WO2021195525A1

WO2021195525A1 - Crispr-cas13 crrna arrays

Info

Publication number: WO2021195525A1
Application number: PCT/US2021/024406
Authority: WO
Inventors: Douglas Matthew ANDERSON
Original assignee: University Of Rochester
Priority date: 2020-03-27
Filing date: 2021-03-26
Publication date: 2021-09-30
Also published as: EP4127170A1; JP2023519344A; US20230103771A1

Abstract

The disclosure provides tandem arrays of CRISPR RNAs and methods of use.

Description

CRISPR-Casl3 crRNA Arrays

CROSS-REFERENCE TO RELATED APPLICATIONS The present application claims priority to U.S. Provisional Application Serial No. 63/000,757, filed on March 27, 2020, which is incorporated by reference herein in its entirety.

BACKGROUND

Mammalian guide-RNA expression cassettes are generally created by cloning annealed oligonucleotides comprising the guide sequence into a cassette comprised of a mammalian Pol III promoter, a Direct Repeat and a terminator of 6 or more Ts. Commonly, multiple guide-RNAs are expressed by adding addition Pol III promoter cassettes, however this can significantly increase the complexity and size of the vector. Generation of tandem crRNA arrays would significantly decrease the size requirements of the vector; however, nucleotide synthesis of long arrays is prohibited due to size and the repeat nature of DR sequences.

SUMMARY OF THE INVENTION

In one embodiment, the disclosure provides a tandem array comprising at least two CRISPR RNA (crRNA), wherein each crRNA comprises a guide sequence and a direct repeat (DR) sequence.

In one embodiment, each guide sequence in the tandem array is different. In one embodiment, each DR sequence in the tandem array is different. In one embodiment, each DR sequence comprises a nucleotide mutation within the loop region of the DR sequence.

In one embodiment, each DR sequence comprises a T17 or T18 nucleotide mutation. In one embodiment, each crRNA comprises a DR sequence independently selected from SEQ ID NOs: 265-274. In one embodiment, each DR sequence is 3’ from the guide sequence.

In one embodiment, each guide sequence is independently substantially complementary to a Coronavirus genomic mRNA sequence or a Coronavirus subgenomic mRNA sequence. In one embodiment, each guide sequence is substantially complementary to a Coronavirus leader sequence, Coronavirus S sequence, Coronavirus E sequence, Coronavirus M sequence, N sequence, or Coronavirus S2M sequence. In one embodiment, each guide sequence is independently substantially complementary to a sequence at least 80% homologous to a sequence selected from SEQ ID NOs: 168-174, 176-181, 186, and 187. In one embodiment, each guide sequence comprises a sequence at least 80% homologous to a sequence selected from SEQ ID NOs: 189-224.In one embodiment, the tandem array comprises a sequence at least 80% homologous to SEQ ID NO:275. In one embodiment, each guide sequence is independently substantially complementary to an influenza vims genomic RNA sequence or an influenza vims subgenomic RNA sequence. In one embodiment, each guide sequence is substantially complementary to an influenza vims PB2 sequence, influenza vims PB 1 sequence, influenza vims PA sequence, influenza vims NP sequence, or influenza vims M sequence. In one embodiment, each guide sequence is independently substantially complementary to a sequence at least 80% homologous to a sequence selected from SEQ ID NOs: 225- 244. In one embodiment, each guide sequence comprises a sequence at least 80% homologous to a sequence selected from SEQ ID NOs: 245-249. In one embodiment, the tandem array comprises a sequence at least 80% homologous to a sequence selected from SEQ ID NO:276-279.

In one embodiment, the disclosure provides a composition comprising a tandem array of the disclosure. In one embodiment, the composition further comprises a Cas protein. In one embodiment, the Cas protein is Casl3. In one embodiment, the Cas protein comprises a sequence at least 80% identical to a sequence selected from SEQ ID NOs: 1-47. In one embodiment, the Cas protein further comprises a localization signal or export signal. In one embodiment, the Cas protein comprises an NES, wherein the NES comprises a sequence at least 80% identical to SEQ ID NO:58-59. In one embodiment, the Cas protein comprises a nuclear localization signal (NLS), wherein the NLS comprises a sequence at least 80% identical to SEQ ID NO: 50-57 and 323-935. In one embodiment, the Cas protein comprises a localization signal, wherein the localization signal comprises a sequence at least 80% identical to SEQ ID NO: 60-66.

In one embodiment, the disclosure provides a method of generating a tandem array comprising at least two CRISPR RNA (crRNA), wherein each crRNA comprises a guide sequence and a direct repeat (DR) sequence. In one embodiment, the method comprises: ligating at least two the crRNA sequences, wherein each crRNA sequence comprises a unique DR sequence, wherein the ligation generates the tandem array.

In one embodiment, the disclosure provides a method of decreasing the number of two or more unique target RNA in a subject. In one embodiment, the method comprises administering to the subject a tandem array of the disclosure and a Cas protein or nucleic acid encoding a Cas protein; or administering a composition the disclosure. In one embodiment, the tandem array comprises at least two unique crRNA sequences which are substantially complementary to the target RNA sequences.

In one embodiment, the disclosure provides a method for treating a viral infection. In one embodiment, the method comprises administering to the subject: (a) tandem array comprising at least two CRISPR RNA (crRNA), wherein each crRNA comprises a guide sequence substantially complementary to a viral RNA sequence and a direct repeat (DR) sequence; and (b) a Cas protein or nucleic acid encoding the Cas protein.

In one embodiment, the Cas protein is Cas 13. In one embodiment, the Cas protein comprises a sequence at least 80% identical to a sequence selected from SEQ ID NOs: 1-47. In one embodiment, the Cas protein further comprises a localization signal or export signal. In one embodiment, the Cas protein comprises an NES, wherein the NES comprises a sequence at least 80% identical to SEQ ID NO:58-59.

In one embodiment, the Cas protein comprises a nuclear localization signal (NLS), wherein the NLS comprises a sequence at least 80% identical to SEQ ID NO: 50-57 and 323-935. In one embodiment, the Cas protein comprises a localization signal, wherein the localization signal comprises a sequence at least 80% identical to SEQ ID NO: 60-66. In one embodiment, the Cas protein comprises a sequence at least 80% identical to SEQ ID NOs: 68-100.

In one embodiment, the nucleic acid encoding the Cas protein comprises a sequence at least 80% identical to SEQ ID NOs: 132-133. In one embodiment, the nucleic acid encoding the Cas protein comprises a sequence at least 80% identical to SEQ ID NOs: 147-166.

In one embodiment, the viral infection is a coronavirus infection and wherein each crRNA independently comprises a guide sequence substantially complementary to a Coronavirus genomic mRNA sequence or a Coronavirus subgenomic mRNA sequence.

In one embodiment, each crRNA independently comprises a guide sequence substantially complementary to a Coronavirus leader sequence, Coronavirus S sequence, Coronavirus E sequence, Coronavirus M sequence, N sequence, or Coronavirus S2M sequence. In one embodiment, each crRNA independently comprises a guide sequence substantially complementary to a sequence at least at least 80% homologous to a sequence selected from SEQ ID NOs: 168-174, 176-181, 186, and 187. In one embodiment, each crRNA independently comprises a guide sequence substantially at least 80% homologous to a sequence selected from SEQ ID NOs: 189-224. In one embodiment, the tandem array comprises a sequence at least 80% homologous to SEQ ID NO: 275.

In one embodiment, the viral infection is an influenza infection and wherein each crRNA independently comprises a guide sequence substantially complementary to an influenza virus genomic RNA sequence or an influenza virus subgenomic RNA sequence. In one embodiment, each crRNA independently comprises a guide sequence substantially complementary an influenza vims PB2 sequence, influenza vims PB 1 sequence, influenza vims PA sequence, influenza vims NP sequence, or influenza vims M sequence. In one embodiment, each crRNA independently comprises a guide sequence substantially complementary to a sequence at least at least 80% homologous to a sequence selected from SEQ ID NOs:225-244. In one embodiment, each crRNA independently comprises a guide sequence substantially at least 80% homologous to a sequence selected from SEQ ID NOs: 245-264. In one embodiment, the tandem array comprises a sequence at least 80% homologous to a sequence selected from SEQ ID NO: 276-279.

In one embodiment, the disclosure provides a delivery system comprising: a packaging plasmid a transfer plasmid, and an envelope plasmid, wherein the packaging plasmid comprises a nucleic acid sequence encoding a gag-pol polyprotein; the transfer plasmid comprises a nucleic acid sequence encoding a tandem array comprising at least two CRISPR RNA (crRNA), wherein each crRNA comprises a guide sequence and a direct repeat (DR) sequence and a nucleic acid sequence encoding a Cas protein; and the envelope plasmid comprises a nucleic acid sequence encoding an envelope protein.

In one embodiment, the Cas protein comprises a sequence at least 80% identical to a sequence selected from SEQ ID NOs: 1-47. In one embodiment, the Cas protein further comprises a localization signal or export signal. In one embodiment, the localization signal or export signal comprises a sequence 80% identical to a sequence selected from SEQ ID NOs:50-66 and 323-935. In one embodiment, the envelope protein is a coronavirus spike glycoprotein. In one embodiment, the envelope protein comprises a sequence at least 80% identical to a sequence selected from SEQ ID NO: 101-129.

In one embodiment, each crRNA independently comprises a guide sequence substantially complementary to a Coronavirus genomic mRNA sequence or a Coronavirus subgenomic mRNA sequence. In one embodiment, each crRNA independently comprises a guide sequence substantially complementary to a Coronavirus leader sequence, Coronavirus S sequence, Coronavirus E sequence, Coronavirus M sequence, N sequence, or Coronavirus S2M sequence. In one embodiment, each crRNA independently compnses a guide sequence substantially complementary to a sequence at least at least 80% homologous to a sequence selected from SEQ ID NOs: 168-174, 176-181, 186, and 187. In one embodiment, crRNA independently comprises a guide sequence substantially at least 80% homologous to a sequence selected from SEQ ID NOs: 189-224. In one embodiment, the tandem array comprises a sequence at least 80% homologous to SEQ ID NO: 275.

In one embodiment, each crRNA independently comprises a guide sequence substantially complementary to an influenza virus genomic RNA sequence or an influenza vims subgenomic RNA sequence. In one embodiment, each crRNA independently comprises a guide sequence substantially complementary an influenza vims PB2 sequence, influenza vims PB 1 sequence, influenza vims PA sequence, influenza vims NP sequence, or influenza vims M sequence. In one embodiment, each crRNA independently compnses a guide sequence substantially complementary to a sequence at least at least 80% homologous to a sequence selected from SEQ ID NOs:225-244. In one embodiment, each crRNA independently compnses a guide sequence substantially at least 80% homologous to a sequence selected from SEQ ID NOs: 245-264. In one embodiment, the tandem array comprises a sequence at least 80% homologous to a sequence selected from SEQ ID NO: 276-279.

BRIEF DESCRIPTION OF THE DRAWINGS

The following detailed description of various embodiments of the invention will be better understood when read in conjunction with the appended drawings. For the purpose of illustrating the invention, there are shown in the drawing’s illustrative embodiments. It should be understood, however, that the invention is not limited to the precise arrangements and instrumentalities of the embodiments shown in the drawings.

Figure 1 depicts a schematic of the Coronavirus genomic and subgenomic mR As.

Figure 2 depicts a schematic of the eraseR platform.

Figure 3 depicts a schematic of delivery via pseudotyped integration-deficient lentiviral vectors.

Figure 4, comprising Figure 4A through Figure 4C, depicts a schematic of guide-RNA testing, lentiviral production and cellular targeting. Figure 4A depicts a schematic of the design of luciferase report construct encoding 5’ and 3’ CoV target sequences. Figure 4B depict a schematic demonstrating the lentiviral constructs encoding CRISPR-Casl3 components can be packaged into non-integrating lentiviral particles pseudotyped with viral envelope proteins, for example, the Spike glycoprotein from SARS-CoV-2 coronavirus, which provides specificity for entry into ACE2 receptor expressing cells. This allows for specific targeting of ‘coronavirus-targeted’ cell types. Figure 4C depicts a schematic demonstrating that post-transduction, processing and formation of non-integrating lentiviral episomes allows for transient expression of CRISPR-Cas 13 components for acute targeted degradation of CoY genomic and subgenomic viral mRNAs.

Figure 5 depicts SARS-CoV-2 leader sequence conservation and targeting sites.

Figure 6 depicts tiling of SARS-CoV-2 Leader crRNAs.

Figure 7, comprising Figure 7A through Figure 7C depicts validated CRISPR-Cas 13 guide-RNAs targeting the SARS-CoV-2 Leader Sequence. Figure 7A depicts a schematic depicting the Luciferase reporter containing the SARS-2-CoV Leader sequence and crRNA target sites locations. Figure 7B depicts a sequence alignment of tiling crRNAs targeting SARS-CoV-2 Leader sequence. Transcriptional Regulatory Sequence (TRS) is highlighted in yellow. Figure 7C depicts cell-based luciferase assays demonstrating robust knockdown of CoV Leader Luc reporter activity in cells with crRNAs targeting SARS-CoV-2 leader sequence (crRNAs A through G) or Luciferase coding sequence (Luc), relative to a non-targeting crRNA.

Figure 8, comprising Figure 8A through Figure 8C depicts, validated CRISPR-Casl3 guide- RNAs targeting the SARS-CoV-2 Stem-loop Like-2 (S2M) Sequence. Figure 8A depicts a schematic depicting the Luciferase reporter containing the SARS-2-CoV S2M sequence and crRNA target sites locations. Figure 8B depicts a sequence alignment of tiling crRNAs targeting SARS-CoV-2 S2M sequence. Figure 8C depicts cell-based luciferase assays demonstrating robust knockdown of CoV S2M Luc reporter activity in cells with crRNAs targeting SARS-CoV-2 S2M sequence (crRNAs A through F) or Luciferase coding sequence (Luc), relative to anon-targeting crRNA.

Figure 9, comprising Figure 9A through Figure 9E, depicts one-step directional assembly of CRISPR-Casl3 crRNA arrays. Figure 9A is a schematic depicting the genomic organization of a bacterial CRISPR-Casl3 locus, which typically consists of a single Casl3 protein and CRISPR array containing multiple Spacer and Direct Repeat (DR) sequences. Figure 9B is a schematic demonstrating that each functional CRISPR guide RNA is processed to include a Spacer and Direct Repeat. Spacer sequences are anti-sense to Target sequences and provide target specificity, whereas the DR sequence acts as a handle for binding to Casl3 protein. Figure 9C is a schematic depicting that mammalian crRNA expression cassettes are typically constructed by annealing and ligating oligonucleotides comprising a desired spacer sequence. Figure 9D is a schematic demonstrating that harnessing tolerable nucleotide substitutions within the loop region of the DR, multiple guide-RNAs are efficiently generated in an ordered array Figure 9E depicts potential tolerable nucleotide substitutions within the loop region of PspCasl3b DR which could be harnessed for array assembly.

Figure 10, comprising Figure 10A through Figure IOC, depicts the identification and validation of non-essential loop residues in Casl3b Direct Repeat (DR). Figure 10A depicts all possible mutations at positions T17 and T18 of the PspCasl3b Direct Repeat. Figure 10B is a schematic depicting the Luciferase reporter and crRNA target sites locations. Figure IOC depicts experimental results demonstrating CRISPR-Casl3b knockdown of Luciferase activity with two independent guide RNAs containing individual DR loop mutations.

Figure 10, comprising Figure 10A through Figure IOC, depicts the identification and validation of non-essential loop residues in Casl3b Direct Repeat (DR). Figure 10A depicts all possible mutations at positions T17 and T18 of the PspCasl3b Direct Repeat. Figure 10B is a schematic depicting the Luciferase reporter and crRNA target sites locations. Figure IOC depicts experimental results demonstrating CRISPR-Casl3b knockdown of Luciferase activity with two independent guide RNAs containing individual DR loop mutations. Figure 11, comprising Figure 11A through Figure 11C, depicts targeted knockdown of a SARS- CoV-2 Luciferase Reporter with a Guide-RNA array. Figure 11A is a schematic depicting the lentiviral gene transfer plasmids encoding CRISPR-Casl3 expression cassettes encoding either single or triple guide RNA arrays. Figure 1 IB is a schematic of a Luciferase reporter containing multiple SARS-CoV-2 viral sequences within the 5’ and 3’ UTRs. Figure 11C depicts experimental results demonstrating relative luciferase activity knockdown through expression of CRISPR-Casl3 RNA targeting components driven by single (LDR-D) or triple guide-RNAs (LDR-D/N-B/S2M-D) targeting the SARS-CoV-2 luciferase reporter, relative to negative control non-targeting crRNA (NC).

Figure 12 is a schematic of the CRISPR-Casl3 expression cassette encoding triple guide RNAs can be packaged in AAV viral vectors.

Figure 13, comprising Figure 13A and Figure 13B, is a schematic of the influenza vims. Figure 13A is a schematic of Influenza viral RNAs (vRNAs). Influenza is an enveloped, negative-sense RNA vims which is composed of 8 vRNA segments. Figure 13A is a schematic of influenza vims particles. All eight vRNAs are packed within an enveloped vims which utilizes viral proteins HA and NA for host cell binding and fusion.

Figure 14, comprising Figure 14A and Figure 14B, is a schematic of the Packaging and Delivery CRISPR-Casl3 RNA editing components to target Influenza. Figure 14A is a schematic demonstrating that the CRISPR-Casl3 editing components, including a CRISPR guide RNA array and Casl3 protein, can be packaged into viral gene therapy vectors, for example, integration deficient lentiviral vectors. Pseudotyping of lentiviral vectors with Influenza NA and HA envelope proteins is one method for delivery to host cells targeted by Influenza vims. Figure 14A is a schematic demonstrating that upon viral vector fusion and delivery, expression of CRISPR-Casl3 components will result in targeted degradation of vRNAs or viral mRNAs. For targeting of vRNAs, robust nuclear localization of Casl3 protein may be necessary.

Figure 15, comprising Figure 15A and Figure 15B, depicts experimental results demonstrating pseudotyping lentiviral vectors with SARS-CoV spike envelope proteins. Figure 15A is a schematic demonstrating that N and C-terminal modifications (4LV) are required for pseudotyping lentivims with CoV Spike proteins from SARS-Cov-1 and SARS-CoV-2. Figure 15B depicts experimental results demonstrating that wild type (WT) CoV spike proteins are not suitable for pseudotyping lentivims for transduction of HEK293T cells orHEK293T cells expressing human ACE2 (ACE2-HEK293T). Expression of the human ACE2 receptor in HEK293T cells is both necessary and sufficient for transduction by 4LV pseudotyped lentiviral vectors. VSV-G envelopes allow for pseudotyping lentivims for broad transduction of many cell types in vitro, independent of ACE2 expression. Figure 16, comprising Figure 16A and Figure 16B, depicts experimental results demonstrating the activity of Casl3b crRNAs targeting Positive- and Negative-sense highly conserved Influenza A RNA sequences. Figure 16A depicts experimental results of guide RNAs targeting positive-sense conserved RNA sequences in Influenza A Segments 1, 2, 3, 5 and 7. Figure 16B depicts experimental results of negative-sense conserved RNA sequences in Influenza A Segments 1, 2, 3, 5 and 7. All Influenza A targeting crRNAs showed robust knockdown efficiency of luciferase reporters carrying corresponding Influenza A Segment-specific target sequences, relative to a non-targeting (NT) crRNA.

DETAILED DESCRIPTION

In some embodiments, the disclosure provides tandem arrays of crRNA sequences. In one embodiment, the tandem array comprises one or more, two or more, three or more, four or more, five or more, six or more, seven or more, or eight or more unique crRNA sequences.

In one embodiment, the crRNA sequences of the tandem array comprise a guide sequence and a direct repeat (DR) sequence. In one embodiment, each DR sequence is unique. In one embodiment, the tandem array can be formed via a single ligation step.

Definitions

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs.

Generally, the nomenclature used herein and the laboratory procedures in cell culture, molecular genetics, organic chemistry, and nucleic acid chemistry and hybridization are those well-known and commonly employed in the art.

Standard techniques are used for nucleic acid and peptide synthesis. The techniques and procedures are generally performed according to conventional methods in the art and various general references (e.g., Sambrook and Russell, 2012, Molecular Cloning, A Laboratory Approach, Cold Spring Harbor Press, Cold Spring Harbor, NY, and Ausubel et ak, 2012, Current Protocols in Molecular Biology, John Wiley & Sons, NY), which are provided throughout this document.

The nomenclature used herein, and the laboratory procedures used in analytical chemistry and organic syntheses described below are those well-known and commonly employed in the art. Standard techniques or modifications thereof are used for chemical syntheses and chemical analyses.

The term "a," "an," "the" and similar terms used in the context of the present invention (especially in the context of the claims) are to be construed to cover both the singular and plural unless otherwise indicated herein or clearly contradicted by the context. “About” as used herein when referring to a measurable value such as an amount, a temporal duration, and the like, is meant to encompass variations of ±20%, or ±10%, or ±5%, or ±1%, or ±0.1% from the specified value, as such variations are appropriate to perform the disclosed methods.

“Antisense” refers particularly to the nucleic acid sequence of the non-coding strand of a double stranded DNA molecule encoding a protein, or to a sequence which is substantially homologous to the non-codmg strand. As defined herein, an antisense sequence is complementary to the sequence of a double stranded DNA molecule encoding a protein. It is not necessary that the antisense sequence be complementary solely to the coding portion of the coding strand of the DNA molecule. The antisense sequence may be complementary to regulatory sequences specified on the coding strand of a DNA molecule encoding a protein, which regulatory sequences control expression of the coding sequences.

A “disease” is a state of health of an animal wherein the animal cannot maintain homeostasis, and wherein if the disease is not ameliorated then the animal’s health continues to deteriorate.

In contrast, a “disorder” in an animal is a state of health in which the animal is able to maintain homeostasis, but in which the animal’s state of health is less favorable than it would be in the absence of the disorder. Left untreated, a disorder does not necessarily cause a further decrease in the animal’s state of health.

A disease or disorder is “alleviated” if the severity of a sign or symptom of the disease or disorder, the frequency with which such a sign or symptom is experienced by a patient, or both, is reduced.

“Encoding” refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (i.e., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom. Thus, a gene encodes a protein if transcription and translation of mRNA corresponding to that gene produces the protein in a cell or other biological system. Both the coding strand, the nucleotide sequence of which is identical to the mRNA sequence and is usually provided in sequence listings, and the non-coding strand, used as the template for transcription of a gene or cDNA, can be referred to as encoding the protein or other product of that gene or cDNA.

The terms “patient,” “subject,” “individual,” and the like are used interchangeably herein, and refer to any animal or cell whether in vitro or in vivo, amenable to the methods described herein. In one embodiment, the subjects include vertebrates and invertebrates. Invertebrates include, but are not limited to, Drosophila melanogaster and Caenorhabditis elegans. Vertebrates include, but are not limited to, primates, rodents, domestic animals or game animals. Primates include, but are not limited to, chimpanzees, cynomologous monkeys, spider monkeys, and macaques (e g., Rhesus). Rodents include, but are not limited to, mice, rats, woodchucks, ferrets, rabbits and hamsters. Domestic and game animals include, but are not limited to, cows, horses, pigs, deer, bison, buffalo, feline species (e.g., domestic cat), canine species (e.g., dog, fox, wolf), avian species (e.g., chicken, emu, ostrich), and fish (e.g., zebrafish, trout, catfish and salmon). In some embodiments, the subject is a mammal, e.g., a primate, e.g., a human. In certain non-limiting embodiments, the patient, subject or individual is a human.

By the term “specifically binds,” as used herein with respect to an antibody, is meant an antibody which recognizes a specific antigen, but does not substantially recognize or bind other molecules in a sample. For example, an antibody that specifically binds to an antigen from one species may also bind to that antigen from one or more species. But, such cross-species reactivity does not itself alter the classification of an antibody as specific. In another example, an antibody that specifically binds to an antigen may also bind to different allelic forms of the antigen. However, such cross reactivity does not itself alter the classification of an antibody as specific.

In some instances, the terms “specific binding” or “specifically binding,” can be used in reference to the interaction of an antibody, a protein, or a peptide with a second chemical species, to mean that the interaction is dependent upon the presence of a particular structure (e.g., an antigenic determinant or epitope) on the chemical species; for example, an antibody recognizes and binds to a specific protein structure rather than to proteins generally. If an antibody is specific for epitope “A”, the presence of a molecule containing epitope A (or free, unlabeled A), in a reaction containing labeled “A” and the antibody, will reduce the amount of labeled A bound to the antibody.

A “coding region” of a gene consists of the nucleotide residues of the coding strand of the gene and the nucleotides of the non-coding strand of the gene which are homologous with or complementary to, respectively, the coding region of an mRNA molecule which is produced by transcription of the gene.

A “coding region” of a mRNA molecule also consists of the nucleotide residues of the mRNA molecule which are matched with an anti-codon region of a transfer RNA molecule during translation of the mRNA molecule or which encode a stop codon. The coding region may thus include nucleotide residues comprising codons for amino acid residues which are not present in the mature protein encoded by the mRNA molecule (e.g., ammo acid residues in a protein export signal sequence).

“Complementary” as used herein to refer to a nucleic acid, refers to the broad concept of sequence complementarity between regions of two nucleic acid strands or between two regions of the same nucleic acid strand. It is known that an adenine residue of a first nucleic acid region is capable of forming specific hydrogen bonds (“base pairing”) with a residue of a second nucleic acid region which is antiparallel to the first region if the residue is thymine or uracil. Similarly, it is known that a cytosine residue of a first nucleic acid strand is capable of base pairing with a residue of a second nucleic acid strand which is antiparallel to the first strand if the residue is guanine. A first region of a nucleic acid is complementary to a second region of the same or a different nucleic acid if, when the two regions are arranged in an antiparallel fashion, at least one nucleotide residue of the first region is capable of base pairing with a residue of the second region. In one embodiment, the first region comprises a first portion and the second region comprises a second portion, whereby, when the first and second portions are arranged in an antiparallel fashion, at least about 50%, at least about 75%, at least about 90%, or at least about 95% of the nucleotide residues of the first portion are capable of base pairing with nucleotide residues in the second portion. In one embodiment, all nucleotide residues of the first portion are capable of base pairing with nucleotide residues in the second portion.

The term “DNA” as used herein is defined as deoxyribonucleic acid.

The term “expression” as used herein is defined as the transcription and/or translation of a particular nucleotide sequence dnven by its promoter.

The term “expression vector” as used herein refers to a vector containing a nucleic acid sequence coding for at least part of a gene product capable of being transcribed. In some cases, RNA molecules are then translated into a protein, polypeptide, or peptide. In other cases, these sequences are not translated, for example, in the production of antisense molecules, siRNA, ribozymes, and the like. Expression vectors can contain a variety of control sequences, which refer to nucleic acid sequences necessary for the transcription and possibly translation of an operatively linked coding sequence in a particular host organism. In addition to control sequences that govern transcription and translation, vectors and expression vectors may contain nucleic acid sequences that serve other functions as well.

As used herein the term “wild type” is a term of the art understood by skilled persons and means the typical form of an organism, strain, gene or characteristic as it occurs in nature as distinguished from mutant or variant forms.

The term “homology” refers to a degree of complementarity. There may be partial homology or complete homology (i.e., identity). Homology is often measured using sequence analysis software (e.g., Sequence Analysis Software Package of the Genetics Computer Group. University of Wisconsin Biotechnology Center. 1710 University Avenue. Madison, Wis. 53705). Such software matches similar sequences by assigning degrees of homology to various substitutions, deletions, insertions, and other modifications. Conservative substitutions typically include substitutions within the following groups: glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid, asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine.

By “nucleic acid” is meant any nucleic acid, whether composed of deoxyribonucleosides or ribonucleosides, and whether composed of phosphodiester linkages or modified linkages such as phosphotriester, phosphoramidate, siloxane, carbonate, carboxymethylester, acetamidate, carbamate, thioether, bridged phosphoramidate, bridged methylene phosphonate, phosphorothioate, methylphosphonate, phosphorodithioate, bridged phosphorothioate or sulfone linkages, and combinations of such linkages. The term nucleic acid also specifically includes nucleic acids composed of bases other than the five biologically occurring bases (adenine, guanine, thymine, cytosine and uracil). The term “nucleic acid” typically refers to large polynucleotides.

Conventional notation is used herein to describe polynucleotide sequences: the left-hand end of a single -stranded polynucleotide sequence is the 5'-end; the left-hand direction of a double-stranded polynucleotide sequence is referred to as the 5 '-direction.

The direction of 5' to 3' addition of nucleotides to nascent RNA transcripts is referred to as the transcription direction. The DNA strand having the same sequence as an mRNA is referred to as the “coding strand”; sequences on the DNA strand which are located 5' to a reference point on the DNA are referred to as “upstream sequences”; sequences on the DNA strand which are 3' to a reference point on the DNA are referred to as “downstream sequences.”

In the context of the present invention, the following abbreviations for the commonly occurring nucleic acid bases are used. “A” refers to adenosine, “C” refers to cytosine, “G” refers to guanosine, “T” refers to thymidine, and “U” refers to uridine.

As used herein, the terms “peptide,” “polypeptide,” and “protein” are used interchangeably, and refer to a compound comprised of amino acid residues covalently linked by peptide bonds. A protein or peptide must contain at least two amino acids, and no limitation is placed on the maximum number of amino acids that can comprise a protein's or peptide's sequence. Polypeptides include any peptide or protein comprising two or more amino acids joined to each other by peptide bonds. As used herein, the term refers to both short chains, which also commonly are referred to in the art as peptides, oligopeptides and oligomers, for example, and to longer chains, which generally are referred to in the art as proteins, of which there are many types. “Polypeptides” include, for example, biologically active fragments, substantially homologous polypeptides, oligopeptides, homodimers, heterodimers, variants of polypeptides, modified polypeptides, derivatives, analogs, fusion proteins, among others. The polypeptides include natural peptides, recombinant peptides, synthetic peptides, or a combination thereof. The term “RNA” as used herein is defined as ribonucleic acid.

“Variant” as the term is used herein, is a nucleic acid sequence or a peptide sequence that differs in sequence from a reference nucleic acid sequence or peptide sequence respectively, but retains essential biological properties of the reference molecule. Changes in the sequence of a nucleic acid variant may not alter the amino acid sequence of a peptide encoded by the reference nucleic acid, or may result in amino acid substitutions, additions, deletions, fusions and truncations. Changes in the sequence of peptide variants are typically limited or conservative, so that the sequences of the reference peptide and the variant are closely similar overall and, in many regions, identical. A variant and reference peptide can differ in amino acid sequence by one or more substitutions, additions, deletions in any combination. A variant of a nucleic acid or peptide can be a naturally occurring such as an allelic variant, or can be a variant that is not known to occur naturally. Non-naturally occurring variants of nucleic acids and peptides may be made by mutagenesis techniques or by direct synthesis.

A “vector” is a composition of matter which comprises an isolated nucleic acid and which can be used to deliver the isolated nucleic acid to the interior of a cell. Numerous vectors are known in the art including, but not limited to, linear polynucleotides, polynucleotides associated with ionic or amphiphilic compounds, plasmids, and viruses. Thus, the term “vector” includes an autonomously replicating plasmid or a virus. The term should also be construed to include non-plasmid and non-viral compounds which facilitate transfer of nucleic acid into cells, such as, for example, polylysine compounds, liposomes, and the like. Examples of viral vectors include, but are not limited to, adenoviral vectors, adeno-associated virus vectors, retroviral vectors, and the like.

As used herein, the term “guide sequence,” “spacer sequence” “crRNA,” “guide RNA,” or “single guide RNA,” or “gRNA” refers to a polynucleotide comprising any polynucleotide sequence having sufficient complementarity with a target nucleic acid sequence to hybridize with the target nucleic acid sequence and to direct sequence-specific binding of a RNA-targeting complex comprising the guide sequence and a CRISPR effector protein to the target nucleic acid sequence. In some example embodiments, the degree of complementarity, when optimally aligned using a suitable alignment algorithm, is about or more than about 50%, 60%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%, or more. Optimal alignment may be determined with the use of any suitable algorithm for aligning sequences, non limiting example of which include the Smith-Waterman algorithm, the Needleman-Wunsch algorithm, algorithms based on the Burrows-Wheeler Transform (e g., the Burrows Wheeler Aligner), ClustalW, Clustal X, BLAT, Novoalign (Novocraft Technologies; available at www.novocraft.com), ELAND (Illumina, San Diego, Calif.), SOAP (available at soap.genomics.org.cn), and Maq (available at maq.sourceforge.net). The ability of a guide sequence (within a nucleic acid-targeting guide RNA) to direct sequence -specific binding of a nucleic acid-targeting complex to a target nucleic acid sequence may be assessed by any suitable assay. For example, the components of a nucleic acid-targeting CRISPR system sufficient to form a nucleic acid-targeting complex, including the guide sequence to be tested, may be provided to a host cell having the corresponding target nucleic acid sequence, such as by transfection with vectors encoding the components of the nucleic acid-targeting complex, followed by an assessment of preferential targeting (e.g., cleavage) within the target nucleic acid sequence, such as by Surveyor assay as described herein. Similarly, cleavage of a target nucleic acid sequence may be evaluated in a test tube by providing the target nucleic acid sequence, components of a nucleic acid-targeting complex, including the guide sequence to be tested and a control guide sequence different from the test guide sequence, and comparing binding or rate of cleavage at the target sequence between the test and control guide sequence reactions. Other assays are possible, and will occur to those skilled in the art. A guide sequence, and hence a nucleic acid-targeting guide may be selected to target any target nucleic acid sequence The target sequence may be DNA. The target sequence may be any RNA sequence. In some embodiments, the target sequence may be a sequence within a RNA molecule selected from the group consisting of messenger RNA (mRNA), pre-mRNA, ribosomal RNA (rRNA), transfer RNA (tRNA), micro-RNA (miRNA), small interfering RNA (siRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), double stranded RNA (dsRNA), non-coding RNA (ncRNA), long non-coding RNA (IncRNA), and small cytoplasmatic RNA (scRNA). In some preferred embodiments, the target sequence may be a sequence within a RNA molecule selected from the group consisting of mRNA, pre-mRNA, and rRNA. In some preferred embodiments, the target sequence may be a sequence within a RNA molecule selected from the group consisting of ncRNA, and IncRNA. In some more preferred embodiments, the target sequence may be a sequence within an mRNA molecule or a pre-mRNA molecule.

Ranges: throughout this disclosure, various aspects of the invention can be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 2.7, 3, 4, 5, 5.3, and 6. This applies regardless of the breadth of the range.

Proteins

In one aspect, the present disclosure is based on the development of novel editing proteins which provide targeted RNA cleavage. In some embodiment, the proteins comprise a localization signal. In one embodiment, the localization signal localizes the protein to the site in which a target RNA is located. In one embodiment, the protein comprises a nuclear localization signal (NLS), to target RNA in the nucleus. In one embodiment, the protein comprises an nuclear export signal (NES), to target RNA in the cytoplasm. In one embodiment, the fusion protein comprises a purification and/or detection tag.

In one aspect, the present disclosure is based on the development of novel editing proteins which provide targeted RNA cleavage and are effectively delivered. In some embodiment, the proteins comprise a localization signal. In one embodiment, the localization signal localizes the protein to the site in which a target RNA is located. In one embodiment, the protein comprises a purification and/or detection tag.

In one aspect, the present disclosure is based on the development of novel editing proteins which are capable of modulating the cleavage and/or polyadenylation of nuclear RNA and are effectively delivered to the nucleus. In some embodiment, the proteins comprise a cleavage and/or polyadenylation protein. In some embodiment, the proteins comprise a nuclear localization signal. In one embodiment, the protein comprises a purification and/or detection tag.

Editing Protein

In one embodiment, the editing protein includes, but is not limited to, a CRISPR-associated (Cas) protein, a zinc finger nuclease (ZFN) protein, and a protein having a DNA or RNA binding domain.

Non-limiting examples of Cas proteins include Casl, CaslB, Cas2, Cas3, Cas4, Cas5, Cas6,

Cas7, Cas8, Cas9, CaslO, Csyl, Csy2, Csy3, Csel, Cse2, Cscl, Csc2, Csa5, Csn2. Csm2, Csm3, Csm4, Csm5, Csm6, Cmrl, Cmr3, Cmr4, Cmr5, Cmr6, Csbl, Csb2, Csb3, Csxl7, Csxl4, CsxlO, Csxl6, CsaX, Csx3, Csxl, Csxl5, Csfl, Csf2, Csf3, Csf4, SpCas9, StCas9, NmCas9, SaCas9, CjCas9, CjCas9, AsCpfl, LbCpfl, FnCpfl, VRER SpCas9, VQR SpCas9, xCas9 3.7, homologs thereof, orthologs thereof, or modified versions thereof. In some embodiments, the Cas protein has DNA or RNA cleavage activity. In some embodiments, the Cas protein directs cleavage of one or both strands of a nucleic acid molecule at the location of a target sequence, such as within the target sequence and/or within the complement of the target sequence. In some embodiments, the Cas protein directs cleavage of one or both strands within about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 50, 100, 200, 500, or more base pairs from the first or last nucleotide of a target sequence. In one embodiment, the Cas protein is Cas9, Cas 13, or Cpfl. In one embodiment, Cas protein is catalytically deficient (dCas).

In one embodiment, the Cas protein has RNA binding activity. In one embodiment, Cas protein is Casl3. In one embodiment, the Cas protein is PspCasl3b, PspCasl3b Truncation, AdmCasl3d, AspCasl3b, AspCasl3c, BmaCasl3a, BzoCasl3b, CamCasl3a, CcaCasl3b, Cga2Casl3a, CgaCasl3a, EbaCasl3a, EreCasl3a, EsCasl3d, FbrCasl3b, FnbCasl3c, FndCasl3c, FnfCasl3c, FnsCasl3c, FpeCasl3c, FulCasl3c, HheCasl3a, LbfCasl3a, LbmCasl3a, LbnCasl3a, LbuCasl3a, LseCasl3a, LshCasl3a, LspCasl3a, Lwa2casl3a, LwaCasl3a, LweCasl3a, PauCasl3b, PbuCasl3b, PgiCasl3b, PguCasl3b, Pin2Casl3b, Pin3Casl3b, PinCasl3b, Pprcasl3a, PsaCasl3b, PsmCasl3b, RaCasl3d, RanCasl3b, RcdCasl3a, RcrCasl3a, RcsCasl3a, RfxCasl3d, UrCasl3d, dPspCasl3b, PspCasl3b_A133H, PspCasl3b_A1058H, dPspCasl3b truncation, dAdmCasl3d, dAspCasl3b, dAspCasl3c, dBmaCasl3a, dBzoCasl3b, dCamCasl3a, dCcaCasl3b, dCga2Casl3a, dCgaCasl3a, dEbaCasl3a, dEreCasl3a, dEsCasl3d, dFbrCasl3b, dFnbCasl3c, dFndCasl3c, dFnfCasl3c, dFnsCasl3c, dFpeCasl3c, dFulCasl3c, dHheCasl3a, dLbfCasl3a, dLbmCasl3a, dLbnCasl3a, dLbuCasl3a, dLseCasl3a, dLshCasl3a, dLspCasl3a, dLwa2casl3a, dLwaCasl3a, dLweCasl3a, dPauCasl3b, dPbuCasl3b, dPgiCasl3b, dPguCasl3b, dPin2Casl3b, dPin3Casl3b, dPinCasl3b, dPprCasl3a, dPsaCasl3b, dPsmCasl3b, dRaCasl3d, dRanCasl3b, dRcdCasl3a, dRcrCasl3a, dRcsCasl3a, dRfxCasl3d, or dUrCasl3d. Additional Cas proteins are known in the art (e g., Konermann et al., Cell, 2018, 173:665-676 el4, Yan et al., Mol Cell, 2018, 7:327-339 e5; Cox, D.B.T., et al, Science, 2017, 358: 1019-1027; Abudayyeh et al., Nature, 2017, 550: 280-284, Gootenberg et al., Science, 2017, 356: 438-442; and East-Seletsky et al., Mol Cell, 2017, 66: 373-383 e3, which are herein incorporated by reference).

In one embodiment, the Cas protein comprises a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs: 1-49. In one embodiment, the Cas protein comprises a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs: 1-47. In one embodiment, the Cas protein comprises a sequence of one of SEQ ID NOs: 1-49. In one embodiment, the Cas protein comprises a sequence of one of SEQ ID NOs: 1-47.

Localization Signal

In some embodiments, the protein may contain a localization signal, such as an nuclear localization signal (NLS), nuclear export signal (NES) or other localization signals to localize to organelles, such as mitochondria, or to localize in the cytoplasm. In one embodiment, the localization signal localizes the protein to the site in which a target RNA is located. Nuclear Localization Signal

In one embodiment, the protein comprises a NLS. In one embodiment, the NLS is a retrotransposon NLS. In one embodiment, the NLS is derived from Tyl, yeast GAL4, SKI3, L29 or histone H2B proteins, polyoma vims large T protein, VP1 or VP2 capsid protein, SV40 YP1 or VP2 capsid protein, Adenovirus Ela or DBP protein, influenza vims NS1 protein, hepatitis vims core antigen or the mammalian lamin, c-myc, max, c-myb, p53, c-erbA, jun, Tax, steroid receptor or Mx proteins, Nucleoplasmin (NPM2), Nucleophosmin (NPM1), or simian vims 40 ("SV40") T-antigen. In one embodiment, the NLS is a Tyl or Ty 1-derived NLS, a Ty2 or Ty2-derived NLS or a MAK11 or MAK11- derived NLS. In one embodiment, the Tyl NLS comprises an amino acid sequence of SEQ ID NO:50. In one embodiment, the Ty2 NLS comprises an ammo acid sequence of SEQ ID NO:51. In one embodiment, the MAK11 NLS comprises an amino acid sequence of SEQ ID NO:52. In one embodiment, the NLS comprises a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs: 50-57 and 323-935. In one embodiment, the NLS comprises a sequence of one of SEQ ID NOs: 50-57 and 323-935.

In one embodiment, the NLS is a Ty 1-like NLS. For example, in one embodiment, the Ty 1 -like NLS comprises KKRX motif. In one embodiment, the Tyl-like NLS comprises KKRX motif at the N- terminal end. In one embodiment, the Tyl-like NLS comprises KKR motif. In one embodiment, the Tyl- like NLS comprises KKR motif at the C-terminal end. In one embodiment, the Tyl-like NLS comprises a KKRX and a KKR motif. In one embodiment, the Tyl-like NLS comprises a KKRX at the N-terminal end and a KKR motif at the C-terminal end. In one embodiment, the Tyl-like NLS comprises at least 20 amino acids. In one embodiment, the Tyl-like NLS comprises between 20 and 40 amino acids. In one embodiment, the Tyl-like NLS comprises a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs: 323-935. In one embodiment, the NLS comprises a sequence of one of SEQ ID NOs: 323-935, wherein the sequence comprises one or more, two or more, three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, or ten or more, insertions, deletions or substitutions In one embodiment, the Tyl-like NLS comprises a sequence of one of SEQ ID NOs: 323-935. In one embodiment, the NLS comprises two copies of the same NLS. For example, in one embodiment, the NLS comprises a multimer of a first Ty 1-derived NLS and a second Tyl-derived NLS.

Nuclear Export Signal

In one embodiment, the protein comprises a Nuclear Export Signal (NES). In one embodiment, the NES is attached to the N-terminal end of the Cas protein. In one embodiment, the NES localizes the protein to the cytoplasm for targeting cytoplasmic RNA. In one embodiment, the NES comprises an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NOs:58 or 59. In one embodiment, the NES comprises an amino acid sequence of SEQ ID NOs: 58 or 59.

Organelle Localization Signal

In one embodiment, the protein comprises a localization signal that localizes the protein to an organelle. In one embodiment, the localization signal localizes the protein to the nucleolus, ribosome, vesicle, rough endoplasmic reticulum, Golgi apparatus, cytoskeleton, smooth endoplasmic reticulum, mitochondria, vacuole, cytosol, lysosome, or centriole. A number of localization signals are known in the art.

In one embodiment, the protein comprises a localization signal that localizes the protein to an organelle or extracellularly. In one embodiment, the localization signal localizes the protein to the nucleolus, ribosome, vesicle, rough endoplasmic reticulum, Golgi apparatus, cytoskeleton, smooth endoplasmic reticulum, mitochondria, vacuole, cytosol, lysosome, or centriole.

A number of localization signals are known in the art. Exemplary localization signals include, but are not limited to lx mitochondrial targeting sequence, 4x mitochondrial targeting sequence, secretory signal sequence (IL-2), myristylation, Calsequestrin leader, KDEL retention and peroxisome targeting sequence.

In one embodiment, the localization signal comprises sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NOs:60-66. In one embodiment, the localization signal comprises sequence of SEQ ID NOs: 60-66. Purification and/or Detection Tag

In some embodiments, the protein may contain a purification and/or detection tag. In one embodiment, the tag is on the N-terminal end of the protein. In one embodiment, the tag is a 3xFLAG tag. In one embodiment, the tag comprises an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO:67. In one embodiment, the tag comprises an amino acid sequence of SEQ ID NO: 67.

Cleavage and/or Polyadenylation Proteins

In one aspect, fusion proteins comprises an editing protein and a cleavage and/or polyadenylation protein which are effectively delivered to the nucleus. In one embodiment, the cleavage and/or polyadenylation protein is an RNA binding protein of the human 3’ end processing machinery. In one embodiment, the cleavage and/or polyadenylation protein is CPSF30, WDR33, orNUDT21. In one embodiment, the cleavage and/or polyadenylation protein is NUDT21. In one embodiment, the cleavage and/or polyadenylation protein is NUDT21 , a NUDT21 mutation, a NUDT21 dimer, a NUDT21 fusion protein or any combination thereof. In one embodiment, the cleavage and/or polyadenylation protein is human NUDT21, Worm NUDT21, Fly NUDT21, Zebrafish NUDT21, NUDT21 R63S, NUDT21 F103A, or a tandem dimer of NUDT21.

In one embodiment, the cleavage and/or polyadenylation protein comprises an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs:298-307. In one embodiment, the cleavage and/or polyadenylation protein comprises an amino acid sequence of one of SEQ ID NOs: 298-307.

Fusion Proteins

Fusion Protein comprising a Cas Protein and Localization Signal

In one embodiment, the proteins of the disclosure are effectively delivered to the nucleus, an organelle, the cytoplasm or extracellularly and allow for targeted RNA cleavage. In one embodiment, the protein comprises an amino acid sequence 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID N0s:68-100. In one embodiment, the protein comprises an amino acid sequence of one of SEQ ID NOs: 68-100.

Fusion Protein comprising a Cas Protein and a Cleavage and/or Polyadenylation Protein

In one embodiment, the proteins of the disclosure are effectively delivered to the nucleus and allow for targeted RNA cleavage and/or polyadenylation. In one embodiment, the protein comprises an amino acid sequence 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs:308-310. In one embodiment, the protein comprises an amino acid sequence of one of SEQ ID NOs: 308-310.

Proteins, Peptides and Fusion Proteins

The proteins of the present disclosure may be made using chemical methods. For example, protein can be synthesized by solid phase techniques (Roberge J Y et al (1995) Science 269: 202-204), cleaved from the resin, and purified by preparative high-performance liquid chromatography. Automated synthesis may be achieved, for example, using the ABI 431 A Peptide Synthesizer (Perkin Elmer) in accordance with the instructions provided by the manufacturer.

The proteins of the present disclosure may be made using recombinant protein expression. The recombinant expression vectors of the disclosure comprise a nucleic acid of the invention in a form suitable for expression of the nucleic acid in a host cell, which means that the recombinant expression vectors include one or more regulatory sequences, selected on the basis of the host cells to be used for expression, that is operatively-linked to the nucleic acid sequence to be expressed. Within a recombinant expression vector, “operably-linked” is intended to mean that the nucleotide sequence of interest is linked to the regulatory sequences in a manner that allows for expression of the nucleotide sequence (e.g., in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell).

The term “regulatory sequence” is intended to include promoters, enhancers and other expression control elements (e.g., polyadenylation signals). Such regulatory sequences are described, for example, in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990). Regulatory sequences include those that direct constitutive expression of a nucleotide sequence in many types of host cell and those that direct expression of the nucleotide sequence only in certain host cells (e.g., tissue-specific regulatory sequences). It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, etc. The expression vectors of the invention can be introduced into host cells to thereby produce proteins or peptides, including fusion proteins or peptides, encoded by nucleic acids as described herein.

The recombinant expression vectors of the invention can be designed for production of variant proteins in prokaryotic or eukaryotic cells. For example, proteins of the invention can be expressed in bacterial cells such as Escherichia coli, insect cells (using baculovirus expression vectors) yeast cells or mammalian cells. Suitable host cells are discussed further in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990). Alternatively, the recombinant expression vector can be transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase.

Expression of proteins in prokaryotes is most often carried out in Escherichia coli with vectors containing constitutive or inducible promoters directing the expression of either fusion or non-fusion proteins. Fusion vectors add a number of amino acids to a protein encoded therein, to the amino or C terminus of the recombinant protein. Such fusion vectors typically serve three purposes: (i) to increase expression of recombinant protein; (ii) to increase the solubility of the recombinant protein; and (iii) to aid in the purification of the recombinant protein by acting as a ligand in affinity purification. Often, in fusion expression vectors, a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant protein to enable separation of the recombinant protein from the fusion moiety subsequent to purification of the fusion protein. Such enzymes, and their cognate recognition sequences, include Factor Xa, thrombin, PreScission, TEV and enterokinase. Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith and Johnson, 1988. Gene 67: 31-40), pMAL (New England Biolabs, Beverly, Mass.) and pRITS (Pharmacia, Piscataway, N.J.) that fuse glutathione S-transferase (GST), maltose E binding protein, or protein A, respectively, to the target recombinant protein.

Examples of suitable inducible non-fusion E. coli expression vectors include pTrc (Amrann et al., (1988) Gene 69:301-315) and pET l id (Studier et al., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990) 60-89) — not accurate, pETl la-d have N terminal T7 tag.

One strategy to maximize recombinant protein expression in E. coli is to express the protein in a host bacterium with an impaired capacity to proteolytically cleave the recombinant protein. See, e g , Gottesman, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990) 119-128. Another strategy is to alter the nucleic acid sequence of the nucleic acid to be inserted into an expression vector so that the individual codons for each amino acid are those preferentially utilized in E. coli (see, e.g., Wada, et al., 1992. Nucl. Acids Res. 20: 2111-2118). Such alteration of nucleic acid sequences of the invention can be carried out by standard DNA synthesis techniques. Another strategy to solve codon bias is by using BL21-codon plus bacterial strains (Invitrogen) or Rosetta bacterial strain (Novagen), these strains contain extra copies of rare E. coli tRNA genes.

In another embodiment, the expression vector encoding for the protein of the disclosure is a yeast expression vector. Examples of vectors for expression in yeast Saccharomyces cerevisiae include pYepSecl (Baldari, et al., 1987. EMBO J. 6: 229-234), pMFa (Kuijan and Herskowitz, 1982. Cell 30: 933-943), pJRY88 (Schultz et af, 1987. Gene 54: 113-123), pYES2 (Invitrogen Corporation, San Diego, Calif.), and picZ (InVitrogen Corp, San Diego, Calif.).

Alternatively, polypeptides of the present invention can be produced in insect cells using baculovirus expression vectors. Baculovirus vectors available for expression of proteins in cultured insect cells (e g., SF9 cells) include the pAc series (Smith, et al., 1983. Mol. Cell. Biol.

3: 2156-2165) and the pVL series (Lucklow and Summers, 1989. Virology 170: 31-39).

In yet another embodiment, a nucleic acid of the disclosure is expressed in mammalian cells using a mammalian expression vector. Mammalian cell lines available in the art for expression of a heterologous polypeptide include, but are not limited to, Chinese hamster ovary (CHO) cells, HeLa cells, baby hamster kidney cells, NSO mouse melanoma cells, YB2/0 rat myeloma cells, human embryonic kidney cells, human embryonic retina cells and many others. Examples of mammalian expression vectors include pCDM8 (Seed, 1987. Nature 329: 840) and pMT2PC (Kaufman, et al., 1987. EMBO J. 6: 187-195), pIRESpuro (Clontech), pUB6 (Invitrogen), pCEP4 (Invitrogen) pREP4 (Invitrogen), pcDNA3 (Invitrogen). When used in mammalian cells, the expression vector's control functions are often provided by viral regulatory elements. For example, commonly used promoters are derived from polyoma, adenovirus 2, cytomegalovirus, Rous Sarcoma Virus, and simian virus 40. For other suitable expression systems for both prokaryotic and eukaryotic cells see, e.g., Chapters 16 and 17 of Sambrook, et al., Molecular Cloning: A Laboratory Manual. 2nd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989.

In another embodiment, the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentially in a particular cell type (e.g., tissue- specific regulatory elements are used to express the nucleic acid). Tissue-specific regulatory elements are known in the art. Non-limiting examples of suitable tissue-specific promoters include the albumin promoter (liver-specific; Pinkert, et al., 1987. Genes Dev. 1: 268-277), lymphoid-specific promoters (Calame and Eaton, 1988. Adv. Immunol. 43: 235-275), in particular promoters of T cell receptors (Winoto and Baltimore, 1989. EMBO J. 8: 729-733) and immunoglobulins (Baneiji, et al., 1983. Cell 33: 729-740; Queen and Baltimore, 1983. Cell 33: 741-748), neuron-specific promoters (e.g., the neurofilament promoter; Byrne and Ruddle, 1989. Proc. Natl. Acad. Sci. USA 86: 5473-5477), pancreas-specific promoters (Edlund, et al., 1985. Science 230: 912-916), and mammary gland-specific promoters (e.g., milk whey promoter; U.S. Pat. No. 4,873,316 and European Application Publication No. 264, 166). Developmentally- regulated promoters are also encompassed, e.g., the murinehox promoters (Kessel and Gruss, 1990. Science 249: 374-379) and the alpha-fetoprotein promoter (Campes and Tilghman, 1989. Genes Dev. 3: 537-546).

The invention should also be construed to include any form of a protein having substantial homology to a protein disclosed herein. In one embodiment, a protein which is “substantially homologous” is about 50% homologous, about 70% homologous, about 80% homologous, about 90% homologous, about 91% homologous, about 92% homologous, about 93% homologous, about 94% homologous, about 95% homologous, about 96% homologous, about 97% homologous, about 98% homologous, or about 99% homologous to amino acid sequence of a fusion-protein disclosed herein.

The protein may alternatively be made by recombinant means or by cleavage from a longer polypeptide. The composition of a protein may be confirmed by amino acid analysis or sequencing.

The variants of the protein according to the present invention may be (i) one in which one or more of the amino acid residues are substituted with a conserved or non-conserved amino acid residue and such substituted amino acid residue may or may not be one encoded by the genetic code, (ii) one in which there are one or more modified amino acid residues, e.g., residues that are modified by the attachment of substituent groups, (iii) one in which the peptide is an alternative splice variant of the protein of the present invention, (iv) fragments of the peptides and/or (v) one in which the protein is fused with another peptide, such as a leader or secretory sequence or a sequence which is employed for purification (for example, His-tag) or for detection (for example, Sv5 epitope tag). The fragments include peptides generated via proteolytic cleavage (including multi-site proteolysis) of an original sequence. Variants may be post-translationally, or chemically modified. Such variants are deemed to be within the scope of those skilled in the art from the teaching herein.

As known in the art the “similarity” between two fusion proteins is determined by comparing the amino acid sequence and its conserved amino acid substitutes of one polypeptide to a sequence of a second polypeptide. Variants are defined to include peptide sequences different from the original sequence. In one embodiment, variants are different from the original sequence in less than 40% of residues per segment of interest different from the original sequence in less than 25% of residues per segment of interest, different by less than 10% of residues per segment of interest, or different from the original protein sequence in just a few residues per segment of interest and at the same time sufficiently homologous to the original sequence to preserve the functionality of the original sequence and/or the ability to stimulate the differentiation of a stem cell into the osteoblast lineage. The present invention includes amino acid sequences that are at least 60%, 65%, 70%, 72%, 74%, 76%, 78%, 80%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% similar or identical to the original amino acid sequence. The degree of identity between two peptides is determined using computer algorithms and methods that are widely known for the persons skilled in the art. The identity between two amino acid sequences may be determined by using the BLASTP algorithm [BLAST Manual, Altschul, S., et al., NCBI NLM NIH Bethesda, Md. 20894, Altschul, S., et al., J. Mol. Biol. 215: 403-410 (1990)].

The protein of the disclosure can be post-translationally modified. For example, post- translational modifications that fall within the scope of the present invention include signal peptide cleavage, glycosylation, acetylation, isoprenylation, proteolysis, myristoylation, protein folding and proteolytic processing, etc. Some modifications or processing events require introduction of additional biological machinery. For example, processing events, such as signal peptide cleavage and core glycosylation, are examined by adding canine microsomal membranes or Xenopus egg extracts (U.S. Pat. No. 6,103,489) to a standard translation reaction.

The protein of the disclosure may include unnatural amino acids formed by post- translational modification or by introducing unnatural amino acids during translation. A variety of approaches are available for introducing unnatural amino acids during protein translation.

A protein of the disclosure may be phosphorylated using conventional methods such as the method described in Reedijk et al. (The EMBO Journal 11(4): 1365, 1992).

Cyclic derivatives of the fusion proteins of the invention are also part of the present invention. Cyclization may allow the protein to assume a more favorable conformation for association with other molecules. Cyclization may be achieved using techniques known in the art. For example, disulfide bonds may be formed between two appropriately spaced components having free sulfhydryl groups, or an amide bond may be formed between an amino group of one component and a carboxyl group of another component. Cyclization may also be achieved using an azobenzene-containing amino acid as described by Ulysse, L., et al., J. Am. Chem. Soc. 1995, 117, 8466-8467. The components that form the bonds may be side chains of amino acids, non amino acid components or a combination of the two. In an embodiment of the invention, cyclic peptides may comprise a beta-turn in the right position. Beta-turns may be introduced into the peptides of the invention by adding the amino acids Pro-Gly at the right position.

It may be desirable to produce a cyclic protein which is more flexible than the cyclic peptides containing peptide bond linkages as described above. A more flexible peptide may be prepared by introducing cysteines at the right and left position of the peptide and forming a disulfide bridge between the two cysteines. The two cysteines are arranged so as not to deform the beta-sheet and turn. The peptide is more flexible as a result of the length of the disulfide linkage and the smaller number of hydrogen bonds in the beta-sheet portion. The relative flexibility of a cyclic peptide can be determined by molecular dynamics simulations.

The invention also relates to peptides comprising a fusion protein comprising Casl3 and a RNase protein, wherein the fusion protein is itself fused to, or integrated into, a target protein, and/or a targeting domain capable of directing the chimeric protein to a desired cellular component or cell type or tissue. The chimeric proteins may also contain additional amino acid sequences or domains. The chimeric proteins are recombinant in the sense that the various components are from different sources, and as such are not found together in nature (i.e., are heterologous).

In one embodiment, the targeting domain can be a membrane spanning domain, a membrane binding domain, or a sequence directing the protein to associate with for example vesicles or with the nucleus. In one embodiment, the targeting domain can target a peptide to a particular cell type or tissue. For example, the targeting domain can be a cell surface ligand or an antibody against cell surface antigens of a target tissue. A targeting domain may target the peptide of the invention to a cellular component.

A peptide of the invention may be synthesized by conventional techniques. For example, the peptides or chimeric proteins may be synthesized by chemical synthesis using solid phase peptide synthesis. These methods employ either solid or solution phase synthesis methods (see for example, J. M. Stewart, and J. D. Young, Solid Phase Peptide Synthesis, 2^nd Ed., Pierce Chemical Co., Rockford Ill. (1984) and G. Barany and R. B. Merrifield, The Peptides: Analysis Synthesis, Biology editors E. Gross and J. Meienhofer Vol. 2 Academic Press, New York, 1980, pp. 3-254 for solid phase synthesis techniques; and M Bodansky, Principles of Peptide Synthesis, Springer-Verlag, Berlin 1984, and E. Gross and J. Meienhofer, Eds., The Peptides: Analysis, Synthesis, Biology, suprs, Vol 1, for classical solution synthesis). By way of example, a peptide of the invention may be synthesized using 9-fluorenyl methoxycarbonyl (Fmoc) solid phase chemistry with direct incorporation of phosphothreonine as the N-fluorenylmethoxy-carbonyl-O- benzyl-L-phosphothreonine derivative.

N-terminal or C-terminal fusion proteins comprising a peptide or chimeric protein of the invention conjugated with other molecules may be prepared by fusing, through recombinant techniques, the N-terminal or C-terminal of the peptide or chimeric protein, and the sequence of a selected protein or selectable marker with a desired biological function. The resultant fusion proteins contain the protein fused to the selected protein or marker protein as described herein. Examples of proteins which may be used to prepare fusion proteins include immunoglobulins, glutathione- S-transferase (GST), hemagglutinin (HA), and truncated myc.

Peptides of the invention may be developed using a biological expression system. The use of these systems allows the production of large libraries of random peptide sequences and the screening of these libraries for peptide sequences that bind to particular proteins. Libraries may be produced by cloning synthetic DNA that encodes random peptide sequences into appropriate expression vectors (see Christian et al 1992, J. Mol. Biol. 227:711; Devlin et al, 1990 Science 249:404; Cwirla et al 1990, Proc. Natl. Acad, Sci. USA, 87:6378). Libraries may also be constructed by concurrent synthesis of overlapping peptides (see U.S. Pat. No. 4,708,871).

The peptides and chimeric proteins of the invention may be converted into pharmaceutical salts by reacting with inorganic acids such as hydrochloric acid, sulfuric acid, hydrobromic acid, phosphoric acid, etc., or organic acids such as formic acid, acetic acid, propionic acid, glycolic acid, lactic acid, pyruvic acid, oxalic acid, succinic acid, malic acid, tartaric acid, citric acid, benzoic acid, salicylic acid, benezenesulfonic acid, and toluenesulfonic acids.

Nucleic Acids

In one aspect, the present disclosure novel nucleic acid molecules encoding editing proteins which provide targeted RNA cleavage. In some embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a localization signal. In one embodiment, the localization signal localizes the protein to the site in which a target RNA is located. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a nuclear localization signal (NLS), to target RNA in the nucleus. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a nuclear export signal (NES), to target RNA in the cytoplasm. Other localization signals can be used (and which are known in the art) to target RNA in organelles, such as mitochondria. In other embodiments, the nucleic acid molecule does not comprise a nucleic acid sequence encoding an localization signal, to target RNA in the cytoplasm. In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a purification and/or detection tag.

The present disclosure also provides targeting nucleic acids, including CRISPR RNAs (crRNAs), for targeting the protein of the disclosure to a target RNA.

In one aspect, the present disclosure novel nucleic acid molecules encoding editing proteins which provide targeted RNA cleavage. In some embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a localization signal. In one embodiment, the localization signal localizes the protein to the site in which a target RNA is located. Thus, the disclosure provides nucleic acid molecules encoding proteins for targeted RNA cleavage which are capable of localization.

Editing Protein

In one embodiment, the nucleic acid molecule comprises a sequence nucleic acid encoding an editing protein. In one embodiment, the editing protein includes, but is not limited to, a CRISPR- associated (Cas) protein, a zinc finger nuclease (ZFN) protein, and a protein having a DNA or RNA binding domain.

In one embodiment, the Cas protein has RNA binding activity. In one embodiment, Cas protein is Casl3. In one embodiment, the Cas protein is PspCasl3b, PspCasl3b Truncation, AdmCasl3d, AspCasl3b, AspCasl3c, BmaCasl3a, BzoCasl3b, CamCasl3a, CcaCasl3b, Cga2Casl3a, CgaCasl3a, EbaCasl3a, EreCasl3a, EsCasl3d, FbrCasl3b, FnbCasl3c, FndCasl3c, FnfCasl3c, FnsCasl3c, FpeCasl3c, FulCasl3c, HheCasl3a, LbfCasl3a, LbmCasl3a, LbnCasl3a, LbuCasl3a, LseCasl3a, LshCasl3a, LspCasl3a, Lwa2casl3a, LwaCasl3a, LweCasl3a, PauCasl3b, PbuCasl3b, PgiCasl3b, PguCasl3b, Pin2Casl3b, Pin3Casl3b, PinCasl3b, Pprcasl3a, PsaCasl3b, PsmCasl3b, RaCasl3d, RanCasl3b, RcdCasl3a, RcrCasl3a, RcsCasl3a, RfxCasl3d, UrCasl3d, dPspCasl3b, PspCasl3b_A133H, PspCasl3b_A1058H, dPspCasl3b tmncation, dAdmCasl3d, dAspCasl3b, dAspCasl3c, dBmaCasl3a, dBzoCasl3b, dCamCasl3a, dCcaCasl3b, dCga2Casl3a, dCgaCasl3a, dEbaCasl3a, dEreCasl3a, dEsCasl3d, dFbrCasl3b, dFnbCasl3c, dFndCasl3c, dFnfCasl3c, dFnsCasl3c, dFpeCasl3c, dFulCasl3c, dHheCasl3a, dLbfCasl3a, dLbmCasl3a, dLbnCasl3a, dLbuCasl3a, dLseCasl3a, dLshCasl3a, dLspCasl3a, dLwa2casl3a, dLwaCasl3a, dLweCasl3a, dPauCasl3b, dPbuCasl3b, dPgiCasl3b, dPguCasl3b, dPin2Casl3b, dPin3Casl3b, dPinCasl3b, dPprCasl3a, dPsaCasl3b, dPsmCasl3b, dRaCasl3d, dRanCasl3b, dRcdCasl3a, dRcrCasl3a, dRcsCasl3a, dRIxCasl3d, or dUrCasl3d. Additional Cas proteins are known in the art (e.g., Konermann et al., Cell, 2018, 173:665-676 el4, Yan et al., Mol Cell, 2018, 7:327-339 e5; Cox, D.B.T., et al., Science, 2017, 358: 1019-1027; Abudayyeh et al., Nature, 2017, 550: 280-284, Gootenberg et al., Science, 2017, 356: 438-442; and East-Seletsky et al., Mol Cell, 2017, 66: 373-383 e3, which are herein incorporated by reference).

In one embodiment, the nucleic acid sequence encoding a Cas protein comprises a nucleic acid sequence encoding an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs: 1-49. In one embodiment, the nucleic acid sequence encoding a Cas protein comprises a nucleic acid sequence encoding an amino acid sequence of one of SEQ ID NOs: 1-49. In one embodiment, the nucleic acid sequence encoding a Cas protein comprises a nucleic acid sequence encoding an amino acid sequence of one of SEQ ID NOs: 1-47.

In one embodiment, the nucleic acid sequence encoding a Cas protein comprises a nucleic acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs: 132-135. In one embodiment, the nucleic acid sequence encoding a Cas protein comprises a nucleic acid sequence of one of SEQ ID NOs: 132-135. In one embodiment, the nucleic acid sequence encoding a Cas protein comprises a nucleic acid sequence of one of SEQ ID NOs: 132 or 133.

Localization Signal

In some embodiments, the nucleic acid molecule comprises a nucleic acid sequence encoding a localization signal, such as a nuclear localization signal (NLS), nuclear export signal (NES) or other localization signals to localize to the cytoplasm or to organelles, such as mitochondria. In one embodiment, the localization signal localizes the protein to the site in which the target RNA is located.

Nuclear Localization Signal

In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a nuclear localization signal (NLS). In one embodiment, the NLS is a retrotransposon NLS. In one embodiment, the NLS is derived from Tyl, yeast GAL4, SKI3, L29 or histone H2B proteins, polyoma virus large T protein, VP1 or VP2 capsid protein, SV40 VP1 or VP2 capsid protein, Adenovirus El a or DBP protein, influenza virus NS1 protein, hepatitis vims core antigen or the mammalian lamin, c-myc, max, c-myb, p53, c-erbA, jun, Tax, steroid receptor or Mx proteins, Nucleoplasmin (NPM2), Nucleophosmin (NPM1), or simian vims 40 ("SV40") T-antigen. In one embodiment, the NLS is a Tyl or Tyl-derived NLS, a Ty2 or Ty2-derived NLS or a MAK11 or MAK11 -derived NLS. In one embodiment, the Tyl NLS comprises an amino acid sequence of SEQ ID NO:50. In one embodiment, the Ty2 NLS comprises an amino acid sequence of SEQ ID NO:51. In one embodiment, the MAK11 NLS comprises an amino acid sequence of SEQ ID NO:52. In one embodiment, the nucleic acid sequence encoding a NLS comprises a nucleic acid sequence encoding an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs: 50-57 and 323-935. In one embodiment, the nucleic acid sequence encoding a NLS comprises a nucleic acid sequence encoding an amino acid sequence of one of SEQ ID NOs: 50-57 and 323-935.

In one embodiment, the NLS is a Ty 1-like NLS. For example, in one embodiment, the Ty 1-like NLS comprises KKRX motif. In one embodiment, the Tyl-like NLS comprises KKRX motif at the N- terminal end. In one embodiment, the Tyl-like NLS comprises KKR motif. In one embodiment, the Tyl- like NLS comprises KKR motif at the C-terminal end. In one embodiment, the Tyl-like NLS comprises a KKRX and a KKR motif. In one embodiment, the Tyl-like NLS comprises a KKRX at the N-terminal end and a KKR motif at the C-terminal end. In one embodiment, the Tyl-like NLS comprises at least 20 amino acids. In one embodiment, the Tyl-like NLS comprises between 20 and 40 amino acids. In one embodiment, the nucleic acid sequence encoding a Tyl-like NLS comprises a nucleic acid sequence encoding an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs: 323-935. In one embodiment, the nucleic acid sequence encoding a Tyl-like NLS comprises a nucleic acid sequence encoding an amino acid sequence of one of SEQ ID NOs: 323-935, wherein the sequence comprises one or more, two or more, three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, or ten or more, insertions, deletions or substitutions. In one embodiment, the nucleic acid sequence encoding a Tyl-like NLS comprises a nucleic acid sequence encoding an amino acid sequence of one of SEQ ID NOs: 323- 935. In one embodiment, the nucleic acid sequence encoding an NLS encodes two copies of the same NLS. For example, in one embodiment, the nucleic acid sequence encodes a multimer of a first Tyl- derived NLS and a second Tyl -derived NLS.

In one embodiment, the nucleic acid sequence encoding a NLS comprises a nucleic acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 136. In one embodiment, the nucleic acid sequence encoding a NLS comprises a nucleic acid sequence of SEQ ID NO: 136.

Nuclear Export Signal

In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a Nuclear Export Signal (NES). In one embodiment, the NES localizes the protein to the cytoplasm for targeting cytoplasmic RNA. In one embodiment, the nucleic acid sequence encoding the NES comprises a sequence encoding an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NOs: 58 or 59. In one embodiment, the nucleic acid sequence encoding the NES comprises a sequence encoding an amino acid sequence of SEQ ID NOs: 58 or 59.

In one embodiment, the nucleic acid sequence encoding the NES comprises a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NOs: 137 or 138. In one embodiment, the nucleic acid sequence encoding the NES comprises a sequence of SEQ ID NOs: 137 or 138.

Organelle Localization Signal

In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a localization signal that localizes the protein to an organelle or extracellularly. In one embodiment, the localization signal localizes the protein to the nucleolus, ribosome, vesicle, rough endoplasmic reticulum, Golgi apparatus, cytoskeleton, smooth endoplasmic reticulum, mitochondria, vacuole, cytosol, lysosome, or centriole. A number of localization signals are known in the art.

Exemplary localization signals include, but are not limited to lx mitochondrial targeting sequence, 4x mitochondrial targeting sequence, secretory signal sequence (IL-2), myristylation, Calsequestrin leader, KDEL retention and peroxisome targeting sequence.

In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a localization signal. In one embodiment, the localization signal localizes the protein to an organelle or extracellularly. In one embodiment, the nucleic acid sequence encoding the localization signal comprises a sequence encoding an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a localization signal. In one embodiment, the localization signal localizes the protein to an organelle or extracellularly. In one embodiment, the nucleic acid sequence encoding the localization signal comprises a sequence encoding an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs: 60-66. In one embodiment, the nucleic acid sequence encoding the localization signal comprises a sequence encoding an amino acid sequence of one of SEQ ID NOs: 60-66.

In one embodiment, the nucleic acid sequence encoding the localization signal comprises a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs: 139-145. In one embodiment, the nucleic acid sequence encoding the localization signal comprises a sequence of one of SEQ ID NOs: 139-145.

Purification and/or Detection Tag

In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a purification and/or detection tag. In one embodiment, the tag is on the N-terminal end of the protein. In one embodiment, the tag is a 3xFLAG tag. In one embodiment, nucleic acid sequence encoding a purification and/or detection tag encodes an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO:67. In one embodiment, nucleic acid sequence encoding a purification and/or detection tag encodes an amino acid sequence of SEQ ID NO:67.

In one embodiment, nucleic acid sequence encoding a purification and/or detection tag comprises sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 146. In one embodiment, nucleic acid sequence encoding a purification and/or detection tag comprises a sequence of SEQ ID NO: 146.

Cleavage and/or Polyadenylation Proteins

In one aspect, In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a cleavage and/or polyadenylation protein. In one embodiment, the cleavage and/or polyadenylation protein is an RNA binding protein of the human 3’ end processing machinery. In one embodiment, the cleavage and/or polyadenylation protein is CPSF30, WDR33, orNUDT21. In one embodiment, the cleavage and/or polyadenylation protein is NUDT21. In one embodiment, the cleavage and/or polyadenylation protein is NUDT21 , a NUDT21 mutation, a NUDT21 dimer, a NUDT21 fusion protein or any combination thereof. In one embodiment, the cleavage and/or polyadenylation protein is human NUDT21, Worm NUDT21, Fly NUDT21, Zebrafish NUDT21, NUDT21 R63S, NUDT21 F103A, or a tandem dimer of NUDT21.

In one embodiment, the nucleic acid sequence encoding the cleavage and/or polyadenylation protein encodes an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs:298-307. In one embodiment, the nucleic acid sequence encoding the cleavage and/or polyadenylation protein encodes amino acid sequence of one of SEQ ID NOs: 298-307.

In one embodiment, nucleic acid sequence encoding a cleavage and/or polyadenylation protein comprises sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO:311-319. In one embodiment, nucleic acid sequence encoding a cleavage and/or polyadenylation protein comprises a sequence of SEQ ID NO:311-319.

Fusion Proteins

Fusion Protein comprising a Cas Protein and Localization Signal

In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a protein of the disclosure, which is effectively delivered to the nucleus, an organelle, the cytoplasm or extracellularly and allow for targeted RNA cleavage. In one embodiment, the nucleic acid sequence encoding a protein encodes an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs: 68-100. In one embodiment, the nucleic acid sequence encoding a protein encodes an amino acid sequence of one of SEQ ID NOs: 68- 100

In one embodiment, the nucleic acid sequence encoding a protein comprises a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs: 147-166. In one embodiment, the nucleic acid sequence encoding a protein comprises a sequence of one of SEQ ID NOs: 147-166.

In one embodiment, the nucleic acid molecule comprises a nucleic acid sequence encoding a protein of the disclosure, which allow for targeted RNA cleavage and/or polyadenylation. In one embodiment, the nucleic acid sequence encoding a protein encodes an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID N0s:308-310. In one embodiment, the nucleic acid sequence encoding a protein encodes an amino acid sequence of one of SEQ ID NOs: 308-310.

In one embodiment, the nucleic acid sequence encoding a protein comprises a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs: 320-322. In one embodiment, the nucleic acid sequence encoding a protein comprises a sequence of one of SEQ ID NOs: 320-322.

Targeting Nucleic Acids and CRISPR RNAs (crRNAs)

In one aspect, the disclosure provides CRISPR RNAs (crRNAs) for targeting Cas to a target RNA. In one embodiment, crRNA comprises guide sequence. In one embodiment, the crRNA comprises a direct repeat (DR) sequence. In one embodiment the crRNA comprises a direct repeat sequence and a guide sequence fused or linked to a guide sequence or spacer sequence. In one embodiment the direct repeat sequence may be located upstream (i.e., 5') from the guide sequence or spacer sequence. In other embodiments, the direct repeat sequence may be located downstream (i.e., 3') from the guide sequence or spacer sequence.

In some embodiments, the crRNA comprises a stem loop. In one embodiment, the crRNA comprises a single stem loop. In one embodiment, the direct repeat sequence forms a stem loop. In one embodiment, the direct repeat sequence forms a single stem loop.

In one embodiment, the spacer length of the guide RNA is from 15 to 35 nt. In one embodiment, the spacer length of the guide RNA is at least 15 nucleotides. In one embodiment the spacer length is from 15 to 17 nt, e.g., 15, 16, or 17 nt, from 17 to 20 nt, e.g., 17, 18, 19, or 20 nt, from 20 to 24 nt, e.g., 20, 21, 22, 23, or 24 nt, from 23 to 25 nt, e.g., 23, 24, or 25 nt, from 24 to 27 nt, e.g., 24, 25, 26, or 27 nt, from 27-30 nt, e.g., 27, 28, 29, or 30 nt, from 30-35 nt, e.g., 30, 31, 32, 33, 34, or 35 nt, or 35 nt or longer.

In general, a guide sequence is any polynucleotide sequence having sufficient complementarity with a target polynucleotide sequence to hybridize with the target sequence and direct sequence-specific binding of a CRISPR complex to the target sequence. In some embodiments, the degree of complementarity between a guide sequence and its corresponding target sequence, when optimally aligned using a suitable alignment algorithm, is about or more than about 50%, 60%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%, or more. Optimal alignment may be determined with the use of any suitable algorithm for aligning sequences, non-limiting example of which include the Smith-Waterman algorithm, the Needleman-Wunsch algorithm, algorithms based on the Burrows-Wheeler Transform (e.g. the Burrows Wheeler Aligner), ClustalW, Clustal X, BLAT, Novoalign (Novocraft Technologies; available at www.novocraft.com), ELAND (Illumina, San Diego, Calif.), SOAP (available at soap.genomics.org.cn), and Maq (available at maq.sourceforge.net). In some embodiments, a guide sequence is about or more than about 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45,

50, 75, or more nucleotides in length. In some embodiments, a guide sequence is less than about 75, 50, 45, 40, 35, 30, 25, 20, 15, 12, or fewer nucleotides in length. Preferably the guide sequence is 1030 nucleotides long. The ability of a guide sequence to direct sequence-specific binding of a CRISPR complex to a target sequence may be assessed by any suitable assay. For example, the components of a CRISPR system sufficient to form a CRISPR complex, including the guide sequence to be tested, may be provided to a host cell having the corresponding target sequence, such as by transfection with vectors encoding the components of the CRISPR sequence, followed by an assessment of preferential cleavage within the target sequence, such as by Surveyor assay as described herein. Similarly, cleavage of a target polynucleotide sequence may be evaluated in a test tube by providing the target sequence, components of a CRISPR complex, including the guide sequence to be tested and a control guide sequence different from the test guide sequence, and comparing binding or rate of cleavage at the target sequence between the test and control guide sequence reactions. Other assays are possible, and will occur to those skilled in the art.

In some embodiments of CRISPR-Cas systems, the degree of complementarity between a guide sequence and its corresponding target sequence can be about or more than about 50%, 60%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%, or 100%; a guide or RNA or sgRNA can be about or more than about 5,

10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 75, or more nucleotides in length; or guide or RNA or sgRNA can be less than about 75, 50, 45, 40, 35, 30, 25, 20, 15, 12, or fewer nucleotides in length; and advantageously tracr RNA is 30 or 50 nucleotides in length. However, an aspect of the disclosure is to reduce off-target interactions, e.g., reduce the guide interacting with a target sequence having low complementarity. Indeed, in the examples, it is shown that the disclosure involves mutations that result in the CRISPR-Cas system being able to distinguish between target and off-target sequences that have greater than 80% to about 95% complementarity, e.g., 83%-84% or 88-89% or 94-95% complementarity (for instance, distinguishing between a target having 18 nucleotides from an off-target of 18 nucleotides having 1, 2 or 3 mismatches). Accordingly, in the context of the present disclosure the degree of complementarity between a guide sequence and its corresponding target sequence is greater than 94.5% or 95% or 95.5% or 96% or 96.5% or 97% or 97.5% or 98% or 98.5% or 99% or 99.5% or 99.9%, or 100%. Off target is less than 100% or 99.9% or 99.5% or 99% or 99% or 98.5% or 98% or 97.5% or 97% or 96.5% or 96% or 95.5% or 95% or 94.5% or 94% or 93% or 92% or 91% or 90% or 89% or 88% or 87% or 86% or 85% or 84% or 83% or 82% or 81% or 80% complementarity between the sequence and the guide, with it advantageous that off target is 100% or 99.9% or 99.5% or 99% or 99% or 98.5% or 98% or 97.5% or 97% or 96.5% or 96% or 95.5% or 95% or 94.5% complementarity between the sequence and the guide.

In one embodiment, the crRNA comprises a sequence substantially complementary to a viral RNA sequence. In one embodiment, the crRNA compnses a sequence substantially complementary to a Coronavirus genomic mRNA sequence or a Coronavirus subgenomic mRNA sequence. For example, in one embodiment, the crRNA comprises a sequence substantially complementary to a Coronavirus leader sequence, S sequence, E sequence, M sequence, N sequence, or S2M sequence. In one embodiment, the crRNA comprises a sequence substantially complementary to a Coronavirus leader sequence, N sequence, or S2M sequence.

In one embodiment, the crRNA comprises a sequence that is substantially complementary to a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to a sequence selected from SEQ ID NOs: 167-187, or a fragment thereof. In one embodiment, the crRNA comprises a sequence that is substantially complementary to a sequence selected from SEQ ID NOs: 167-187, or a fragment thereof.

In one embodiment, the crRNA comprises a sequence that is substantially complementary to a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to a fragment of a sequence selected from SEQ ID NOs: 167, 175, or 182-185. In one embodiment, the crRNA comprises a sequence that is substantially complementary to a fragment of a sequence selected from SEQ ID NOs: 167, 175, or 182-185.

In one embodiment, the crRNA comprises a sequence that is substantially complementary to a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to a sequence selected from SEQ ID NOs: 168-174, 176-181, 186, and 187. In one embodiment, the crRNA comprises a sequence that is substantially complementary to a sequence selected from SEQ ID NOs: 168-174, 176-181, 186, and 187.

In one embodiment, the crRNA comprises a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to a sequence selected from SEQ ID NOs: 189-224. In one embodiment, the crRNA comprises a sequence selected from SEQ ID NOs: 189- 224.

In one embodiment, the disclosure provides crRNA having a sequence substantially complementary to an influenza virus sequence. In one embodiment, the crRNA comprises a substantially complementary to an influenza virus genomic mRNA sequence or a subgenomic mRNA sequence. For example, in one embodiment, the crRNA comprises a sequence substantially complementary to an Influenza vims PB2 sequence, PB1 sequence, PA sequence, HA sequence, NP sequence, NA sequence, M sequence or NS sequence. In one embodiment, the crRNA comprises a sequence substantially complementary to an Influenza vims PB2 sequence, PB1 sequence, PA sequence, NP sequence, or M sequence.

In one embodiment, the crRNA comprises a sequence that is substantially complementary to a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to a sequence selected from SEQ ID NOs:225-244, or a fragment thereof. In one embodiment, the crRNA comprises a sequence that is substantially complementary to a sequence selected from SEQ ID NOs: 225-244, or a fragment thereof.

In one embodiment, the crRNA comprises a sequence that is substantially complementary to a viral RNA sequence. In one embodiment, the crRNA comprises a sequence that is substantially complementary to a sequence a positive-sense viral RNA sequence. In one embodiment, the crRNA comprises a sequence that is substantially complementary to a sequence a negative-sense viral RNA sequence. In one embodiment, the crRNA comprises a sequence that at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to a sequence selected from SEQ ID NOs: 245-264. In one embodiment, the crRNA comprises a sequence selected from SEQ ID NOs: 245-264.

In one embodiment, the crRNA comprises a direct repeat (DR) sequence. In one embodiment, the DR sequence is 5’ of the sequence substantially complementary to the target sequence. For example, in one embodiment, the DR sequence is 5’ of the sequence substantially complementary to a Coronavirus genomic mRNA sequence or a Coronavirus subgenomic mRNA sequence. In one embodiment, the DR sequence is 5 ’ of the sequence substantially complementary to an influenza vims genomic RNA sequence or a influenza vims subgenomic RNA sequence. In one embodiment, the DR sequence is 5 ’ of the sequence substantially complementary to an expanded RNA repeat sequence. In one embodiment, the DR sequence enhances the activity of Casl3 targeting to a target sequence, Casl3 catalytic activity, or both. For example, in one embodiment, the DR sequence comprises a mutation. For example, in one embodiment, the DR sequence comprises a T17C point mutation. In one embodiment, the DR sequence comprises a T18C point mutation. In one embodiment, the DR sequence is 5’ of a sequence at least 80% homologous to a sequence selected from SEQ ID NOs: 189-224 and 245-264.

In one embodiment, the DR sequence is 3’ of the sequence substantially complementary to the target sequence. For example, in one embodiment, the DR sequence is 3’ of the sequence substantially complementary to a Coronavirus genomic mRNA sequence or a Coronavirus subgenomic mRNA sequence. In one embodiment, the DR sequence is 3’ of the sequence substantially complementary to an Influenza vims genomic mRNA sequence or an Influenza vims subgenomic mRNA sequence. In one embodiment, the DR sequence is 3’ of a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to a sequence selected from SEQ ID NOs: 189-224 and 245-264.

In one embodiment, selection of a 5 ’ or 3 ’ DR sequence is dependent on the Cas protein ortholog used. In one embodiment the DR sequence comprises a sequence selected from SEQ ID NOs: 265-274.

Tandem Arrays

In one embodiment, the invention provides tandem CRISPR RNA (crRNA) arrays. In one embodiment, the tandem crRNA arrays allow for a single promoter to drive expression of multiple crRNAs. In one embodiment, the tandem array comprises one or more, two or more, three or more, four or more, five or more six or more, seven or more or eight or more crRNA sequences. In one embodiment, each crRNA in the tandem crRNA array comprises a direct repeat (DR) sequence and a spacer sequence. In one embodiment the direct repeat sequence may be located upstream (i.e., 5') from the guide sequence or spacer sequence. In other embodiments, the direct repeat sequence may be located downstream (i.e., 3') from the guide sequence or spacer sequence.

In one embodiment, the DR sequence is specific for an associated Cas protein. For example, in one embodiment, the Cas protein is Cas 13 and the direct repeat sequence compnses a sequence of one of SEQ ID NOs: 265-274. In one embodiment, the direct repeat sequence includes a single mutation in the poly T stretch. For example, in one embodiment, the direct repeat sequence comprises a sequence selected from SEQ ID NOs: 268-274.

In one embodiment, each crRNA in the tandem crRNA array comprises a different direct repeat sequence. For example, in one embodiment, nucleotide substitutions within the loop region of the direct repeat, multiple guide-RNAs provides for efficiently generated ordered arrays of crRNAs.

In one embodiment, the tandem array comprises at least two or more crRNA, wherein each crRNA comprises a sequence substantially complementary to a target RNA. For example, in one embodiment, each crRNA comprises a different sequence substantially complementary to a different sequence in a single target RNA. In one embodiment, each crRNA comprises a different sequence substantially complementary to a different sequence in a different target RNAs. In one embodiment, the different target RNAs are related to a single disease, disorder or infection. For example, in one embodiment, the different target RNAs are each viral RNA sequences of a virus.

For example, in one embodiment, each crRNA comprises a different sequence substantially complementary to a different sequence within a genomic coronavirus RNA sequence and/or a sub- genomic coronavirus RNA sequence. In one embodiment, the crRNA comprises a substantially complementary to a corona virus genomic mRNA sequence or a Coronavirus subgenomic mRNA sequence. For example, in one embodiment, the crRNA comprises a sequence substantially complementary to a Coronavirus leader sequence, S sequence, E sequence, M sequence, N sequence, or S2M sequence. In one embodiment, the crRNA comprises a sequence substantially complementary to a Coronavirus leader sequence, N sequence, or S2M sequence.

In one embodiment, the tandem array comprises at least two or more crRNA comprising sequences substantially complementary to a genomic coronavirus RNA sequence and/or a sub-genomic coronavirus RNA sequence. In one embodiment, the tandem array comprises at least two or more crRNA comprising a substantially complementary to a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to a sequence selected from SEQ ID NOs: 167-188 or a fragment thereof. In one embodiment, the tandem array comprises at least two or more crRNA comprising a substantially complementary to a sequence selected from SEQ ID NOs: 167-188, or a fragment thereof.

In one embodiment, the tandem array comprises at least two or more crRNA comprising a substantially complementary to a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to a sequence selected from SEQ ID NOs: 168-174, 176- 181, 186, and 187. In one embodiment, the tandem array comprises at least two ormore crRNA comprising a substantially complementary to a sequence selected from SEQ ID NOs: 168-174, 176-181, 186, and 187.

In one embodiment, the tandem array comprises at least two or more crRNA comprising a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to a sequence selected from SEQ ID NOs: 189-224. In one embodiment, the tandem array comprises at least two or more crRNA comprising a sequence selected from SEQ ID NOs: 189-224.

In one embodiment, the tandem array comprises a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to SEQ ID NO:275. In one embodiment, the tandem array comprises a sequence of SEQ ID NO: 275.

In one embodiment, the tandem array comprises at least two or more crRNA each independently comprising sequences substantially complementary to an influenza vims sequence. In one embodiment, the tandem array comprises at least two or more crRNA each comprising a sequence substantially complementary to an influenza vims genomic mRNA sequence or a subgenomic mRNA sequence. In one embodiment, the tandem array comprises at least two or more crRNA each comprising a sequence substantially complementary to an Influenza virus PB2 sequence, PB1 sequence, PA sequence, HA sequence, NP sequence, NA sequence, M sequence or NS sequence.

In one embodiment, the tandem array comprises at least two or more crRNA comprising a substantially complementary to a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to a sequence selected from SEQ ID NOs: 225-244 or a fragment thereof. In one embodiment, the tandem array comprises at least two or more crRNA comprising a substantially complementary to a sequence selected from SEQ ID NOs: 225-244, or a fragment thereof.

In one embodiment, the tandem array comprises at least two or more crRNA comprising a sequence each targeting a different positive sense vRNA segment 1, 2, 3, 5 or 7. In one embodiment, the tandem array comprises at least two or more crRNA comprising a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to a sequence selected from SEQ ID NOs: 216-225. In one embodiment, the tandem array comprises at least two or more crRNA comprising a sequence selected from SEQ ID NOs: 245-264. In one embodiment, the tandem array comprises at least two or more crRNA comprising a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to a sequence selected from SEQ ID NOs: 255-259. In one embodiment, the tandem array comprises at least two or more crRNA comprising a sequence selected from SEQ ID NOs: 255-259.

In one embodiment, the tandem array comprises at least two or more crRNA comprising a sequence each targeting a different negative sense vRNA segment 1, 2, 3, 5 or 7. In one embodiment, the tandem array comprises at least two or more crRNA comprising a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to a sequence selected from SEQ ID NOs: 245-249. In one embodiment, the tandem array comprises at least two or more crRNA comprising a sequence selected from SEQ ID NOs: 245-249. In one embodiment, the tandem array comprises at least two or more crRNA comprising a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to a sequence selected from SEQ ID NOs: 260-264. In one embodiment, the tandem array comprises at least two or more crRNA comprising a sequence selected from SEQ ID NOs: 260-264.

In one embodiment, the tandem array comprises at least two or more crRNA comprising a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to a sequence selected from SEQ ID NOs: 250-254. In one embodiment, the tandem array comprises at least two or more crRNA comprising a sequence selected from SEQ ID NOs: 250-254.

In one embodiment, the tandem array comprises a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to one of SEQ ID NOs: 276- 279. In one embodiment, the tandem array comprises a sequence of SEQ ID NOs: 276-279.

In one embodiment, the tandem array comprises at least two or more crRNA each independently comprising sequences substantially complementary to mRNA sequences within a cellular pathway. In some embodiments, the cellular pathway lead, for example, to aberrant control of cellular processes, with uncontrolled growth and increased cell survival. For example, in one embodiment, each crRNA independently comprises a sequence substantially complementary to an mRNA sequence within the RAS, JAK-STAT, PI3K/AKT ErbB, the p53-mediated apoptosis, GSK3, Hippo, Wnt, Estrogen, Insulin, mTOR,NF-kB, Notch, TGF- b, Toll-like Receptor, VEGF, AMPK or MAPK cellular signaling pathways.

In one embodiment, the tandem array comprises at least two or more crRNA each independently comprising sequences substantially complementary to mRNA sequences for use in biofuel production in microorganisms or plants, Bioengineering CAR-T cells, silencing stress response pathways, immune cell inflammation pathways. Targeting multiple different types or subtypes of infectious vims.

In one embodiment, the crRNA comprises a direct repeat (DR) sequence. In one embodiment, the DR sequence is 5’ of the sequence substantially complementary to the target sequence. For example, in one embodiment, the DR sequence is 5’ of the sequence substantially complementary to a Coronavirus genomic mRNA sequence or a Coronavirus subgenomic mRNA sequence. In one embodiment, the DR sequence enhances the activity of Casl3 targeting to a target sequence, Casl3 catalytic activity, or both. For example, in one embodiment, the DR sequence comprises a mutation. For example, in one embodiment, the DR sequence comprises a T17C point mutation. In one embodiment, the DR sequence comprises a T18C point mutation. In one embodiment, the DR sequence comprises a T17A point mutation. In one embodiment, the DR sequence comprises a T18A point mutation. In one embodiment, the DR sequence comprises a T17G point mutation. In one embodiment, the DR sequence comprises a T18G point mutation. In one embodiment, the DR sequence is 5’ of a sequence at least 80% homologous to a sequence selected from SEQ ID NOs: 189-224. In one embodiment, the DR sequence is 3’ of the sequence substantially complementary to the target sequence. For example, in one embodiment, the DR sequence is 3 ’ of the sequence substantially complementary to a corona vims genomic mRNA sequence or a Coronavirus subgenomic mRNA sequence. In one embodiment, the DR sequence is 3’ of a sequence at least 80% homologous to a sequence selected from SEQ ID NOs: 189-224. In one embodiment, selection of a 5’ or 3’ DR sequence is dependent on the Cas protein ortholog used. In one embodiment the DR sequence comprises a sequence selected from SEQ ID NOs: 265-274.

In general, a “guide sequence,” which is used interchangeably with the term “spacer sequence” is any polynucleotide sequence having sufficient complementarity with a target polynucleotide sequence to hybridize with the target sequence and direct sequence-specific binding of a CRISPR complex to the target sequence. In some embodiments, the degree of complementarity between a guide sequence and its corresponding target sequence, when optimally aligned using a suitable alignment algorithm, is about or more than about 50%, 60%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%, or more. Optimal alignment may be determined with the use of any suitable algorithm for aligning sequences, non-limiting example of which include the Smith-Waterman algorithm, the Needleman-Wunsch algorithm, algorithms based on the Burrows-Wheeler Transform (e.g. the Burrows Wheeler Aligner), ClustalW, Clustal X, BLAT, Novoalign (Novocraft Technologies; available at www.novocraft.com), ELAND (Illumina, San Diego, Calif.), SOAP (available at soap.genomics.org.cn), and Maq (available at maq.sourceforge.net). In some embodiments, a guide sequence is about or more than about 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 75, or more nucleotides in length. In some embodiments, a guide sequence is less than about 75, 50, 45, 40, 35, 30, 25, 20, 15, 12, or fewer nucleotides in length. Preferably the guide sequence is 10 30 nucleotides long. The ability of a guide sequence to direct sequence-specific binding of a CRISPR complex to a target sequence may be assessed by any suitable assay. For example, the components of a CRISPR system sufficient to form a CRISPR complex, including the guide sequence to be tested, may be provided to a host cell having the corresponding target sequence, such as by transfection with vectors encoding the components of the CRISPR sequence, followed by an assessment of preferential cleavage within the target sequence, such as by Surveyor assay as described herein. Similarly, cleavage of a target polynucleotide sequence may be evaluated in a test tube by providing the target sequence, components of a CRISPR complex, including the guide sequence to be tested and a control guide sequence different from the test guide sequence, and comparing binding or rate of cleavage at the target sequence between the test and control guide sequence reactions. Other assays are possible, and will occur to those skilled in the art.

10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 75, or more nucleotides in length; or guide or RNA or sgRNA can be less than about 75, 50, 45, 40, 35, 30, 25, 20, 15, 12, or fewer nucleotides in length; and advantageously tracr RNA is 30 or 50 nucleotides in length. However, an aspect of the invention is to reduce off-target interactions, e.g., reduce the guide interacting with a target sequence having low complementarity. Indeed, in the examples, it is shown that the invention involves mutations that result in the CRISPR-Cas system being able to distinguish between target and off-target sequences that have greater than 80% to about 95% complementarity, e.g., 83%-84% or 88-89% or 94-95% complementarity (for instance, distinguishing between a target having 18 nucleotides from an off-target of 18 nucleotides having 1, 2 or 3 mismatches). Accordingly, in the context of the present invention the degree of complementarity between a guide sequence and its corresponding target sequence is greater than 94.5% or 95% or 95.5% or 96% or 96.5% or 97% or 97.5% or 98% or 98.5% or 99% or 99.5% or 99.9%, or 100%. Off target is less than 100% or 99.9% or 99.5% or 99% or 99% or 98.5% or 98% or 97.5% or 97% or 96.5% or 96% or 95.5% or 95% or 94.5% or 94% or 93% or 92% or 91% or 90% or 89% or 88% or 87% or 86% or 85% or 84% or 83% or 82% or 81% or 80% complementarity between the sequence and the guide, with it advantageous that off target is 100% or 99.9% or 99.5% or 99% or 99% or 98.5% or 98% or 97.5% or 97% or 96.5% or 96% or 95.5% or 95% or 94.5% complementarity between the sequence and the guide.

Nucleic Acids

The isolated nucleic acid sequences of the disclosure can be obtained using any of the many recombinant methods known in the art, such as, for example by screening libraries from cells expressing the gene, by deriving the gene from a vector known to include the same, or by isolating directly from cells and tissues containing the same, using standard techniques. Alternatively, the gene of interest can be produced synthetically, rather than cloned.

The isolated nucleic acid may comprise any type of nucleic acid, including, but not limited to DNA and RNA. For example, in one embodiment, the composition comprises an isolated DNA molecule, including for example, an isolated cDNA molecule, encoding a protein of the disclosure. In one embodiment, the composition comprises an isolated RNA molecule encoding a protein of the disclosure, or a functional fragment thereof.

The nucleic acid molecules of the present invention can be modified to improve stability in serum or in growth medium for cell cultures. Modifications can be added to enhance stability, functionality, and/or specificity and to minimize immunostimulatory properties of the nucleic acid molecule of the invention. For example, in order to enhance the stability, the 3 ’-residues may be stabilized against degradation, e.g., they may be selected such that they consist of purine nucleotides, particularly adenosine or guanosine nucleotides. Alternatively, substitution of pyrimidine nucleotides by modified analogues, e.g., substitution of uridine by 2’-deoxythymidine is tolerated and does not affect function of the molecule.

In one embodiment of the present invention the nucleic acid molecule may contain at least one modified nucleotide analogue. For example, the ends may be stabilized by incorporating modified nucleotide analogues.

Non-limiting examples of nucleotide analogues include sugar- and or backbone -modified ribonucleotides (i.e., include modifications to the phosphate-sugar backbone). For example, the phosphodiester linkages of natural RNA may be modified to include at least one of a nitrogen or sulfur heteroatom. In exemplary backbone-modified ribonucleotides the phosphoester group connecting to adjacent ribonucleotides is replaced by a modified group, e.g., of phosphothioate group. In exemplary sugar-modified ribonucleotides, the 2’ OH-group is replaced by a group selected from H, OR, R, halo,

SH, SR, NFF, NHR, NR or ON, wherein R is C -G, alkyl, alkenyl or alkynyl and halo is F, Cl, Br or I. Other examples of modifications are nucleobase-modified ribonucleotides, i.e., ribonucleotides, containing at least one non-naturally occurring nucleobase instead of a naturally occurring nucleobase. Bases may be modified to block the activity of adenosine deaminase. Exemplary modified nucleobases include, but are not limited to, uridine and/or cytidine modified at the 5-position, e.g., 5-(2-amino)propyl uridine, 5-bromo uridine; adenosine and/or guanosines modified at the 8 position, e.g., 8-bromo guanosine; deaza nucleotides, e.g., 7-deaza-adenosine; 0- and N-alkylated nucleotides, e.g., N6-methyl adenosine are suitable. It should be noted that the above modifications may be combined.

In some instances, the nucleic acid molecule comprises at least one of the following chemical modifications: 2’-H, 2’-0-methyl, or 2’-OH modification of one or more nucleotides. In certain embodiments, a nucleic acid molecule of the invention can have enhanced resistance to nucleases. For increased nuclease resistance, a nucleic acid molecule, can include, for example, T -modified ribose units and/or phosphorothioate linkages. For example, the 2’ hydroxyl group (OH) can be modified or replaced with a number of different “oxy” or “deoxy” substituents. For increased nuclease resistance the nucleic acid molecules of the invention can include 2’-0-methyl, 2’-fluorine, 2’-0-methoxyethyl, 2’-0- aminopropyl, 2’-amino, and/or phosphorothioate linkages. Inclusion of locked nucleic acids (FNA), ethylene nucleic acids (ENA), e.g., 2’-4’-ethylene-bridged nucleic acids, and certain nucleobase modifications such as 2-amino-A, 2-thio (e.g., 2-thio-U), G-clamp modifications, can also increase binding affinity to a target.

In one embodiment, the nucleic acid molecule includes a 2’-modified nucleotide, e.g., a 2’-deoxy, 2’-deoxy-2’-fluoro, 2’-0-methyl, 2’-0-methoxyethyl (2’-0-M0E), 2’-0-aminopropyl (2’-0-AP), 2 -0- dimethylaminoethyl (2’-0-DMA0E), 2’-0-dimethylaminopropyl (2’-0-DMAP), 2 -0- dimethylaminoethyloxyethyl (2’-0-DMAE0E), or 2’-0-N-methylacetamido (2’-0-NMA). In one embodiment, the nucleic acid molecule includes at least one 2’ -O-methyl -modified nucleotide, and in some embodiments, all of the nucleotides of the nucleic acid molecule include a 2’-0-methyl modification.

In certain embodiments, the nucleic acid molecule of the invention has one or more of the following properties:

Nucleic acid agents discussed herein include otherwise unmodified RNA and DNA as well as RNA and DNA that have been modified, e.g., to improve efficacy, and polymers of nucleoside surrogates. Unmodified RNA refers to a molecule in which the components of the nucleic acid, namely sugars, bases, and phosphate moieties, are the same or essentially the same as that which occur in nature, or as occur naturally in the human body. The art has referred to rare or unusual, but naturally occurring, RNAs as modified RNAs, see, e.g., Fimbach et al. (Nucleic Acids Res., 1994, 22:2183-2196). Such rare or unusual RNAs, often termed modified RNAs, are typically the result of a post-transcriptional modification and are within the term unmodified RNA as used herein. Modified RNA, as used herein, refers to a molecule in which one or more of the components of the nucleic acid, namely sugars, bases, and phosphate moieties, are different from that which occur in nature, or different from that which occurs in the human body. While they are referred to as “modified RNAs” they will of course, because of the modification, include molecules that are not, strictly speaking, RNAs. Nucleoside surrogates are molecules in which the ribophosphate backbone is replaced with a non-ribophosphate construct that allows the bases to be presented in the correct spatial relationship such that hybridization is substantially similar to what is seen with a ribophosphate backbone, e.g., non-charged mimics of the ribophosphate backbone.

Modifications of the nucleic acid of the invention may be present at one or more of, a phosphate group, a sugar group, backbone, N-terminus, C-terminus, or nucleobase.

The present invention also includes a vector in which the isolated nucleic acid of the present invention is inserted. The art is replete with suitable vectors that are useful in the present invention.

In brief summary, the expression of natural or synthetic nucleic acids encoding a protein of the disclosure is typically achieved by operably linking a nucleic acid encoding the protein of the disclosure or portions thereof to a promoter, and incorporating the construct into an expression vector. The vectors to be used are suitable for replication and, optionally, integration in eukaryotic cells. Typical vectors contain transcription and translation terminators, initiation sequences, and promoters useful for regulation of the expression of the desired nucleic acid sequence.

The vectors of the present invention may also be used for nucleic acid immunization and gene therapy, using standard gene delivery protocols. Methods for gene delivery are known in the art. See, e.g., U.S. Pat. Nos. 5,399,346, 5,580,859, 5,589,466, incorporated by reference herein in their entireties. In another embodiment, the invention provides a gene therapy vector.

The isolated nucleic acid of the invention can be cloned into a number of types of vectors. For example, the nucleic acid can be cloned into a vector including, but not limited to a plasmid, a phagemid, a phage derivative, an animal virus, and a cosmid. Vectors of particular interest include expression vectors, replication vectors, probe generation vectors, and sequencing vectors.

Further, the vector may be provided to a cell in the form of a viral vector. Viral vector technology is well known in the art and is described, for example, in Sambrook et al. (2012, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York), and in other virology and molecular biology manuals. Vimses, which are useful as vectors include, but are not limited to, retrovimses, adenoviruses, adeno- associated viruses, herpes vimses, and lentiviruses. In general, a suitable vector contains an origin of replication functional in at least one organism, a promoter sequence, convenient restriction endonuclease sites, and one or more selectable markers, (e.g., WO 01/96584; WO 01/29058; and U.S. Pat. No. 6,326,193).

Delivery Systems and Methods

In one aspect, the disclosure relates to the development of novel lentiviral packaging and delivery systems. The lentiviral particle delivers the viral enzymes as proteins. In this fashion, lentiviral enzymes are short lived, thus limiting the potential for off-target editing due to long term expression though the entire life of the cell. Thus, in one embodiment, the disclosure provides novel delivery systems for delivering a gene or genetic material.

The incorporation of editing components, or traditional CRISPR-Cas editing components as proteins in lentiviral particles is advantageous, given that their required activity is only required for a short period of time. Thus, in one embodiment, the disclosure provides a lentiviral delivery system and methods of delivering the compositions of the invention, editing genetic material, and nucleic acid delivery using lentiviral delivery systems.

In one embodiment, the delivery system comprises (1) a packaging plasmid (2) a transfer plasmid, and (3) an envelope plasmid. In one embodiment, the delivery system comprises (1) a packaging plasmid (2) an envelope plasmid, and (3) a VPR plasmid. In one embodiment, the packaging plasmid comprises a nucleic acid sequence encoding a gag-pol polyprotein. In one embodiment, the gag-pol polyprotein comprises catalytically dead integrase. In one embodiment, the gag-pol polyprotein comprises a mutation selected from D116N, D116A, D116E, D64V, D64E, and D64A.

In one embodiment, the transfer plasmid comprises a nucleic acid sequence encoding a crRNA sequence and Cas protein of the disclosure. For example, in one embodiment the transfer plasmid comprises a nucleic acid sequence encoding a crRNA sequence and a protein of the disclosure comprising a Cas protein. In one embodiment, the transfer plasmid comprises a nucleic acid sequence encoding a crRNA sequence and a protein of the disclosure comprising a Cas protein and a localization signal. In one embodiment, the transfer plasmid comprises a nucleic acid sequence encoding a crRNA sequence and a protein of the disclosure comprising a Cas protein and a NLS, NES or other localization signal.

For example, in one embodiment, the transfer plasmid comprises a nucleic acid sequence encoding a tandem crRNA array of the disclosure. In one embodiment, the tandem array comprises one or more, two or more, three or more, four or more, five or more six or more, seven or more or eight or more crRNA sequences. In one embodiment, each crRNA in the tandem crRNA array comprises a direct repeat (DR) sequence and a spacer sequence. In one embodiment the direct repeat sequence may be located upstream (i.e., 5') from the guide sequence or spacer sequence. In other embodiments, the direct repeat sequence may be located downstream (i.e., 3') from the guide sequence or spacer sequence.

In one embodiment, the tandem array comprises at least two or more crRNA, wherein each crRNA comprises a sequence substantially complementary to a target RNA. For example, in one embodiment, each crRNA comprises a different sequence substantially complementary to a different sequence in a single target RNA. In one embodiment, each crRNA comprises a different sequence substantially complementary to a different sequence in a different target RNAs. In one embodiment, the different target RNAs are related to a single disease, disorder or infection. For example, in one embodiment, the different target RNAs are each viral RNA sequences of a vims.

In one embodiment, the tandem array comprises at least two or more crRNA comprising a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to a sequence selected from SEQ ID NOs: 189-224. In one embodiment, the tandem array comprises at least two or more crRNA comprising a sequence selected from SEQ ID NOs: 189-22.

In one embodiment, the tandem array comprises at least two or more crRNA each independently comprising sequences substantially complementary to an influenza virus sequence. In one embodiment, the tandem array comprises at least two or more crRNA each comprising a sequence substantially complementary to an influenza virus genomic mRNA sequence or a subgenomic mRNA sequence. In one embodiment, the tandem array comprises at least two or more crRNA each comprising a sequence substantially complementary to an Influenza virus PB2 sequence, PB1 sequence, PA sequence, HA sequence, NP sequence, NA sequence, M sequence or NS sequence.

In one embodiment, the tandem array comprises at least two or more crRNA comprising a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to a sequence selected from SEQ ID NOs: 245-249. In one embodiment, the tandem array comprises at least two or more crRNA comprising a sequence selected from SEQ ID NOs: 245-249.

In one embodiment, the tandem array comprises a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to one of SEQ ID NO:276-279. In one embodiment, the tandem array comprises a sequence of one of SEQ ID NO: 276-279. In one embodiment, the tandem array comprises at least two or more crRNA each independently comprising sequences substantially complementary to mRNA sequences within a cellular pathway. In some embodiments, the cellular pathway lead, for example, to aberrant control of cellular processes, with uncontrolled growth and increased cell survival. For example, in one embodiment, each crRNA independently comprises a sequence substantially complementary to an mRNA sequence within the RAS, JAK-STAT, PI3K/AKT, or MAPK cellular pathway.

In one embodiment, nucleic acid sequence encoding Cas protein comprises a sequence encoding an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to one of SEQ ID NOs: 1-47 or 68-100. In one embodiment, nucleic acid sequence encoding Cas protein comprises a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to one of SEQ ID NOs: 132-133 or 14-166.

In one embodiment, the transfer plasmid comprises a sequence of SEQ ID NO:283.

In one embodiment, the envelope plasmid comprises a nucleic acid sequence encoding an envelope protein. In one embodiment, the envelope protein can be selected based on the desired cell type. In one embodiment, the envelope plasmid comprises a nucleic acid sequence encoding an HIV envelope protein. In one embodiment, the envelope plasmid compnses a nucleic acid sequence encoding a vesicular stomatitis virus g-protein (VSV-g) envelope protein. In one embodiment, the envelope plasmid comprises a nucleic acid sequence encoding an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to SEQ ID NO: 130. In one embodiment, the envelope plasmid comprises a nucleic acid sequence encoding an amino acid sequence of SEQ ID NO: 130.

In one embodiment, the envelope plasmid compnses a nucleic acid sequence encoding a coronavirus spike protein or a coronavirus spike protem-derived protein. For example in one embodiment, the envelope plasmid comprises a nucleic acid sequence encoding an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to one of SEQ ID NOs: 101-129. In one embodiment, the envelope plasmid comprises a nucleic acid sequence encoding an amino acid sequence of one of SEQ ID NOs: 101-129.

In one embodiment, viral envelope proteins from coronaviruses are not efficient for pseudotyping of lentiviral vectors. Thus, in one embodiment, the disclosure also provides novel coronavirus envelope proteins for use in pseudotyping a lentiviral vector. In one embodiment, the coronavirus envelope protein comprises an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to one of SEQ ID NOs: 101-129. In one embodiment, the coronavirus envelope protein comprises an amino acid sequence of one of SEQ ID NOs: 101-129.

In one embodiment, the YPR plasmid comprises a nucleic acid sequence encoding a fusion protein comprising VPR, and a Cas protein of the disclosure..

In one embodiment, the packaging plasmid, transfer plasmid, and envelope plasmid are introduced into a cell. In one embodiment, the cell transcribes and translates the nucleic acid sequence encoding the gag-pol protein encoded by the packaging plasmid to produce the gag-pol polyprotein. In one embodiment, the cell transcribes and translates the nucleic acid sequence encoding the envelope protein of the envelope plasmid to produce the envelope protein. In one embodiment, the cell transcribes the nucleic acid sequence encoding the crRNA sequence or crRNA array of the transfer plasmid to produce the crRNA or crRNA array. In one embodiment, the cell transcribes and translates the nucleic acid sequence encoding the Cas protein of the transfer plasmid to produce the Cas or Cas fusion protein.

In one embodiment, the transcribed transfer plasmid and gag-pol proteins are packaged into a lentiviral vector. In one embodiment, the lentiviral vectors are collected from the cell media. In one embodiment, the viral particles transduce a target cell, wherein the transcribed the crRNA and Cas protein are cleaved and the translated thereby generating the Cas protein and crRNA, wherein the crRNA binds to the Cas protein and directs it to an RNA having a sequence substantially complementary to the crRNA sequence. In one embodiment, the packaging plasmid, transfer plasmid, and envelope plasmid are introduced into a cell. In one embodiment, the cell transcribes and translates the nucleic acid sequence encoding the gag-pol protein encoded by the packaging plasmid to produce the gag-pol polyprotein. In one embodiment, the cell transcribes and translates the nucleic acid sequence encoding the envelope protein of the envelope plasmid to produce the envelope protein. In one embodiment, the cell transcribes the nucleic acid sequence encoding the gene to produce the gene. In one embodiment, the cell transcribes and translates the nucleic acid sequence encoding the gene of the transfer plasmid to produce a protein.

In one embodiment, the transcribed transfer plasmid and gag-pol proteins are packaged into a lentiviral vector. In one embodiment, the lentiviral vectors are collected from the cell media. In one embodiment, the viral particles transduce a target cell, wherein the transcribed gene is delivered to the cell and inserted into the genome.

In one embodiment, the transcribed transfer plasmid and gag-pol proteins are packaged into a lentiviral vector. In one embodiment, the lentiviral vectors are collected from the cell media. In one embodiment, the viral particles transduce a target cell, wherein the transcribed and translated gene is delivered to the cell.

In one embodiment, the gene or protein is delivered to a respiratory, vascular, renal, or cardiovascular cell type. Thus, in one embodiment the envelope protein is derived from a coronavirus. In one embodiment, the coronavirus envelope protein comprises an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to one of SEQ ID NOs: 101-129. In one embodiment, the coronavirus envelope protein comprises an amino acid sequence of one of SEQ ID NOs: 101-129.

Further, a number of additional viral based systems have been developed for gene transfer into mammalian cells. For example, retroviruses provide a convenient platform for gene delivery systems. A selected gene can be inserted into a vector and packaged in retroviral particles using techniques known in the art. The recombinant vims can then be isolated and delivered to cells of the subject either in vivo or ex vivo. A number of retroviral systems are known in the art. In some embodiments, adenovirus vectors are used. A number of adenovirus vectors are known in the art. In one embodiment, lenti virus vectors are used. For example, vectors derived from retroviruses such as the lentivirus are suitable tools to achieve long-term gene transfer since they allow long-term, stable integration of a transgene and its propagation in daughter cells. Lentiviral vectors have the added advantage over vectors derived from onco-retroviruses such as murine leukemia viruses in that they can transduce non-proliferating cells, such as hepatocytes. They also have the added advantage of low immunogenicity.

In one embodiment, the composition includes a vector derived from an adeno-associated vims (AAV). The term "AAV vector" means a vector derived from an adeno-associated vims serotype, including without limitation, AAV-1, AAV-2, AAV-3, AAV-4, AAV-5, AAV-6, AAV-7, AAV-8, and AAV-9. AAV vectors have become powerful gene delivery tools for the treatment of various disorders. AAV vectors possess a number of features that render them ideally suited for gene therapy, including a lack of pathogenicity, minimal immunogenicity, and the ability to transduce postmitotic cells in a stable and efficient manner. Expression of a particular gene contained within an AAV vector can be specifically targeted to one or more types of cells by choosing the appropriate combination of AAV serotype, promoter, and delivery method.

For example, in one embodiment, the AAV vector comprises a crRNA having substantially complementary to a Coronavims genomic mRNA sequence or a Coronavims subgenomic mRNA sequence. In one embodiment, the AAV vector comprises a crRNA array comprising two or more crRNA having substantially complementary to a Coronavims genomic mRNA sequence or a Coronavims subgenomic mRNA sequence. In one embodiment, the AAV vector comprises a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to SEQ ID NO: 284. In one embodiment, the transfer plasmid comprises a sequence of SEQ ID NO: 284.

In one embodiment, the AAV vector comprises a crRNA having substantially complementary to an influenza vims genomic RNA sequence or an influenza vims subgenomic RNA sequence. In one embodiment, the transfer plasmid comprises a crRNA array comprising two or more crRNA having substantially complementary to an influenza vims genomic RNA sequence or an influenza vims subgenomic RNA sequence.

AAV vectors can have one or more of the AAV wild-type genes deleted in whole or part, preferably the rep and/or cap genes, but retain functional flanking ITR sequences. Despite the high degree of homology, the different serotypes have tropisms for different tissues. The receptor for AAV 1 is unknown; however, AAV1 is known to transduce skeletal and cardiac muscle more efficiently than AAV2. Since most of the studies have been done with pseudotyped vectors in which the vector DNA flanked with AAV2 ITR is packaged into capsids of alternate serotypes, it is clear that the biological differences are related to the capsid rather than to the genomes. Recent evidence indicates that DNA expression cassettes packaged in AAV 1 capsids are at least 1 log 10 more efficient at transducing cardiomyocytes than those packaged in AAY2 capsids. In one embodiment, the viral delivery system is an adeno-associated viral delivery system. The adeno-associated virus can be of serotype 1 (AAV 1), serotype 2 (AAV2), serotype 3 (AAV3), serotype 4 (AAV4), serotype 5 (AAV5), serotype 6 (AAV6), serotype 7 (AAV7), serotype 8 (AAV8), or serotype 9 (AAV9).

Desirable AAV fragments for assembly into vectors include the cap proteins, including the vpl, vp2, vp3 and hypervariable regions, the rep proteins, including rep 78, rep 68, rep 52, and rep 40, and the sequences encoding these proteins. These fragments may be readily utilized in a variety of vector systems and host cells. Such fragments may be used alone, in combination with other AAV serotype sequences or fragments, or in combination with elements from other AAV or non-AAV viral sequences. As used herein, artificial AAV serotypes include, without limitation, AAV with a non-naturally occurring capsid protein. Such an artificial capsid may be generated by any suitable technique, using a selected AAV sequence (e.g., a fragment of a vpl capsid protein) in combination with heterologous sequences which may be obtained from a different selected AAV serotype, non-contiguous portions of the same AAV serotype, from a non-AAV viral source, or from a non-viral source. An artificial AAV serotype may be, without limitation, a chimeric AAV capsid, a recombinant AAV capsid, or a “humanized” AAV capsid. Thus exemplary AAVs, or artificial AAVs, suitable for expression of one or more proteins, include AAV2/8 (see U S. Pat. No. 7,282,199), AAV2/5 (available from the National Institutes of Health), AAV2/9 (International Patent Publication No. W02005/033321), AAV2/6 (U.S. Pat. No. 6,156,303), and AAVrh8 (International Patent Publication No. W02003/042397), among others.

In certain embodiments, the vector also includes conventional control elements which are operably linked to the transgene in a manner which permits its transcription, translation and/or expression in a cell transfected with the plasmid vector or infected with the vims produced by the invention. As used herein, “operably linked” sequences include both expression control sequences that are contiguous with the gene of interest and expression control sequences that act in trans or at a distance to control the gene of interest. Expression control sequences include appropriate transcription initiation, termination, promoter and enhancer sequences; efficient RNA processing signals such as splicing and polyadenylation (poly A) signals; sequences that stabilize cytoplasmic mRNA; sequences that enhance translation efficiency (i.e., Kozak consensus sequence); sequences that enhance protein stability; and when desired, sequences that enhance secretion of the encoded product. A great number of expression control sequences, including promoters which are native, constitutive, inducible and/or tissue-specific, are known in the art and may be utilized.

Additional promoter elements, e.g., enhancers, regulate the frequency of transcriptional initiation. Typically, these are located in the region 30-110 bp upstream of the start site, although a number of promoters have recently been shown to contain functional elements downstream of the start site as well. The spacing between promoter elements frequently is flexible, so that promoter function is preserved when elements are inverted or moved relative to one another. In the thymidine kinase (tk) promoter, the spacing between promoter elements can be increased to 50 bp apart before activity begins to decline. Depending on the promoter, it appears that individual elements can function either cooperatively or independently to activate transcription.

One example of a suitable promoter is the immediate early cytomegalovirus (CMV) promoter sequence. This promoter sequence is a strong constitutive promoter sequence capable of driving high levels of expression of any polynucleotide sequence operatively linked thereto. Another example of a suitable promoter is Elongation Growth Factor -la (EF-la). However, other constitutive promoter sequences may also be used, including, but not limited to the simian vims 40 (SV40) early promoter, mouse mammary tumor vims (MMTV), human immunodeficiency vims (HIV) long terminal repeat (LTR) promoter, MoMuLV promoter, an avian leukemia vims promoter, an Epstein-Barr vims immediate early promoter, a Rous sarcoma vims promoter, as well as human gene promoters such as, but not limited to, the actin promoter, the myosin promoter, the hemoglobin promoter, and the creatine kinase promoter. Further, the invention should not be limited to the use of constitutive promoters. Inducible promoters are also contemplated as part of the invention. The use of an inducible promoter provides a molecular switch capable of turning on expression of the polynucleotide sequence which it is operatively linked when such expression is desired, or turning off the expression when expression is not desired. Examples of inducible promoters include, but are not limited to a metallothionine promoter, a glucocorticoid promoter, a progesterone promoter, and a tetracycline promoter.

Enhancer sequences found on a vector also regulates expression of the gene contained therein. Typically, enhancers are bound with protein factors to enhance the transcription of a gene. Enhancers may be located upstream or downstream of the gene it regulates. Enhancers may also be tissue-specific to enhance transcription in a specific cell or tissue type. In one embodiment, the vector of the present invention comprises one or more enhancers to boost transcription of the gene present within the vector.

In order to assess the expression of a fusion protein of the invention, the expression vector to be introduced into a cell can also contain either a selectable marker gene or a reporter gene or both to facilitate identification and selection of expressing cells from the population of cells sought to be transfected or infected through viral vectors. In other aspects, the selectable marker may be carried on a separate piece of DNA and used in a co- transfection procedure. Both selectable markers and reporter genes may be flanked with appropriate regulatory sequences to enable expression in the host cells. Useful selectable markers include, for example, antibiotic -resistance genes, such as neo and the like.

Reporter genes are used for identifying potentially transfected cells and for evaluating the functionality of regulatory sequences. In general, a reporter gene is a gene that is not present in or expressed by the recipient organism or tissue and that encodes a polypeptide whose expression is manifested by some easily detectable property, e.g., enzymatic activity. Expression of the reporter gene is assayed at a suitable time after the DNA has been introduced into the recipient cells. Suitable reporter genes may include genes encoding luciferase, beta-galactosidase, chloramphenicol acetyl transferase, secreted alkaline phosphatase, or the green fluorescent protein gene (e.g., Ui-Tei et al., 2000 FEBS Letters 479: 79-82). Suitable expression systems are well known and may be prepared using known techniques or obtained commercially. In general, the construct with the minimal 5' flanking region showing the highest level of expression of reporter gene is identified as the promoter. Such promoter regions may be linked to a reporter gene and used to evaluate agents for the ability to modulate promoter- driven transcription.

Methods of introducing and expressing genes into a cell are known in the art. In the context of an expression vector, the vector can be readily introduced into a host cell, e.g., mammalian, bacterial, yeast, or insect cell by any method in the art. For example, the expression vector can be transferred into a host cell by physical, chemical, or biological means.

Physical methods for introducing a polynucleotide into a host cell include calcium phosphate precipitation, hpofection, particle bombardment, micromjection, electroporation, and the like. Methods for producing cells comprising vectors and/or exogenous nucleic acids are well-known in the art. See, for example, Sambrook et al. (2012, Molecular Cloning: A Laboratory Manual, Cold Spnng Harbor Laboratory, New York). An exemplary method for the introduction of a polynucleotide into a host cell is calcium phosphate transfection.

Biological methods for introducing a polynucleotide of interest into a host cell include the use of DNA and RNA vectors. Viral vectors, and especially retroviral vectors, have become the most widely used method for inserting genes into mammalian, e.g., human cells. Other viral vectors can be derived from lentivirus, poxviruses, herpes simplex virus I, adenoviruses and adeno-associated viruses, and the like. See, for example, U.S. Pat. Nos. 5,350,674 and 5,585,362. Chemical means for introducing a polynucleotide into a host cell include colloidal dispersion systems, such as macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes. An exemplary colloidal system for use as a delivery vehicle in vitro and in vivo is a liposome (e.g., an artificial membrane vesicle).

In the case where a non-viral delivery system is utilized, an exemplary delivery vehicle is a liposome. The use of lipid formulations is contemplated for the introduction of the nucleic acids into a host cell (in vitro, ex vivo or in vivo). In another aspect, the nucleic acid may be associated with a lipid. The nucleic acid associated with a lipid may be encapsulated in the aqueous interior of a liposome, interspersed within the lipid bilayer of a liposome, attached to a liposome via a linking molecule that is associated with both the liposome and the oligonucleotide, entrapped in a liposome, complexed with a liposome, dispersed in a solution containing a lipid, mixed with a lipid, combined with a lipid, contained as a suspension in a lipid, contained or complexed with a micelle, or otherwise associated with a lipid. Lipid, lipid/DNA or lipid/expression vector associated compositions are not limited to any particular structure in solution. For example, they may be present in a bilayer structure, as micelles, or with a “collapsed” structure. They may also simply be interspersed in a solution, possibly forming aggregates that are not uniform in size or shape. Lipids are fatty substances which may be naturally occurring or synthetic lipids. For example, lipids include the fatty droplets that naturally occur in the cytoplasm as well as the class of compounds which contain long-chain aliphatic hydrocarbons and their derivatives, such as fatty acids, alcohols, amines, amino alcohols, and aldehydes.

Lipids suitable for use can be obtained from commercial sources. For example, dimyristyl phosphatidylcholine (“DMPC”) can be obtained from Sigma, St. Louis, MO; dicetyl phosphate (“DCP”) can be obtained from K & K Laboratories (Plainview, NY); cholesterol (“Choi”) can be obtained from Calbiochem-Behring; dimyristyl phosphatidylglycerol (“DMPG”) and other lipids may be obtained from Avanti Polar Lipids, Inc. (Birmingham, AL). Stock solutions of lipids in chloroform or chloroform/methanol can be stored at about -20°C. Chloroform is used as the only solvent since it is more readily evaporated than methanol. “Liposome” is a generic term encompassing a variety of single and multilamellar lipid vehicles formed by the generation of enclosed lipid bilayers or aggregates Liposomes can be characterized as having vesicular structures with a phospholipid bilayer membrane and an inner aqueous medium. Multilamellar liposomes have multiple lipid layers separated by aqueous medium. They form spontaneously when phospholipids are suspended in an excess of aqueous solution. The lipid components undergo self-rearrangement before the formation of closed structures and entrap water and dissolved solutes between the lipid bilayers (Ghosh et ak, 1991 Glycobiology 5: 505-10). However, compositions that have different structures in solution than the normal vesicular structure are also encompassed. For example, the lipids may assume a micellar structure or merely exist as nonuniform aggregates of lipid molecules. Also contemplated are lipofectamine-nucleic acid complexes.

Regardless of the method used to introduce exogenous nucleic acids into a host cell, in order to confirm the presence of the recombinant DNA sequence in the host cell, a variety of assays may be performed. Such assays include, for example, “molecular biological” assays well known to those of skill in the art, such as Southern and Northern blotting, RT-PCR and PCR; “biochemical” assays, such as detecting the presence or absence of a particular peptide, e.g., by immunological means (ELIS As and Western blots) or by assays described herein to identify agents falling within the scope of the invention.

Systems

In one aspect, the present invention provides a system for decreasing the number of one or more RNA transcripts in a subject. In one embodiment the system comprises, in one or more vectors, a nucleic acid sequence encoding a protein, wherein the protein comprises a CRISPR-associated (Cas) protein, and optionally a localization sequence, such as an NLS, NES, or organelle localization signal; and a nucleic acid sequence encoding a tandem crRNA array.

In one embodiment, the tandem array comprises one or more, two or more, three or more, four or more, five or more six or more, seven or more or eight or more crRNA sequences. In one embodiment, each crRNA comprises a different sequence substantially complementary to a different sequence in a single target RNA. In one embodiment, each crRNA comprises a different sequence substantially complementary to a different sequence in a different target RNAs. In one embodiment, the different target RNAs are related to a single disease, disorder or infection. For example, in one embodiment, the different target RNAs are each viral RNA sequences of a virus.

In one embodiment, the nucleic acid sequence encoding the Cas and the nucleic acid sequence encoding a crRNA are in the same vector. In one embodiment, the nucleic acid sequence encoding the protein and the nucleic acid sequence encoding a crRNA are in different vectors.

In one embodiment, the nucleic acid sequence encoding a protein comprises (1) a nucleic acid sequence encoding an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs: 1-47; and (2) optionally a nucleic acid sequence encoding an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs: 50-66 and 323-935. In one embodiment, the nucleic acid sequence encoding a protein comprises (1) a nucleic acid sequence encoding an amino acid of one of SEQ ID NOs: 1-47; and (2) optionally a nucleic acid sequence encoding an amino acid of one of SEQ ID NOs: 50-66 and 323-935. In one embodiment, the nucleic acid sequence encoding a protein comprises a nucleic acid sequence encoding an amino acid at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs: 68- 100 In one embodiment, the nucleic acid sequence encoding a protein comprises a nucleic acid sequence encoding an amino acid of one of SEQ ID NOs: 68-100.

In one embodiment, the tandem array comprises one or more, two or more, three or more, four or more, five or more six or more, seven or more or eight or more crRNA sequences. In one embodiment, each crRNA in the tandem crRNA array comprises a direct repeat (DR) sequence and a spacer sequence. In one embodiment the direct repeat sequence may be located upstream (i.e., 5') from the guide sequence or spacer sequence. In other embodiments, the direct repeat sequence may be located downstream (i.e., 3') from the guide sequence or spacer sequence.

In one embodiment, the tandem array comprises at least two or more crRNA each independently comprising sequences substantially complementary to an influenza virus sequence. In one embodiment, the tandem array comprises at least two or more crRNA each comprising a sequence substantially complementary to an influenza virus genomic mRNA sequence or a subgenomic mRNA sequence. In one embodiment, the tandem array comprises at least two or more crRNA each comprising a sequence substantially complementary to an Influenza vims PB2 sequence, PB1 sequence, PA sequence, HA sequence, NP sequence, NA sequence, M sequence or NS sequence.

In one embodiment, the tandem array comprises at least two or more crRNA comprising a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to a sequence selected from SEQ ID NOs: 245-264. In one embodiment, the tandem array comprises at least two or more crRNA comprising a sequence selected from SEQ ID NOs: 245-264.

In one embodiment, the tandem array comprises a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to one of SEQ ID NO: 276- 279. In one embodiment, the tandem array comprises a sequence of one of SEQ ID NO: 276-279.

In one embodiment, the tandem array comprises at least two or more crRNA each independently comprising sequences substantially complementary to mRNA sequences within a cellular pathway. In some embodiments, the cellular pathway lead, for example, to aberrant control of cellular processes, with uncontrolled growth and increased cell survival. For example, in one embodiment, each crRNA independently compnses a sequence substantially complementary to an mRNA sequence within the RAS, JAK-STAT, PI3K/AKT, or MAPK cellular pathway.

Compositions and Formulations

In one aspect, the present invention provides compositions for decreasing the number of an RNA transcript in a subject. In one embodiment, the composition comprises a fusion protein, wherein the fusion protein comprises a CRISPR-associated (Cas) protein, and optionally a localization sequence, such as an NLS, NES or organelle localization signal. In one embodiment, the composition comprises a tandem crRNA array. In one embodiment, the tandem crRNA array comprises two or more crRNA which each substantially hybridizes to a target RNA sequence in one or more RNA transcripts. In one embodiment, the composition comprises a protein comprising (1) an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs: 1-47; and (2) optionally an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs: 50-66 and 323-935. In one embodiment, composition comprises a protein comprising (1) an amino acid of one of SEQ ID NOs: 1-47; and (2) optionally an amino acid of one of SEQ ID NOs: 50-66 and 323-935.

In one embodiment, composition comprises a protein comprising an amino acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to one of SEQ ID NOs: 68-100. In one embodiment, the nucleic acid sequence encoding a protein comprises a protein comprising an amino acid sequence of one of SEQ ID NOs: 68-100.

In one embodiment, the composition comprises a tandem crRNA array, wherein the array comprises one or more, two or more, three or more, four or more, five or more six or more, seven or more or eight or more crRNA sequences. In one embodiment, each crRNA in the tandem crRNA array comprises a direct repeat (DR) sequence and a spacer sequence. In one embodiment the direct repeat sequence may be located upstream (i.e., 5') from the guide sequence or spacer sequence. In other embodiments, the direct repeat sequence may be located downstream (i.e., 3') from the guide sequence or spacer sequence.

In one embodiment, the composition comprises a tandem array wherein the tandem array comprises at least two or more crRNA, wherein each crRNA comprises a sequence substantially complementary to a target RNA. For example, in one embodiment, each crRNA comprises a different sequence substantially complementary to a different sequence in a single target RNA. In one embodiment, each crRNA comprises a different sequence substantially complementary to a different sequence in a different target RNAs. In one embodiment, the different target RNAs are related to a single disease, disorder or infection. For example, in one embodiment, the different target RNAs are each viral RNA sequences of a virus.

In one embodiment, the tandem array comprises at least two or more crRNA comprising sequences substantially complementary to a genomic coronavirus RNA sequence and/or a sub-genomic coronavirus RNA sequence. In one embodiment, the tandem array comprises at least two or more crRNA comprising a substantially complementary to a sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% homologous to a sequence selected from SEQ ID NOs: 167-188, or a fragment thereof. In one embodiment, the tandem array comprises at least two or more crRNA comprising a substantially complementary to a sequence selected from SEQ ID NOs: 167-188, or a fragment thereof.

The disclosure also encompasses the use of pharmaceutical compositions of the disclosure to practice the methods of the disclosure. Such a pharmaceutical composition may consist of at least one modulator (e.g., inhibitor or activator) composition of the invention or a salt thereof in a form suitable for administration to a subject, or the pharmaceutical composition may comprise at least one modulator (e.g., inhibitor or activator) composition of the invention or a salt thereof, and one or more pharmaceutically acceptable carriers, one or more additional ingredients, or some combination of these. The compound of the invention may be present in the pharmaceutical composition in the form of a physiologically acceptable salt, such as in combination with a physiologically acceptable cation or anion, as is well known in the art.

In an embodiment, the pharmaceutical compositions useful for practicing the methods of the invention may be administered to deliver a dose of between 1 ng/kg/day and 100 mg/kg/day. In another embodiment, the pharmaceutical compositions useful for practicing the invention may be administered to deliver a dose of between 1 ng/kg/day and 500 mg/kg/day.

The relative amounts of the active ingredient, the pharmaceutically acceptable carrier, and any additional ingredients in a pharmaceutical composition of the invention will vary, depending upon the identity, size, and condition of the subject treated and further depending upon the route by which the composition is to be administered. By way of example, the composition may comprise between 0.1% and 100% (w/w) active ingredient.

Pharmaceutical compositions that are useful in the methods of the invention may be suitably developed for oral, rectal, vaginal, parenteral, topical, pulmonary, intranasal, buccal, ophthalmic, or another route of administration. A composition useful within the methods of the invention may be directly administered to the skin, or any other tissue of a mammal. Other contemplated formulations include liposomal preparations, resealed erythrocytes containing the active ingredient, and immunologically- based formulations. The route(s) of administration will be readily apparent to the skilled artisan and will depend upon any number of factors including the type and severity of the disease being treated, the type and age of the veterinary or human subject being treated, and the like.

The formulations of the pharmaceutical compositions described herein may be prepared by any method known or hereafter developed in the art of pharmacology. In general, such preparatory methods include the step of bringing the active ingredient into association with a carrier or one or more other accessory ingredients, and then, if necessary or desirable, shaping or packaging the product into a desired single- or multi -dose unit.

As used herein, a “unit dose” is a discrete amount of the pharmaceutical composition comprising a predetermined amount of the active ingredient. The amount of the active ingredient is generally equal to the dosage of the active ingredient that would be administered to a subject or a convenient fraction of such a dosage such as, for example, one-half or one-third of such a dosage. The unit dosage form may be for a single daily dose or one of multiple daily doses (e g., about 1 to 4 or more times per day). When multiple daily doses are used, the unit dosage form may be the same or different for each dose.

In one embodiment, the compositions of the invention are formulated using one or more pharmaceutically acceptable excipients or carriers. In one embodiment, the pharmaceutical compositions of the invention comprise a therapeutically effective amount of a compound or conjugate of the invention and a pharmaceutically acceptable carrier. Pharmaceutically acceptable earners that are useful, include, but are not limited to, glycerol, water, saline, ethanol and other pharmaceutically acceptable salt solutions such as phosphates and salts of organic acids. Examples of these and other pharmaceutically acceptable carriers are described in Remington’s Pharmaceutical Sciences (1991, Mack Publication Co., New Jersey).

The carrier may be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and vegetable oils. The proper fluidity may be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prevention of the action of microorganisms may be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In many cases, isotonic agents, for example, sugars, sodium chloride, or polyalcohols such as mannitol and sorbitol are included in the composition. Prolonged absorption of the injectable compositions may be brought about by including in the composition an agent that delays absorption, for example, aluminum monostearate or gelatin. In one embodiment, the pharmaceutically acceptable carrier is not DMSO alone.

Formulations may be employed in admixtures with conventional excipients, i.e., pharmaceutically acceptable organic or inorganic carrier substances suitable for oral, vaginal, parenteral, nasal, intravenous, subcutaneous, enteral, or any other suitable mode of administration, known to the art. The pharmaceutical preparations may be sterilized and if desired mixed with auxiliary agents, e.g., lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure buffers, coloring, flavoring and/or aromatic substances and the like. They may also be combined where desired with other active agents, e.g., other analgesic agents.

As used herein, “additional ingredients” include, but are not limited to, one or more of the following: excipients; surface active agents; dispersing agents; inert diluents; granulating and disintegrating agents; binding agents; lubricating agents; sweetening agents; flavoring agents; coloring agents; preservatives; physiologically degradable compositions such as gelatin; aqueous vehicles and solvents; oily vehicles and solvents; suspending agents; dispersing or wetting agents; emulsifying agents, demulcents; buffers; salts; thickening agents; fdlers; emulsifying agents; antioxidants; antibiotics; antifungal agents; stabilizing agents; and pharmaceutically acceptable polymeric or hydrophobic materials. Other “additional ingredients” that may be included in the pharmaceutical compositions of the invention are known in the art and described, for example in Genaro, ed. (1985, Remington’s Pharmaceutical Sciences, Mack Publishing Co., Easton, PA), which is incorporated herein by reference.

The composition of the invention may comprise a preservative from about 0.005% to 2.0% by total weight of the composition. The preservative is used to prevent spoilage in the case of exposure to contaminants in the environment. Examples of preservatives useful in accordance with the invention included but are not limited to those selected from the group consisting of benzyl alcohol, sorbic acid, parabens, imidurea and combinations thereof. An exemplary preservative is a combination of about 0.5% to 2.0% benzyl alcohol and 0.05% to 0.5% sorbic acid.

In one embodiment, the composition includes an anti-oxidant and a chelating agent that inhibits the degradation of the compound. Exemplary antioxidants for some compounds are BHT, BHA, alpha- tocopherol and ascorbic acid in the range of about 0.01 % to 0.3 % and BTGG in the range of 0.03 % to 0.1 % by weight by total weight of the composition. In one embodiment, the chelating agent is present in an amount of from 0.01% to 0.5% by weight by total weight of the composition. Exemplary chelating agents include edetate salts (e.g. disodium edetate) and citric acid in the weight range of about 0.01% to 0.20%. In some embodiments, the chelating agent is in the range of 0.02% to 0.10% by weight by total weight of the composition. The chelating agent is useful for chelating metal ions in the composition that may be detrimental to the shelf life of the formulation. While BHT and disodium edetate are exemplary antioxidants and chelating agent respectively for some compounds, other suitable and equivalent antioxidants and chelating agents may be substituted therefore as would be known to those skilled in the art.

Liquid suspensions may be prepared using conventional methods to achieve suspension of the active ingredient in an aqueous or oily vehicle. Aqueous vehicles include, for example, water, and isotonic saline. Oily vehicles include, for example, almond oil, oily esters, ethyl alcohol, vegetable oils such as arachis, olive, sesame, or coconut oil, fractionated vegetable oils, and mineral oils such as liquid paraffin. Liquid suspensions may further comprise one or more additional ingredients including, but not limited to, suspending agents, dispersing or wetting agents, emulsifying agents, demulcents, preservatives, buffers, salts, flavorings, coloring agents, and sweetening agents. Oily suspensions may further comprise a thickening agent. Known suspending agents include, but are not limited to, sorbitol syrup, hydrogenated edible fats, sodium alginate, polyvinylpyrrolidone, gum tragacanth, gum acacia, and cellulose derivatives such as sodium carboxymethylcellulose, methylcellulose, hydroxypropylmethylcellulose. Known dispersing or wetting agents include, but are not limited to, naturally-occurring phosphatide s such as lecithin, condensation products of an alkylene oxide with a fatty acid, with a long chain aliphatic alcohol, with a partial ester derived from a fatty acid and a hexitol, or with a partial ester derived from a fatty acid and a hexitol anhydride (e.g., polyoxyethylene stearate, heptadecaethyleneoxycetanol, polyoxyethylene sorbitol monooleate, and polyoxyethylene sorbitan monooleate, respectively). Known emulsifying agents include, but are not limited to, lecithin, and acacia. Known preservatives include, but are not limited to, methyl, ethyl, or n-propyl-para- hydroxybenzoates, ascorbic acid, and sorbic acid. Known sweetening agents include, for example, glycerol, propylene glycol, sorbitol, sucrose, and saccharin. Known thickening agents for oily suspensions include, for example, beeswax, hard paraffin, and cetyl alcohol.

Liquid solutions of the active ingredient in aqueous or oily solvents may be prepared in substantially the same manner as liquid suspensions, the primary difference being that the active ingredient is dissolved, rather than suspended in the solvent. As used herein, an “oily” liquid is one which comprises a carbon-containing liquid molecule and which exhibits a less polar character than water. Liquid solutions of the pharmaceutical composition of the invention may comprise each of the components described with regard to liquid suspensions, it being understood that suspending agents will not necessarily aid dissolution of the active ingredient in the solvent. Aqueous solvents include, for example, water, and isotonic saline. Oily solvents include, for example, almond oil, oily esters, ethyl alcohol, vegetable oils such as arachis, olive, sesame, or coconut oil, fractionated vegetable oils, and mineral oils such as liquid paraffin.

Powdered and granular formulations of a pharmaceutical preparation of the invention may be prepared using known methods. Such formulations may be administered directly to a subject, used, for example, to form tablets, to fill capsules, or to prepare an aqueous or oily suspension or solution by addition of an aqueous or oily vehicle thereto. Each of these formulations may further comprise one or more of dispersing or wetting agent, a suspending agent, and a preservative. Additional excipients, such as fillers and sweetening, flavoring, or coloring agents, may also be included in these formulations.

A pharmaceutical composition of the invention may also be prepared, packaged, or sold in the form of oil-in-water emulsion or a water-in-oil emulsion. The oily phase may be a vegetable oil such as olive or arachis oil, a mineral oil such as liquid paraffin, or a combination of these. Such compositions may further comprise one or more emulsifying agents such as naturally occurring gums such as gum acacia or gum tragacanth, naturally-occurring phosphatides such as soybean or lecithin phosphatide, esters or partial esters derived from combinations of fatty acids and hexitol anhydrides such as sorbitan monooleate, and condensation products of such partial esters with ethylene oxide such as polyoxyethylene sorbitan monooleate. These emulsions may also contain additional ingredients including, for example, sweetening or flavoring agents.

Methods for impregnating or coating a material with a chemical composition are known in the art, and include, but are not limited to methods of depositing or binding a chemical composition onto a surface, methods of incorporating a chemical composition into the structure of a material during the synthesis of the material (i.e., such as with a physiologically degradable material), and methods of absorbing an aqueous or oily solution or suspension into an absorbent material, with or without subsequent drying.

The regimen of administration may affect what constitutes an effective amount. The therapeutic formulations may be administered to the subject either prior to or after a diagnosis of disease. Further, several divided dosages, as well as staggered dosages may be administered daily or sequentially, or the dose may be continuously infused, or may be a bolus injection. Further, the dosages of the therapeutic formulations may be proportionally increased or decreased as indicated by the exigencies of the therapeutic or prophylactic situation.

Administration of the compositions of the present invention to a subject, include a mammal, for example a human, may be carried out using known procedures, at dosages and for periods of time effective to prevent or treat disease. An effective amount of the therapeutic compound necessary to achieve a therapeutic effect may vary according to factors such as the activity of the particular compound employed; the time of administration; the rate of excretion of the compound; the duration of the treatment; other drugs, compounds or materials used in combination with the compound; the state of the disease or disorder, age, sex, weight, condition, general health and pnor medical history of the subject being treated, and like factors well-known in the medical arts. Dosage regimens may be adjusted to provide the optimum therapeutic response. For example, several divided doses may be administered daily, or the dose may be proportionally reduced as indicated by the exigencies of the therapeutic situation. A non-limiting example of an effective dose range for a therapeutic compound of the invention is from about 1 and 5,000 mg/kg of body weight/per day. One of ordinary skill in the art would be able to study the relevant factors and make the determination regarding the effective amount of the therapeutic compound without undue experimentation.

The compound may be administered to a subject as frequently as several times daily, or it may be administered less frequently, such as once a day, once a week, once every two weeks, once a month, or even less frequently, such as once every several months or even once a year or less. It is understood that the amount of compound dosed per day may be administered, in non-limiting examples, every day, every other day, every 2 days, every 3 days, every 4 days, or every 5 days. For example, with every other day administration, a 5 mg per day dose may be initiated on Monday with a first subsequent 5 mg per day dose administered on Wednesday, a second subsequent 5 mg per day dose administered on Friday, and so on. The frequency of the dose will be readily apparent to the skilled artisan and will depend upon any number of factors, such as, but not limited to, the type and severity of the disease being treated, the type and age of the animal, etc.

Actual dosage levels of the active ingredients in the pharmaceutical compositions of this invention may be vaned so as to obtain an amount of the active ingredient that is effective to achieve the desired therapeutic response for a particular subject, composition, and mode of administration, without being toxic to the subject.

A medical doctor, e.g., physician or veterinarian, having ordinary skill in the art may readily determine and prescribe the effective amount of the pharmaceutical composition required. For example, the physician or veterinarian could start doses of the compounds of the invention employed in the pharmaceutical composition at levels lower than that required in order to achieve the desired therapeutic effect and gradually increase the dosage until the desired effect is achieved.

In particular embodiments, it is especially advantageous to formulate the compound in dosage unit form for ease of administration and uniformity of dosage. Dosage unit form as used herein refers to physically discrete units suited as unitary dosages for the subjects to be treated; each unit containing a predetermined quantity of therapeutic compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical vehicle. The dosage unit forms of the invention are dictated by and directly dependent on (a) the unique characteristics of the therapeutic compound and the particular therapeutic effect to be achieved, and (b) the limitations inherent in the art of compounding/formulating such a therapeutic compound for the treatment of a disease in a subject.

In one embodiment, the compositions of the invention are administered to the subject in dosages that range from one to five times per day or more. In another embodiment, the compositions of the invention are administered to the subject in range of dosages that include, but are not limited to, once every day, every two, days, every three days to once a week, and once every two weeks. It will be readily apparent to one skilled in the art that the frequency of administration of the various combination compositions of the invention will vary from subject to subject depending on many factors including, but not limited to, age, disease or disorder to be treated, gender, overall health, and other factors. Thus, the invention should not be construed to be limited to any particular dosage regime and the precise dosage and composition to be administered to any subject will be determined by the attending physical taking all other factors about the subject into account. Compounds of the invention for administration may be in the range of from about 1 mg to about 10,000 mg, about 20 mg to about 9,500 mg, about 40 mg to about 9,000 mg, about 75 mg to about 8,500 mg, about 150 mg to about 7,500 mg, about 200 mg to about 7,000 mg, about 3050 mg to about 6,000 mg, about 500 mg to about 5,000 mg, about 750 mg to about 4,000 mg, about 1 mg to about 3,000 mg, about 10 mg to about 2,500 mg, about 20 mg to about 2,000 mg, about 25 mg to about 1,500 mg, about 50 mg to about 1,000 mg, about 75 mg to about 900 mg, about 100 mg to about 800 mg, about 250 mg to about 750 mg, about 300 mg to about 600 mg, about 400 mg to about 500 mg, and any and all whole or partial increments there between.

In some embodiments, the dose of a compound of the invention is from about 1 mg and about 2,500 mg. In some embodiments, a dose of a compound of the invention used in compositions described herein is less than about 10,000 mg, or less than about 8,000 mg, or less than about 6,000 mg, or less than about 5,000 mg, or less than about 3,000 mg, or less than about 2,000 mg, or less than about 1,000 mg, or less than about 500 mg, or less than about 200 mg, or less than about 50 mg. Similarly, in some embodiments, a dose of a second compound (i.e., a drug used for treating the same or another disease as that treated by the compositions of the invention) as described herein is less than about 1,000 mg, or less than about 800 mg, or less than about 600 mg, or less than about 500 mg, or less than about 400 mg, or less than about 300 mg, or less than about 200 mg, or less than about 100 mg, or less than about 50 mg, or less than about 40 mg, or less than about 30 mg, or less than about 25 mg, or less than about 20 mg, or less than about 15 mg, or less than about 10 mg, or less than about 5 mg, or less than about 2 mg, or less than about 1 mg, or less than about 0.5 mg, and any and all whole or partial increments thereof.

In one embodiment, the present invention is directed to a packaged pharmaceutical composition comprising a container holding a therapeutically effective amount of a compound or conjugate of the invention, alone or in combination with a second pharmaceutical agent; and instructions for using the compound or conjugate to treat, prevent, or reduce one or more symptoms of a disease in a subject.

The term “container” includes any receptacle for holding the pharmaceutical composition. For example, in one embodiment, the container is the packaging that contains the pharmaceutical composition. In other embodiments, the container is not the packaging that contains the pharmaceutical composition, i.e., the container is a receptacle, such as a box or vial that contains the packaged pharmaceutical composition or unpackaged pharmaceutical composition and the instructions for use of the pharmaceutical composition. Moreover, packaging techniques are well known in the art. It should be understood that the instructions for use of the pharmaceutical composition may be contained on the packaging containing the pharmaceutical composition, and as such the instructions form an increased functional relationship to the packaged product. However, it should be understood that the instructions may contain information pertaining to the compound’s ability to perform its intended function, e.g., treating or preventing a disease in a subject, or delivering an imaging or diagnostic agent to a subject.

Routes of administration of any of the compositions of the invention include oral, nasal, parenteral, sublingual, transdermal, transmucosal (e g., sublingual, lingual, (trans)buccal, and (intra)nasal.). intravesical, intraduodenal, intragastrical, rectal, intra-peritoneal, subcutaneous, intramuscular, intradermal, intra-arterial, intravenous, or administration.

Suitable compositions and dosage forms include, for example, tablets, capsules, caplets, pills, gel caps, troches, dispersions, suspensions, solutions, syrups, granules, beads, transdermal patches, gels, powders, pellets, magmas, lozenges, creams, pastes, plasters, lotions, discs, suppositories, liquid sprays for nasal or oral administration, dry powder or aerosolized formulations for inhalation, compositions and formulations for intravesical administration and the like. It should be understood that the formulations and compositions that would be useful in the present invention are not limited to the particular formulations and compositions that are described herein.

Methods of Generating Tandem Arrays

The present invention provides a method of generating a tandem array of the invention. For example, in one embodiment, the tandem array can be generated in a single step. In one embodiment, the generation of the tandem array allows for full-length array transcription.

In one embodiment, the method comprises ligating at least two crRNA sequences, wherein each crRNA sequence comprises a unique direct repeat sequence (DR), wherein the ligation generates the tandem array. In one embodiment, each DR sequence comprises a unique mutation in the poly T stretch of SEQ ID NO: 267. For example, in one embodiment, each DR sequence comprises a unique mutation at T17 or T18 of SEQ ID NO: 267. In one embodiment, one crRNA sequence comprises a wild type DR sequence and each additional crRNA sequence comprises a DR sequence having unique mutation in the poly T stretch of SEQ ID NO: 267. In one embodiment, each DR sequence is independently selected from SEQ ID NOs:268-274.

Methods of Decreasing RNA & Methods of Treatment

In one aspect, the disclosure provides methods of decreasing the number of one or more RNA transcripts in a subject. In one embodiment, the method decrease the number of two or more RNA transcripts in a subject. In one embodiment, the two or more RNA transcripts in a subject are related. For example, in one embodiment, the two or more RNA transcripts are each viral transcripts of the same virus. In one embodiment, the two or more RNA transcripts are each involved the same cellular pathway.

In one embodiment, RNA is localized in the cytoplasm In one embodiment, the RNA is localized in the nucleus. In one embodiment, RNA is localized in an organelle. For example, in one embodiment, the methods decrease RNA localized in the nucleolus, ribosome, vesicle, rough endoplasmic reticulum, Golgi apparatus, cytoskeleton, smooth endoplasmic reticulum, mitochondna, vacuole, cytosol, lysosome, or centriole. In one embodiment, the methods decrease cell-membrane associated RNA. In one embodiment, the methods decrease extracellular RNA.

In one embodiment, the method comprises administering to the subject (1) a nucleic acid molecule encoding a fusion protein of the disclosure comprising a Cas protein and optionally a localization sequence, such as an NLS, NES or organelle localization signal, or a fusion protein of the disclosure comprising a Cas protein and optionally a localization sequence, such as an NLS, NES, or organelle localization signal; and (2) a nucleic acid molecule encoding a crRNA array comprising two or more crRNA.

In some embodiments, the RNA cytoplasmic. In such embodiments, the method comprises administering to the subject (1) a protein of the disclosure comprising a Cas protein and a NES or a nucleic acid molecule encoding a protein of the disclosure comprising a Cas protein and a NES; and (2) a nucleic acid molecule encoding a crRNA array comprising two or more crRNA.

In some embodiments, the RNA nuclear. In such embodiments, the method comprises administering to the subject (1) a protein of the disclosure comprising a Cas protein and a NLS or a nucleic acid molecule encoding a protein of the disclosure comprising a Cas protein and a NLS; and (2) a nucleic acid molecule encoding a crRNA array comprising two or more crRNA.

In one embodiment, the subject is a cell. In one embodiment, the cell is a prokaryotic cell or eukaryotic cell. In one embodiment, the cell is a eukaryotic cell. In one embodiment, the cell is a plant, animal, or fungi cell. In one embodiment, the cell is a plant cell. In one embodiment, the cell is an animal cell. In one embodiment, the cell is a yeast cell.

In one embodiment, the subject is a mammal. For example, in one embodiment, the subject is a human, non-human primate, dog, cat, horse, cow, goat, sheep, rabbit, pig, rat, or mouse. In one embodiment, the subject is a non-mammalian subject. For example, in one embodiment, the subject is a zebrafish, fruit fly, or roundworm.

In one embodiment, the amount of viral RNA is reduced in vitro. In one embodiment, the amount of viral RNA is reduced in vivo. In one aspect, the present invention provides methods cleaving of a one or more target viral RNA in a subject. In one embodiment, the method comprises administering to the subject (1) a nucleic acid molecule encoding a protein of the disclosure comprising a Cas protein and optionally a localization sequence, such as an NLS, NES, or organelle localization signal, or a protein of the disclosure comprising a Cas protein and optionally a localization sequence, such as an NLS, NES, or organelle localization signal; and (2) a nucleic acid molecule encoding a crRNA array comprising two or more crRNA, wherein each crRNA independently comprises a sequence substantially complementary to a RNA sequence in the target viral RNA.

Methods of Treatment and Use

The present invention provides methods of treating, reducing the symptoms of, and/or reducing the risk of developing a disease or disorder in a subject. For example, in one embodiment, methods of the invention of treat, reduce the symptoms of, and/or reduce the risk of developing a disease or disorder in a mammal. In one embodiment, the methods of the invention of treat, reduce the symptoms of, and/or reduce the risk of developing a disease or disorder in a plant. In one embodiment, the methods of the invention of treat, reduce the symptoms of, and/or reduce the risk of developing a disease or disorder in a yeast organism.

In one embodiment, the disease or disorder is caused by an activation of a cellular pathway. In some embodiments, the cellular pathway lead, for example, to aberrant control of cellular processes, with uncontrolled growth and increased cell survival. For example, in one embodiment, each crRNA independently comprises a sequence substantially complementary to an mRNA sequence within the RAS, JAK-STAT, PI3K/AKT, or MAPK cellular pathway.

In one embodiment, the method comprises administering to the subject (1) a protein of the disclosure or a nucleic acid molecule encoding a protein of the disclosure, and (2) a nucleic acid molecule encoding a crRNA array comprising two or more crRNA, wherein each crRNA independently comprises a sequence substantially complementary to a nucleotide sequence of a RNA transcript of the pathway. In one embodiment, the crRNA array comprising two or more crRNA, wherein each crRNA independently comprises a sequence substantially complementary to a nucleotide sequence of an mRNA sequence within the RAS, JAK-STAT, PI3K/AKT, or MAPK cellular pathway. In one embodiment, the Cas protein cleaves the RNA transcript(s).

In one embodiment, the disease or disorder includes, but is not limited to, cancer, heart disease, atherosclerosis, cardiac fibrosis, cardiac arrhythmia, hypertension, respiratory disease, stroke,

Alzheimer’s disease, diabetes, nephritis, liver disease.

In one embodiment, the disease or disorder the infection of vims infection. In one embodiment, the disease or disorder is caused by an vims infection. In one embodiment, the vims infection is infection of an RNA vims. For example, in one embodiment, the vims infection is infection of a positive sense ssRNA vims, a negative sense ssRNA vims, adsRNA vims, or a ssRNA-RT vims. In one embodiment, the vims infection is infection of an DNA vims. For example, in one embodiment, the vims infection is infection of a dsDNA vims, a ssDNA vims, or a dsDNA-RT vims. Thus, in one embodiment, the disease or disorder is may be treated, reduced, or the risk can be reduced via an element that prevents or reduces a viral RNA transcnpt. Thus, in one embodiment, the disease or disorder is may be treated, reduced, or the risk can be reduced via an element that prevents or reduces viral mRNA transcript, or prevents or reduces translation of viral protein.

In one embodiment, the method comprises administering to the subject (1) a protein of the disclosure or a nucleic acid molecule encoding a protein of the disclosure, and (2) a nucleic acid molecule encoding a crRNA array comprising two or more crRNA, wherein each crRNA independently comprises a sequence substantially complementary to a nucleotide sequence complimentary to a viral RNA transcript. In one embodiment, the Cas protein cleaves the viral RNA transcript.

In one embodiment, the virus is an RNA vims. In one embodiment, the vims produces RNA during its lifecycle. In one embodiment, the vims is a human vims, a plant vims or an animal vims. Exemplary vimses include, but are not limited to, vimses of families Adenoviridae, Adenoviridae, Alphaflexiviridae, Anelloviridae, Arenavims, Arteriviridae, Asfarviridae, Astroviridae, Benyviridae, Betaflexiviridae, Bimaviridae, Bomaviridae, Bromoviridae, Caliciviridae, Caulimoviridae, Circoviridae, Closteroviridae, Coronaviridae, Filoviridae, Flaviviridae, Gemmivindae, Flantavindae, Flepadnaviridae, Hepevindae, Herpesviridae, Kitaviridae, Luteoviridae, Nairovindae, Nanoviridae, Nimaviridae, Orthomyxoviridae, Paramyxoviridae, Phenuiviridae, Picomaviridae, Polyomaviridae, Pospiviridae, Potyviridae, Poxviridae, Reoviridae, Retroviridae, Retrovims, Rhabdoviridae, Secoviridae, Togaviridae, Tombusviridae, Tospoviridae, Tymoviridae, and Yirgaviridae. For example, exemplary vimses include, but are not limited to, African swme fever, Avian hepatitis E, Avian infectious laryngotracheitis, Avian nephritis virus, Bamboo mosaic vims, Banana bunchy top vims, Barley stripe mosaic vims, Barley yellow dwarf vims, Potato leafroll vims, Boma disease, Brome mosaic vims, wheat, Cauliflower mosaic vims, Chikungunya, Eastern equine encephalitis vims, Citms leprosis, Citms sudden death associated vims, Citms tristeza vims, Coconut cadang-cadang viroid, Curly top vims, African cassava mosaic vims, Cytomegalovirus, Epstein-Barr vims, Dengue, Yellow fever, West Nile, Zika, Ebola vims, Marburg vims, Equine arteritis vims, Porcine reproductive and respiratory syndrome vims, Equine infectious anemia, Foot and mouth disease, Foot and mouth disease, Enterovimses, Rhinovimses, Hepatitis B vims,

Hepatitis E vims, HIV, HIV-1, HIV-2, Infectious bursal disease vims (poultry), Infectious pancreatic necrosis (salmon), Infectious canine hepatitis, aviadenovimses of fowl, Influenza vimses, Lassa vims, Lymphocytic choriomeningitis vims, Monkeypox, Nairobi sheep disease, Newcastle disease vims (poultry), Norwalk vims, Numerous examples of crop damaging vimses, including Potato vims Y,

Porcine circovims 2, Beak and feather disease vims (poultry), Potato vims M, Rabies vims, Respiratory and enteric adenovimses, Respiratory syncytial vims, Rice stripe necrosis vims, Rift Valley fever, rotavimses, SARS-CoV-2, MERS, Sheeppox vims, Lumpy skin disease vims, SinNombre vims, Andes vims, SV40, Tobacco ringspot vims, Tomato bushy stunt vims, Tomato spotted wilt vims, Torque teno vims, Venezuelan equine encephalitis vims, Vesicular stomatitis Indiana vims, Viral hemorrhagic septicemia (trout), and White spot syndrome vims (shrimp).

In one embodiment, exemplary vimses include, but are not limited to, Primate T-lymphotropic vims 1, Primate T-lymphotropic vims 2, Primate T-lymphotropic vims 3, Human immunodeficiency vims 1, Human immunodeficiency vims 2, Simian foamy vims, Human picobimavims, Colorado tick fever vims, Changuinola vims, Great Island vims, Lebombo vims, Orungo vims, Rotavims A, Rotavims B, Rotavims C, Banna vims, Boma disease vims, Lake Victoria Marburgvims, Reston ebolavims, Sudan ebolavims, Tai forest ebolavims, Zaire vims, Human parainfluenza vims 2, Human parainfluenza vims 4, Mumps vims, Newcastle disease vims, Human parainfluenza vims 1, Human parainfluenza vims 3, Hendra vims, Nipah vims, Measles vims, Human respiratory syncytial vims, Human metapneumovims, Chandipura vims, Isfahan vims, Piry vims, Vesicular stomatitis Alagoas vims, Vesicular stomatitis Indiana vims, Vesicular stomatitis New Jersey vims, Australian bat lyssavims, Duvenhage vims, European bat lyssavims 1, European bat lyssavims 2, Mokola vims, Rabies vims, Guanarito vims, Junin vims, Lassa vims, Lymphocytic choriomeningitis vims, Machupo vims, Pichinde vims, Sabia vims, Whitewater Arroyo vims, Bunyamwera vims, Bwamba vims, California encephalitis vims, Carapam vims, Catu vims, Guama vims, Guaroa vims, Kairi vims, Marituba vims, Oriboca vims, Oropouche vims, Shuni vims, Tacaiuma vims, Wyeomyia vims, Andes vims, Bayou vims, Black creek canal vims, Dobrava-Belgrade vims, Hantaan vims, Laguna Negra vims, New York vims, Puumala vims, Seoul virus, Sin Nombre virus, Cnmean-Congo haemorrhagic fever virus, Dugbe vims, Candiru vims, Punta Toro vims, Rift Valley fever vims, Sandfly fever Naples vims, Influenza A vims, Influenza B vims, Influenza C vims, Dhori vims, Thogoto vims, Hepatitis delta vims, Human coronavims 229E, Human coronavims NL63, Human coronavims HKU1, Human coronavims OC43, SARS coronavims, Human torovims, Human enterovims A, Human enterovims B, Human enterovims C, Human enterovims D, Human rhinovims A, Human rhinovims B, Human rhinovims C, Encephalomyocarditis vims,

Theilovims, Equine rhinitis A vims, Foot and mouth disease vims, Hepatitis A vims, Human parechovims, Ljungan vims, Aichi vims, Human astrovims, Human astrovims 2, Human astrovims 3, Human astrovims 4, Human astrovims 5, Human astrovims 6, Human astrovims 7, Human astrovims 8, Norwalk vims, Sapporo vims, Aroa vims, Banzi vims, Dengue vims, Ilheus vims, Japanese encephalitis vims, Kokobera vims, Kyasanur forest disease vims, Louping ill vims, Murray Valley encephalitis vims, Ntaya vims, Omsk haemorrhagic fever vims, Powassan vims, Rio Bravo vims, St Louis encephalitis vims, Tick-bome encephalitis vims, Usutu vims, Wesselsbron vims, West Nile vims, Yellow fever vims, Zika vims, Hepatitis C vims, Hepatitis E vims, Barmah Forest vims, Chikungunya vims, Eastern equine encephalitis vims, Everglades vims, Getah vims, Mayaro vims, Mucambo vims, O'nyong-nyong vims, Pixuna vims, Ross River vims, Semliki Forest vims, Sindbis vims, Venezuelan equine encephalitis vims, Western equine encephalitis vims, Whataroa vims, Rubella vims.

In one embodiment, exemplary vimses include, but are not limited to, Ranid herpesvirus 1, Ranid herpesvirus 2, Ranid herpesvirus 3, Anguillid herpesvirus 1, Cyprinid herpesvirus 1, Cyprinid herpesvirus 2, Cyprinid herpesvirus 3, Acipenserid herpesvirus 2, Ictalurid herpesvirus 1, Ictalurid herpesvirus 2, Salmonid herpesvirus 1, Salmonid herpesvirus 2, Salmonid herpesvirus 3, Gallid alphaherpesvims 1, Psittacid alphaherpesvims 1, Anatid alphaherpesvims 1, Columbid alphaherpesvims 1, Gallid alphaherpesvims 2, Gallid alphaherpesvims 3, Meleagrid alphaherpesvims 1, Spheniscid alphaherpesvims 1, Chelonid alphaherpesvims 5, Testudinid alphaherpesvims 3, Ateline alphaherpesvims

1, Bovine alphaherpesvims 2, Cercopithecine alphaherpesvims 2, Human alphaherpesvims 1, Human alphaherpesvims 2, Leporid alphaherpesvims 4, Macacine alphaherpesvims 1, Macropodid alphaherpesvims 1, Macropodid alphaherpesvims 2, Panine alphaherpesvims 3, Papiine alphaherpesvims

2, Pteropodid alphaherpesvims 1, Saimiriine alphaherpesvims 1, Bovine alphaherpesvims 1, Bovine alphaherpesvims 5, Bubaline alphaherpesvims 1, Canid alphaherpesvims 1, Caprine alphaherpesvims 1, Cercopithecine alphaherpesvims 9, Cervid alphaherpesvims 1, Cervid alphaherpesvims 2, Equid alphaherpesvims 1, Equid alphaherpesvims 3, Equid alphaherpesvims 4, Equid alphaherpesvims 8, Equid alphaherpesvims 9, Felid alphaherpesvims 1, Human alphaherpesvims 3, Monodontid alphaherpesvims

1, Phocid alphaherpesvims 1, Suid alphaherpesvims 1, Chelonid alphaherpesvims 6, Aotine betaherpesvims 1, Cebine betaherpesvims 1, Cercopithecine betaherpesvims 5, Human betaherpesvims 5, Macacine betaherpesvirus 3, Macacine betaherpesvirus 8, Mandrilline betaherpesvirus 1, Panine betaherpesvirus 2, Papiine betaherpesvirus 3, Papiine betaherpesvirus 4, Saimiriine betaherpesvirus 4, Murid betaherpesvirus 1, Murid betaherpesvirus 2, Murid betaherpesvirus 8, Elephantid betaherpesvirus 1, Elephantid betaherpesvirus 4, Elephantid betaherpesvirus 5, Human betaherpesvirus 7, Human betaherpesvirus 6A, Human betaherpesvirus 6B, Macacine betaherpesvirus 9, Murid betaherpesvirus 3, Suid betaherpesvirus 2, Caviid betaherpesvirus 2, Tupaiid betaherpesvirus 1, Callitrichine gammaherpesvirus 3, Cercopithecine gammaherpesvirus 14, Gorilline gammaherpesvirus 1, Human gammaherpesvirus 4, Macacine gammaherpesvirus 4, Macacine gammaherpesvirus 10, Panine gammaherpesvirus 1, Papiine gammaherpesvirus 1, Pongine gammaherpesvirus 2, Alcelaphine gammaherpesvirus 1, Alcelaphine gammaherpesvirus 2, Bovine gammaherpesvirus 6, Caprine gammaherpesvirus 2, Hippotragine gammaherpesvirus 1, Ovine gammaherpesvirus 2, Suid gammaherpesvirus 3, Suid gammaherpesvirus 4, Suid gammaherpesvirus 5, Equid gammaherpesvirus 2, Equid gammaherpesvirus 5, Felid gammaherpesvirus 1, Mustelid gammaherpesvirus 1, Phocid gammaherpesvirus 3, Vespertilionid gammaherpesvirus 1, Ateline gammaherpesvirus 2, Ateline gammaherpesvirus 3, Bovine gammaherpesvirus 4, Cricetid gammaherpesvirus 2, Human gammaherpesvirus 8, Macacine gammaherpesvirus 5, Macacine gammaherpesvirus 8, Macacine gammaherpesvirus 11, Macacine gammaherpesvirus 12, Murid gammaherpesvirus 4, Murid gammaherpesvirus 7, Saimiriine gammaherpesvirus 2, Equid gammaherpesvirus 7, Phocid gammaherpesvirus 2, Saguinine gammaherpesvirus 1, Iguanid herpesvirus 2, Haliotid herpesvirus 1, Ostreid herpesvirus 1, Salmonella vims SKML39, Shigella vims AG3, Dickeya vims Limestone, Dickeya vims RC2014, Escherichia vims CBA120, Escherichia vims Phaxl, Salmonella vims 38, Salmonella vims Det7, Salmonella vims GG32, Salmonella vims PM10, Salmonella vims SFP10, Salmonella vims SH19, Salmonella vims SJ3, Escherichia vims KWBSE43-6, Klebsiella vims 0507KN21, Klebsiella vims KpSl 10, Klebsiella vims May, Klebsiella vims Menlow, Serratia vims IME250, Erwinia vims Ea2809, Serratia vims MAM1, Acinetobacter vims Acibel007, Acinetobacter vims AB3, Acinetobacter vims AbKT21III, Acinetobacter vims Abpl, Acinetobacter vims Aci07, Acinetobacter vims Aci08, Acinetobacter vims AS11, Acinetobacter vims AS 12, Acinetobacter vims Fril, Acinetobacter vims IME200, Acinetobacter vims PD6A3, Acinetobacter vims PDAB9, Acinetobacter vims phiABl, Acinetobacter vims SH-Ab 15519, Acinetobacter vims SWHAbl, Acinetobacter vims SWHAb3, Acinetobacter vims WCHABP5, Acintetobacter vims Bl, Acmtetobacter vims B2, Acmtetobacter vims B5, Acintetobacter vims D2, Acintetobacter vims PI, Acintetobacter vims P2, Acintetobacter vims phiAB6, Acinetobacter vims Petty, Vibrio vims Vcl, Vibrio vims A318, Vibrio vims AS51, Vibrio vims Vp670, Marinomonas vims CB5A, Marinomonas vims CPPlm, Vibrio vims VEN, Pseudomonas vims Achelous, Pseudomonas vims Alpheus, Pseudomonas vims Nerthus, Pseudomonas vims Njord, Pseudomonas vims uligo, Pseudomonas vims C171, Pectobacterium vims PP16, Pectobacterium vims PPWS1, Pectobacterium vims PPWS2, Pectobacterium vims CB5, Pectobacterium vims Clickz, Pectobacterium vims fMl, Pectobacterium vims Gaspode, Pectobacterium vims Khlen, Pectobacterium vims Koot, Pectobacterium vims Lelidair, Pectobacterium vims Nobby, Pectobacterium vims Peatl, Pectobacterium vims Phoria, Pectobacterium vims PP90, Pectobacterium vims Zenivior, Dickeya vims BF25-12, Pseudomonas vims NV3, Pseudomonas vims 130-113, Pseudomonas vims 15pyo, Pseudomonas vims Ab05, Pseudomonas vims ABTNL, Pseudomonas vims DL62, Pseudomonas vims kF77, Pseudomonas vims LKD16, Pseudomonas vims LUZ19, Pseudomonas vims MPK6, Pseudomonas vims MPK7, Pseudomonas vims NFS, Pseudomonas vims PAXYB1, Pseudomonas vims phiKMV, Pseudomonas vims PT2, Pseudomonas vims PT5, Pseudomonas vims RLP, Pseudomonas vims LKA1, Pseudomonas vims f2, Aeromonas vims 25AhydR2PP, Aeromonas vims AS7, Aeromonas vims ZPAH7, Yersinia vims ISA08, Aeromonas vims Ahpl, Aeromonas vims CF7, Cronobacter vims DevCD23823, Cronobacter vims GAP227, Salmonella vims Sppl6, Yersinia vims R8-01, Yersinia vims fFleYen301, Yersinia vims Phi80-18, Pectobacterium vims Amol60, Pectobacterium vims PP2, Proteus vims PM85, Proteus vims PM93, Proteus vims PM116, Proteus vims Pm5460, Pectobacterium vims PP1, Erwinia vims Eral03, Erwinia vims S2, Lelliottia vims phD2B, Citrobacter CrRp3, Escherchia vims LL11, Escherichia vims AAPEc6, Escherichia vims ACGC91, Escherichia vims B, Escherichia vims C, Escherichia vims K, Escherichia vims Kl-5, Escherichia vims K1E, Escherichia vims mutPKlA2, Escherichia vims VEc3, Escherichia vims UAB78, Salmonella vims BP12B, Salmonella vims SP6, Burkholderia vims BpAMPl, Ralstonia vims RSPI1, Ralstonia vims RSB1, Ralstonia vims RsoPlIDN, Burkholderia vims JG068, Ralstonia vims RSJ2, Ralstonia vims RSJ5, Ralstonia vims RSPII1, Shigella vims Buco, Escherichia vims Minoma, Klebsiella vims AltoGao, Klebsiella vims BO IE, Klebsiella vims FI 9, Klebsiella vims K244, Klebsiella vims Kp2, Klebsiella vims KP34, Klebsiella vims KPRio2015, Klebsiella vims KpS2, Klebsiella vims KpV41, Klebsiella vims KpV48, Klebsiella vims KpV71, Klebsiella vims KpV74, Klebsiella vims KpV475, Klebsiella vims KPV811, Klebsiella vims myPSH1235, Klebsiella vims SU503, Klebsiella vims SU552A, Shigella vims SFN6B, Enterobacter vims KDA1, Proteus vims PM16, Proteus vims PM75, Dickeya vims Dagda, Dickeya vims Katbat, Dickeya vims Luksen, Dickeya vims Mysterion, Yersinia vims AP10, Erwinia vims FE44, Eschenchia vims 285P, Escherichia vims BA14, Escherichia vims P483, Escherichia vims P694, Escherichia vims S523, Kluyvera vims Kvpl, Pectobacterium vims PP74, Salmonella vims BP12A, Salmonella vims BSP161, Shigella vims A7, Yersinia vims Berlin, Yersinia vims PYPS50, Yersinia vims Yepe2, Yersinia vims Yepf, Citrobacter vims CR8, Vibrio vims ICP3, Vibrio vims N4, Vibrio vims VP4, Enterobacter vims Eapl, Erwinia vims LI, Escherichia vims SRT7, Pseudomonas vims 17A, Pseudomonas vims ghl, Pseudomonas vims Henninger, Pseudomonas vims KNP, Pseudomonas vims PflERZ2017, Pseudomonas virus PhiPSA2, Pseudomonas virus PhiPsal7, Pseudomonas virus PPPL1, Pseudomonas virus shl2, Pseudomonas virus WRT, Yersinia virus fPS9, Yersinia virus fPS53, Yersinia virus fPS59, Yersinia vims fPS54ocr, Pectobacterium vims Jarilo, Citrobacter vims CR44b, Citrobacter vims SH3, Citrobacter vims SH4, Cronobacter vims Dev2, Cronobacter vims GW1, Enterobacter vims EcpYZUOl, Escherichia vims EcoDSl, Escherichia vims F, Escherichia vims GA2A, Escherichia vims IMM002, Escherichia vims K1F, Escherichia vims LM33P1, Escherichia vims PE3-1, Escherichia vims Ro451w, Escherichia vims ST31, Escherichia vims Vecl3, Escherichia vims YZ1, Escherichia vims ZG49, Shigella vims SFPH2, Morganella vims MmPl, Morganella vims MP2, Dickeya virus JA10, Dickeyavims Ninurta, Pectobacterium vims PP47, Pectobacterium vims PP81, Pectobacterium vims PPWS4, Pseudomonas vims PPpW4, Pseudomonas vims 22PfluR64PP, Pseudomonas vims IBBPF7A, Pseudomonas vims PflO, Pseudomonas vims PFP1, Pseudomonas vims PhiSl, Pseudomonas vims UNOSLW1, Pseudomonas vims PspYZU08, Escherichia vims K30, Klebsiella vims 2044-307w, Klebsiella vims BIS33, Klebsiella vims Elenul, Klebsiella vims IL33, Klebsiella vims IME205, Klebsiella vims IME321, Klebsiella vims K5, Klebsiella vims Kll, Klebsiella vims K5-2, Klebsiella vims K5-4, Klebsiella vims KNl-1,

Klebsiella vims KN3-1, Klebsiella vims KN4-1, Klebsiella vims Kpl, Klebsiella vims KP32, Klebsiella vims KR32P92, Klebsiella vims KR32P94, Klebsiella vims KP32il95, Klebsiella vims KP32il96, Klebsiella vims kpssk3, Klebsiella vims KpV289, Klebsiella vims KpV763, Klebsiella vims KpV766, Klebsiella vims KpV767, Klebsiella vims Pharr, Klebsiella vims PRA33, Klebsiella vims SHKpl52234, Klebsiella vims SHKpl52410, Citrobacter vims CFP1, Citrobacter vims SHI, Citrobacter vims SH2, Enterobacter vims E2, Enterobacter vims E3, Enterobacter vims KPN3, Enterobacteria vims T7M, Escherichia vims ECA2, Escherichia vims LL2, Escherichia vims T3, Escherichia vims T3Luria, Leclercia vims 10164-302, Salmonella vims SG-JL2, Serratia vims 2050H2, Serratia virus SM9-3Y, Yersinia vims AP5, Yersinia vims YeFlO, Yersinia vims Ye03- 12, Enterobacteria vims IME390, Escherichia vims 13a, Escherichia vims 64795ecl, Escherichia vims C5, Escherichia vims CICC80001, Escherichia vims Ebrios, Escherichia vims EG1, Escherichia vims HZ2R8, Escherichia vims HZP2, Escherichia vims N30, Escherichia vims NCA, Escherichia vims T7, Salmonella vims 3A8767, Salmonella vims Vi06, Stenotrophomonas vims IME15, Yersinia vims YpPY, Yersinia vims YpsPG, Pseudomonas vims Phi 15, Pectobacterium vims DUPPII, Synechococcus vims SCBP42, Aquamicrobium vims P14, Ashivims S45C4, Agrobacterium vims Atuph02, Agrobacterium vims Atuph03, Ralstonia vims Apl, Ayaqvims S45C18, Prochlorococcus vims SS120-1, Pseudomonas vims Andromeda, Pseudomonas vims Bf7, Escherichia vims J8-65, Escherichia vims Lidtsur, Prochlorococcus vims NATL1A7, Chosvims KM23C739, Rhizobium vims RHEph02, Rhizobium vims RHEph08, Rhizobium vims RHEph09, Vibrio vims Cyclit, Escherichia vims PGT2, Escherichia vims PhiKT, Alteromonas vims H4-4, Foussvims S46C10, Fussvims S30C28, Escherichia vims ECBP5, Pectobacterium vims PP99, Ralstonia virus DURPI, Ralstoma virus RsoPlEGY, Synechococcus STIP37, Jalkavirus S08C159, Ralstonia virus RSB3, Kawavirus SWcelC56, Synechococcus virus SRIP1, Providencia virus PS3, Curvibacter virus P26059B, Ralstonia virus RSB2, Synechococcus virus SCBP2, Krakvirus S39C11, Podovirus Lau218, Pantoea virus LIMElight, Prochlorococcus virus PGSP1, Synechococcus virus SCBP3, Caulobacter virus Lullwater, Vibrio virus KF1, Vibrio virus KF2, Vibrio virus OWB, Vibrio virus VP93, Pseudomonas virus VSW3, Nohivirus S31C1, Oinezvirus S37C6, Rhizobium virus RElEphOl, Pagavirus S05C849, Mesorhizobium virus Lo5R7ANS, Pedosvirus S28C3, Pekhitvirus S04C24, Pelagibacter virus HTVC019P, Pelagivirus S35C6, Caulobacter virus Percy, Delftia virus IMEDE1, Podivirus S05C243, Pseudomonas virus PollyC, Synechococcus virus SCBP4, Powvirus S08C41, Xanthomonas virus f20, Xanthomonas virus BO, Xanthomonas virus XAJ24, Xanthomonas virus XclO, Xylella virus Prado, Synechococcus virus SB28, Sphingomonas virus Scott, Synechococcus virus SRIP2, Ralstonia vims ITL1, Sieqvirus S42C7, Ralstonia vims RPSCl, Stopalavims S38C3, Pelagibacter vims EITVCOllP, Stupnyavims KM16C193, Prochlorococcus vims 951510a, Prochlorococcus vims NATL2A133, Prochlorococcus vims PSSP10, Vibrio vims JSF7, Prochlorococcus vims PSSP7, Synechococcus vims P60, Prochlorococcus vims PSSP3, Synechococcus vims PSSP2, Synechococcus vims Syn5, Votkovvims S28C10, Pantoea vims LIMEzero, Pasteurella vims PHB01, Pasteurella vims PHB02, Escherichia vims GJ1, Escherichia vims ST32, Erwinia vims Faunus, Erwinia vims Y2, Aeromonas vims pAh6C, Pectobacterium vims PM1, Pectobacterium vims PP101, Shewanella vims SppOOl, Shewanella vims SppYZU05, Vibrio vims Ceto, Vibrio vims Thalassa, Vibrio vims JSF10, Vibrio vims JSF12, Vibrio vims phi3, Vibrio vims pVpl, Escherichia vims EPS7, Escherichia vims mar003J3, Escherichia vims sausl32, Salmonella vims 123, Salmonella vims 329, Salmonella vims 118970sal2, Salmonella vims LVR16A, Salmonella vims SI 13, Salmonella vims SI 14, Salmonella vims SI 16, Salmonella vims S124, Salmonella vims S126, Salmonella vims S132, Salmonella vims S133, Salmonella vims S147, Salmonella vims Seafire, Salmonella vims SH9, Salmonella vims STG2, Salmonella vims Stitch, Salmonella vims Sw2, Yersinia vims phiR201, Escherichia vims AKFV33, Escherichia vims BF23, Escherichia vims chee24, Escherichia vims DT5712, Escherichia vims DT57C, Escherichia vims FFH1, Escherichia vims Gostya9, Escherichia vims H8, Escherichia vims mar004NP2, Escherichia vims OSYSP, Escherichia vims phiAPCEc03, Escherichia vims phiLLS, Escherichia vims slur09, Escherichia vims T5, Salmonella vims NRO 1 , Salmonella vims S 131 , Salmonella vims Shivani, Salmonella vims SP01, Salmonella vims SP3, Salmonella vims SPC35, Shigella vims SHSML45, Shigella vims SSP1, Pectobacterium vims DUPPV, Pectobacterium vims Myl, Proteus vims PM 135, Proteus vims Stubb, Vibrio vims PG07, Vibrio vims VspSwl, Aeromonas vims AhSzql, Aeromonas vims AhSzwl, Klebsiella vims IME260, Klebsiella vims Sugarland, Escherichia vims IME542, Escherichia vims ACGM12, Escherichia vims EC3a, Escherichia vims DTL, Escherichia vims IME253, Escherichia virus Rtp, Shigella virus Sfl2, Escherichia virus phiEB49, Escherichia virus AHP42, Escherichia virus AHS24, Escherichia virus AKS96, Escherichia virus Cl 19, Escherichia virus E41c, Escherichia virus Eb49, Escherichia virus Jk06, Escherichia virus KP26, Escherichia virus phiJLA23, Escherichia virus Roguel, Shigella virus Sdl, Shigella virus pSfl, Citrobacter virus DK2017, Citrobacter virus Sazh, Citrobacter virus Stevie, Escherichia virus LL5, Escherichia virus TLS, Salmonella virus 36, Salmonella virus PHB07, Salmonella virus phSE2, Salmonella vims SP126, Salmonella vims YSP2, Escherichia vims 95, Escherichia vims marOOl Jl, Escherichia vims mar002J2, Escherichia vims SECphi27, Escherichia vims swanOl, Escherichia vims IME347, Escherichia vims SRT8, Escherichia vims ADB2, Escherichia vims BIFF, Escherichia vims IME18, Escherichia vims JMPW1, Escherichia vims JMPW2, Escherichia vims SH2, Escherichia vims Tl, Shigella vims 008, Shigella vims ISF001, Shigella vims PSf2, Shigella vims Sfml, Shigella vims SH6, Shigella vims Shfll, Shigella vims ISF002, Cronobacter vims Esp2949-1, Enterobacter vims EcLl, Cronobacter vims PhiCSOl, Escherichia vims ESC041, Pantoeavims AAS23, Escherichia vims NBD2, Enterobacter vims F20, Klebsiella vims 1513, Klebsiella vims GFIK3, Klebsiella vims KLPN1, Klebsiella vims KOX1, Klebsiella vims KP36, Klebsiella vims KpColl, Klebsiella vims KpKT21phil, Klebsiella vims KPNN141, Klebsiella vims KpV522, Klebsiella vims MezzoGao, Klebsiella vims NJR15, Klebsiella vims NJS1, Klebsiella vims NJS2, Klebsiella vims PKP126, Klebsiella vims Sushi, Klebsiella vims TAH8, Klebsiella vims TSK1, Bacillus vims Agate, Bacillus vims Bobb, Bacillus vims Bp8pC, Bacillus vims Bastille, Bacillus vims CAM003, Bacillus vims Evoli, Bacillus vims HoodyT, Bacillus vims AvesoBmore, Bacillus vims B4, Bacillus vims Bigbertha, Bacillus vims Riley, Bacillus vims Spock, Bacillus vims Troll, Bacillus vims Bc431, Bacillus vims Bcpl, Bacillus vims BCP82, Bacillus vims BM15, Bacillus vims Deepblue, Bacillus vims JBP901, Bacillus vims Grass, Bacillus vims NIT1, Bacillus vims SPG24, Bacillus vims BCP78, Bacillus vims TsarBomba, Bacillus vims BPS13, Bacillus vims BPS10C, Bacillus vims Hakuna, Bacillus vims Megatron, Bacillus vims WPh, Bacillus vims Mater, Bacillus vims Moonbeam, Bacillus vims SlOphi, Enterococcus vims ECP3, Enterococcus vims EF24C, Enterococcus vims EFLK1, Enterococcus vims EFDG1, Enterococcus vims EFP01, Enterococcus vims EfV12, Listeria vims A511, Listeria vims AG20, Listeria vims List36, Listeria vims LMSP25, Listeria vims LMTA34, Listena vims LMTA148, Listena vims LP048, Listena vims LP064, Listeria vims LP083-2, Listeria vims P100, Listena vims WIL1, Bacillus vims Camphawk, Bacillus vims SPOl, Bacillus vims CP51, Bacillus vims JL, Bacillus vims Shanette, Staphylococcus vims BS1, Staphylococcus vims BS2, Lactobacillus vims Bacchae, Lactobacillus vims Bromius, Lactobacillus vims Iacchus, Lactobacillus vims Lpa804, Lactobacillus vims Semele, Staphylococcus vims Gl, Staphylococcus vims G15, Staphylococcus vims JD7, Staphylococcus vims K, Staphylococcus vims MCE2014, Staphylococcus vims P108, Staphylococcus vims Rodi, Staphylococcus vims S253, Staphylococcus vims S25-4, Staphylococcus virus SA12, Staphylococcus virus Sbl, Staphylococcus virus SscMl, Staphylococcus virus IPLAC1C, Staphylococcus virus SEP1, Staphylococcus virus Remus, Staphylococcus virus SA11, Staphylococcus virus Stau2, Staphylococcus virus Twort, Brochothrix virus A9, Lactobacillus virus Lb338-1, Lactobacillus virus LP65, Campylobacter virus CP21, Campylobacter virus CP220, Campylobacter virus CPtlO, Campylobacter vims IBB35, Campylobacter vims CP81, Campylobacter vims CP30A, Campylobacter vims CPX, Campylobacter vims Losl, Campylobacter vims NCTC12673, Escherichia vims Alf5, Escherichia vims AY0145A, Escherichia vims EC6, Escherichia vims HY02, Escherichia vims JH2, Escherichia vims TP1, Escherichia vims VpaEl, Escherichia vims wV8, Salmonella vims BPS15Q2, Salmonella vims BPS17L1, Salmonella vims BPS17W1, Salmonella vims FelixOl, Salmonella vims Mushroom, Salmonella vims Si3, Salmonella vims SP116, Salmonella vims UAB87, Erwinia virus Ea214, Erwiniavims M7, Citrobacter vims Moogle, Citrobacter vims Mordin, Shigella vims Sfl3, Shigella vims Sfl4, Shigella vims Sfl7, Escherichia vims SUSP1, Escherichia vims SUSP2, Ralstonia vims RSA1, Ralstonia vims RSY1, Mannheimia vims 1127AP1, Mannheimia vims PHL101, Aeromonas vims phi018P, Vibrio vims Canoe, Pseudoalteromonas vims C5a, Pseudomonas vims Dobby, Pseudomonas vims phiCTX, Erwiniavims EtG, Escherichia vims 186, Salmonella vims PsP3, Salmonella vims SEN1, Erwinia vims ENT90, Klebsiella vims 4LV2017, Salmonella vims Fels2, Salmonella vims RE2010, Salmonella vims SEN8, Salmonella vims SopEphi, Haemophilus vims HP1, Haemophilus vims HP2, Vibrio vims Kappa, Pasteurella vims F108, Burkholderia vims KS14, Burkholderia vims AP3, Burkholderia vims KS5, Vibrio vims K139, Burkholderia vims ST79, Escherichia vims fiAA91ss, Escherichia vims P2, Escherichia vims prol47, Escherichia vims pro483, Escherichia vims Wphi, Yersinia vims L413C, Pseudomonas vims phi3, Salinivibrio vims SMHB1, Klebsiella vims 3LV2017, Salmonella vims SEN4, Cronobacter vims ESSI2, Stenotrophomonas vims Smpl31, Salmonella vims FSLSP004, Burkholderia vims KL3, Burkholderia vims phi52237, Burkholderia vims phiE122, Burkholderia vims phiE202, Vibrio vims PV94, Escherichia vims P88, Escherichia vims Bp7, Escherichia vims IME08, Escherichia vims JS 10, Escherichia vims JS98, Escherichia vims MX01, Escherichia vims QL01, Escherichia vims VR5, Escherichia vims WG01, Escherichia vims VR7, Escherichia vims VR20, Escherichia vims VR25, Escherichia vims VR26, Shigella vims SP18, Salmonella vims Melville, Salmonella vims S16, Salmonella vims STML198, Salmonella vims STP4a, Klebsiella vims JD18, Klebsiella vims PKOl 11, Enterobacter vims PG7, Escherichia vims CC31, Escherichia vims ECD7, Escherichia vims GEC3S, Escherichia vims JSE, Escherichia vims phi 1, Escherichia vims RB49, Citrobacter vims CF1, Citrobacter vims Merlin, Citrobacter vims Moon, Escherichia vims APCEcOl, Escherichia vims HP3, Escherichia vims HX01, Escherichia vims JS09, Escherichia vims 0157tp3, Escherichia vims 0157tp6, Escherichia vims PhAPEC2, Escherichia vims RB69, Escherichia vims STO, Shigella vims SHSML521, Shigella vims UTAM, Vibrio virus KVP40, Vibrio virus ntl, Vibrio virus ValKK3, Enterobacter virus Eap3, Klebsiella virus KP15, Klebsiella virus KP27, Klebsiella virus Matisse, Klebsiella virus Miro, Klebsiella virus PMBT1, Escherichia virus AR1, Escherichia virus C40, Escherichia virus CF2, Escherichia virus El 12, Escherichia virus ECML134, Escherichia virus HY01, Escherichia virus HY03, Escherichia virus Ime09, Escherichia virus RB3, Escherichia virus RB14, Escherichia virus slur03, Escherichia virus slur04, Escherichia virus T4, Shigella virus Pssl, Shigella virus Sf21, Shigella virus Sf22, Shigella virus Sf24, Shigella virus SHBML501, Shigella virus Shfl2, Yersinia virus Dl, Yersinia virus PST, Acinetobacter virus 133, Aeromonas virus 65, Aeromonas virus Aehl, Escherichia virus RB16, Escherichia virus RB32, Escherichia virus RB43, Pseudomonas virus 42, Escherichia virus Av05, Cronobacter virus CR3, Cronobacter virus CR8, Cronobacter virus CR9, Cronobacter virus PBES02, Pectobacterium virus phiTE, Cronobacter virus GAP31, Escherichia virus 4MG, Salmonella vims PYPSE1, Salmonella vims SSE121, Escherichia vims APECc02, Escherichia vims FFH2, Escherichia vims FV3, Escherichia vims JES2013, Escherichia vims Murica, Escherichia vims slurl6, Escherichia vims V5, Escherichia vims V18, Brevibacillus vims Abouo, Brevibacillus vims Davies, Synechococcus vims SMbCMIOO, Erwinia vims Deimos, Erwinia vims Desertfox, Erwinia vims Ea35-70, Erwinia vims RAY, Erwinia vims Simmy50, Erwinia vims SpecialG, Synechococcus vims SShM2, Klebsiella vims K64-1, Klebsiella vims RaK2, Dickeya vims ADI, Erwinia vims Alexandra, Lactobacillus vims LBR48, Synechococcus vims SCAM1, Synechococcus vims SCBWM1, Vibrio vims Aphroditel, Escherichia vims 121Q, Eschierichia vims PBEC04, Synechococcus vims AC2014fSyn7803C8, Synechococcus vims ACG2014f, Synechococcus vims ACG2014fSyn7803US26, Synechococcus vims STIM5, Pseudomonas vims PaBG, Rheinheimera vims Barbal8A, Rheinheimera vims Barbal9A, Rheinheimera vims Barba21A, Rheinheimera vims Barba5S, Rheinheimera vims Barba8S, Burkholderia vims BcepMu, Burkholderia vims phiE255, Synechococcus vims Bellamy, Gordonia vims GMA6, Aeromonas vims 44RR2, Mycobacterium vims Alice, Mycobacterium vims Bxzl, Mycobacterium vims Dandelion, Mycobacterium vims HyRo, Mycobacterium vims 13, Mycobacterium vims Lukilu, Mycobacterium vims Nappy, Mycobacterium vims Sebata, Faecalibacterium vims Brigit, Prochlorococcus vims Syn33, Synechococcus vims SRIM12- 01, Synechococcus vims SRIM12-06, Synechococcus vims SRIM12-08, Salmonella vims SEN34, Acidovorax vims ACPI 7, Xanthomonas vims Carpasina, Xanthomonas vims XcPl, Pseudomonas vims pfl6, Synechococcus vims SCAM3, Ralstonia vims RSF1, Ralstonia vims RSL2, Synechococcus vims SWAM2, Erwinia vims Derbicus, Pseudomonas vims EL, Smorhizobium vims M7, Sinorhizobium vims M12, Sinorhizobium vims N3, Serratia vims BF, Yersinia vims Yen9-04, Faecalibacterium vims Epona, Erwinia vims Asesmo, Erwinia vims EaH2, Prochlorococcus vims MED4-213, Prochlorococcus vims PHM1, Prochlorococcus vims PFIM2, Flavobacterium vims FCL2, Flavobacterium vims FCV1, Pseudomonas vims KIL2, Pseudomonas vims KIL4, Edwardsiella vims GF2, Escherichia vims Goslar, Halomonas virus HAP1, Vibrio virus VP882, Lactobacillus virus Lb, Erwinia virus EaHl, Iodobacter virus PLPE, Delftia virus PhiW14, Klebsiella virus JD001, Klebsiella virus KpV52, Klebsiella virus KpV80, Escherichia virus CVM10, Escherichia virus EC0078, Escherichia virus ep3, Brevibacillus virus Jimmer, Brevibacillus virus Osiris, Synechococcus virus SCAM9, Rhizobium virus RHEph4, Faecalibacterium virus Lagaffc. Synechoccus virus SP4, Synechococcus virus Syn30, Prochlorococcus virus PTIM40, Synechococcus virus SSKS1, Salmonella virus ZCSE2, Clostridium vims phiC2, Clostridium vims phiCD27, Clostridium vims phi CD 119, Erwinia vims Machina, Arthrobacter vims BarretLemon, Arthrobacter vims Beans, Arthrobacter vims Brent, Arthrobacter vims Jawnski, Arthrobacter vims Martha, Arthrobacter vims Piccoletto, Arthrobacter vims Shade, Arthrobacter vims Sonny, Synechococcus vims SCAM7, Acinetobacter vims ME3, Ralstonia vims RSL1, Cronobacter vims GAP32, Pectinobacterium vims CBB, Faecalibacterium vims Mushu, Escherichia vims Mu, Shigella vims SfMu, Elalobacterium vims phiEI, Burkholderia vims Bcepl, Burkholderia vims Bcep43, Burkholderia vims Bcep781, Burkholderia vims BcepNY3, Xanthomonas vims OP2, Synechococcus vims SMbCM6, Pseudomonas vims Ab03, Pseudomonas vims Gl, Pseudomonas vims KPP10, Pseudomonas vims PAKP3, Pseudomonas vims PS24, Synechococcus vims SRIM8, Synechococcus vims SRIM50, Synechococcus vims ACG2014bSyn7803C61, Synechococcus vims ACG2014bSyn9311C4, Synechococcus vims SRIM2, Synechococcus vims SPM2, Pseudomonas vims Noxifer, Acinetobacter vims AB 1, Acinetobacter vims AB2, Acinetobacter vims AbC62, Acinetobacter vims AbP2, Acinetobacter vims AP22, Acinetobacter vims LZ35, Acinetobacter vims WCHABP1, Acinetobacter vims WCHABP12, Pseudomonas vims Psa374, Pseudomonas vims VCM, Pseudomonas vims CAM, Pseudomonas vims CAb02, Pseudomonas vims JG004, Pseudomonas vims MAGI, Pseudomonas vims PA 10, Pseudomonas vims PAKP1, Pseudomonas vims PAKP2, Pseudomonas vims PAKP4, Pseudomonas vims PaPl, Pseudomonas vims phiMK, Pseudomonas vims Zigelbmcke, Prochlorococcus vims PSSM7, Burkholderia vims BcepFl, Pseudomonas vims 141, Pseudomonas vims Ab28, Pseudomonas vims CEBDP1, Pseudomonas vims DL60, Pseudomonas vims DL68, Pseudomonas vims E215, Pseudomonas vims E217, Pseudomonas vims F8, Pseudomonas vims JG024, Pseudomonas vims KPP12, Pseudomonas vims KTN6, Pseudomonas vims LBL3, Pseudomonas vims LMA2, Pseudomonas vims NEI4, Pseudomonas vims PA5, Pseudomonas vims PB1, Pseudomonas vims PS44, Pseudomonas vims SN, Pectinobacterium vims PEAT2, Edwardsiella vims pEtSU, Bordetella vims PHB04, Escherichia phage ESC013, Escherichia vims ESC05, Escherichia vims phAPEC8, Escherichia vims Schickermooser, Klebsiella vims ZCKP1, Pseudomonas vims PA7, Pseudomonas vims phiKZ, Pseudomonas vims SL2, Pseudomonas vims PMW, Agrobacterium vims Atuph07, Synechococcus vims Synl9, Aeromonas vims 56, Aeromonas vims 43, Escherichia vims PI, Escherichia vims RCS47, Salmonella vims SJ46, Pseudoalteromonas vims J2-1, Arthrobacter vims ArVl, Arthrobacter vims Colucci, Arthrobacter virus Trina, Ralstonia virus RP12, Erwinia virus Risingsun, Salmonella virus BP63, Acinetobacter vims Aci05, Acinetobacter vims AciOl-1, Acinetobacter vims Aci02-2, Prochlorococcus vims PSSM2, Dickeya vims JA11, Dickeya vims JA29, Erwinia vims Y3, Agrobacterium vims 7-7-1, Salmonella vims SPN3US, Bacillus vims Shbhl, Bacillus vims 1, Geobacillus vims GBSV1, Pseudomonas vims tabemarius, Synechococcus vims ST4, Faecalibacterium vims Taranis,

Synechococcus vims SIOM18, Yersinia vims R1RT, Yersinia vims TGI, Synechococcus vims STIVI4. Synechococcus vims SSM1, Bacillus vims SP15, Vibrio vims pTDl, Vibrio vims VP4B, Tetrasphaera vims TJE1, Faecalibacterium vims Toutatis, Aeromonas vims 25, Aeromonas vims Aesl2, Aeromonas vims Aes508, Aeromonas vims AS4, Aeromonas vims Asgz, Stenotrophomonas vims IME13, Prochlorococcus vims Synl, Synechococcus vims SRIM44, Vibrio vims MAR, Vibrio vims VHML, Vibrio vims VP585, Escherichia vims ECML4, Salmonella vims Marshall, Salmonella vims Maynard, Salmonella vims SJ2, Salmonella vims STML131, Salmonella vims Vil, Erwinia vims Wellington, Escherichia vims ECML-117, Escherichia vims FECI 9, Escherichia vims WFC, Escherichia vims WFFI, Serratia vims CF1I14, Edwardsiella vims MSW3, Edwardsiella vims PEi21, Erwinia vims Yoloswag, Bacillus vims G, Bacillus vims PBS1, Microcystis vims Ma-LMMOl, Streptococcus vims Cpl, Streptococcus vims Cp7, Lactococcus vims WP2, Bacillus vims B103, Bacillus vims GA1, Bacillus vims phi29, Kurthia vims 6, Actinomyces vims Avl, Mycoplasma vims PI, Staphylococcus vims Andhra, Staphylococcus vims Stl 34, Staphylococcus vims 66, Staphylococcus vims 44AHJD, Staphylococcus vims BP39, Staphylococcus vims CSA13, Staphylococcus vims GRCS, Staphylococcus vims Pabna, Staphylococcus vims phiAG013, Staphylococcus vims PSa3, Staphylococcus vims S24-1, Staphylococcus vims SAP2, Staphylococcus vims SCF11, Staphylococcus vims SLPW, Shigella vims 7502Stx, Shigella vims POCJ13, Escherichia vims 191, Escherichia vims PA2, Escherichia vims TL2011, Shigella vims VASD, Escherichia vims 24B, Escherichia vims 933W, Escherichia vims Min27, Escherichia vims PA28, Escherichia vims Stx2 II, Dinoroseobacter vims DFL12, Pseudomonas vims Bjom, Pseudomonas vims Ab22, Pseudomonas vims CHU, Pseudomonas vims LUZ24, Pseudomonas vims PAA2, Pseudomonas vims PaP3, Pseudomonas vims PaP4, Pseudomonas vims TL, Vibrio vims VC8, Vibrio vims VP2, Vibrio vims VP5, Escherichia vims N4, Flavobacterium vims Fpvl, Flavobacterium vims Fpv4, Streptococcus vims Cl, Escherichia vims APEC5, Escherichia vims APEC7, Escherichia vims Bp4, Escherichia vims ECIUPM, Escherichia vims ECBP1, Escherichia vims G7C, Escherichia vims IME11, Shigella vims Sbl, Escherichia vims C1302, Pseudomonas vims FI 16, Pseudomonas vims H66, Escherichia vims Pollock, Salmonella vims FSL SP-058, Salmonella vims FSL SP-076, Arthrobacter vims Adat, Arthrobacter vims Jasmine, Erwinia vims Ea9-2, Erwinia vims Frozen, Achromobacter vims Axp3, Achromobacter vims JWAlpha, Edwardsiella vims KF1, Burkholderia vims KL4, Pseudomonas vims KPP25, Pseudomonas vims R18, Pseudomonas vims tf, Escherichia vims 172- 1, Escherichia virus ECB2, Escherichia virus NJ01, Escherichia virus phiEco32, Escherichia virus Septimal 1, Escherichia virus SU10, Escherichia virus HK620, Salmonella virus BTP1, Salmonella vims P22, Salmonella vims SElSpa, Salmonella vims ST64T, Shigella vims Sf6, Burkholderia vims Bcep22, Burkholderia vims Bcepil02, Burkholderia vims Bcepmigl, Burkholderia vims DC1, Cellulophaga vims Cba41, Cellulophaga vims Cbal72, Pseudomonas vims Ab09, Pseudomonas vims LIT1, Pseudomonas vims PA26, Pseudomonas vims KPP21, Pseudomonas vims LUZ7, Vibrio vims 48B1, Vibrio vims 51A6, Vibrio vims 51A7, Vibrio vims 52B1, Myxococcus vims Mx8, Bacillus vims Page, Bacillus vims Palmer, Bacillus vims Pascal, Bacillus vims Pony, Bacillus vims Pookie, Brucella vims Pr, Brucella vims Tb, Bordetella vims BPP1, Burkholderia vims BcepC6B, Helicobacter vims 1961P, Helicobacter vims KΉR30, Helicobacter vims KΉR40, Pseudomonas vims phCDa, Escherichia vims Skarpretter, Escherichia vims Sortsne, Klebsiella vims IME279, Escherichia vims phiVIO, Salmonella vims Epsilonl5, Salmonella vims SPN1S, Pseudomonas vims NV1, Pseudomonas vims UFVP2, Escherichia vims PTXU04, Hamiltonella vims APSE1, Lactococcus vims KSY1, Phormidium vims WMP3, Phormidium vims WMP4, Pseudomonas vims 119X, Roseobacter vims SIOl, Vibrio vims VpV262, Streptomyces vims ELB20, Streptomyces vims R4, Streptomyces vims Amela, Streptomyces vims phiCAM, Streptomyces vims Aaronocolus, Streptomyces vims Calibum, Streptomyces vims Danzina, Streptomyces vims Hydra, Streptomyces vims Izzy, Streptomyces vims Lannister, Streptomyces vims Lika, Streptomyces vims Sujidade, Streptomyces vims Zemlya, Streptomyces vims phiHau3, Mycobacterium vims Acadian, Mycobacterium vims Baee, Mycobacterium vims Reprobate, Mycobacterium vims Adawi, Mycobacterium vims Banel, Mycobacterium vims BrownCNA, Mycobacterium vims Chrisnmich, Mycobacterium vims Cooper, Mycobacterium vims JAMaL, Mycobacterium vims Nigel, Mycobacterium vims Stinger, Mycobacterium vims Vincenzo, Mycobacterium vims Zemanar, Mycobacterium vims Apizium, Mycobacterium vims Manad, Mycobacterium vims Oline, Mycobacterium vims Osmaximus, Mycobacterium vims Pgl, Mycobacterium vims Soto, Mycobacterium vims Suffolk, Mycobacterium vims Athena, Mycobacterium vims Bernardo, Mycobacterium vims Gadjet, Mycobacterium vims Pipefish, Mycobacterium vims Godines, Mycobacterium vims Rosebush, Mycobacterium vims TA17a, Mycobacterium vims Babsiella, Mycobacterium vims Bmjita, Mycobacterium vims Hawkeye, Mycobacterium vims Plot, Caulobacter vims CcrBL9, Caulobacter vims CcrSC, Caulobacter vims CcrColossus, Caulobacter vims CcrPW, Caulobacter vims CcrBLIO, Caulobacter vims CcrRogue, Caulobacter vims phiCbK, Caulobacter vims Swift, Salmonella vims SP31, Salmonella vims AG11, Salmonella vims Entl, Salmonella vims fl8SE, Salmonella vims Jersey, Salmonella vims L13, Salmonella vims LSPA1, Salmonella vims SE2, Salmonella vims SETP3, Salmonella vims SETP7, Salmonella vims SETP13, Salmonella vims SP101, Salmonella vims SS3e, Salmonella vims wksl3, Escherichia vims K1G, Escherichia vims K1H, Escherichia virus Klindl, Escherichia virus Klind2, Esherichia virus Golestan, Raoultella virus RP180, Gordonia virus Asapag, Gordonia virus BENtherdunthat, Gordonia virus Getalong, Gordonia virus Kenna, Gordonia virus Horns, Gordonia virus Phistory, Leuconostoc virus Lmdl, Leuconostoc virus LN03, Leuconostoc virus LN04, Leuconostoc virus LN12, Leuconostoc virus LN6B, Leuconostoc virus P793, Leuconostoc virus 1A4, Leuconostoc virus Ln8, Leuconostoc virus Ln9, Leuconostoc virus LN25, Leuconostoc virus LN34, Leuconostoc virus LNTR3, Mycobacterium virus Bongo, Mycobacterium vims Rey, Mycobacterium vims Butters, Mycobacterium vims Michelle, Mycobacterium vims Charlie, Mycobacterium vims Pipsqueaks, Mycobacterium vims Xeno, Mycobacterium vims Panchino, Mycobacterium vims Phrann, Mycobacterium vims Redi, Mycobacterium vims Skinnyp, Gordonia vims BaxterFox, Gordonia vims Yeezy, Gordonia vims Kita, Gordonia vims Nymphadora, Gordonia vims Zirinka, Mycobacterium vims Bignuz, Mycobacterium vims Brusacoram, Mycobacterium vims Donovan, Mycobacterium vims Fishbume, Mycobacterium vims Jebeks, Mycobacterium vims Malithi, Mycobacterium vims Phayonce, Lactobacillus vims B2, Lactobacillus vims Lenus, Lactobacillus vims Nyseid, Lactobacillus vims SAC12, Lactobacillus vims Ldll, Lactobacillus vims ViSo2018a, Lactobacillus vims Maenad, Lactobacillus vims PI, Lactobacillus vims Satyr, Streptomyces vims AbbeyMikolon, Pseudomonas vims Abl8, Pseudomonas vims Abl9, Pseudomonas vims PaMxl 1, Burkholderia vims AH2, Arthrobacter vims Amigo, Arthrobacteria vims Molivia, Propionibacterium vims Anatole, Propionibacterium vims B3, Arthrobacter vims Andrew, Bacillus vims Andromeda, Bacillus vims Blastoid, Bacillus vims Curly, Bacillus vims Eoghan, Bacillus vims Finn, Bacillus vims Glittering, Bacillus vims Riggi, Bacillus vims Taylor, Microbacterium vims Appa, Gordonia vims Apricot, Microbacterium vims Armstrong, Gordonia vims Attis, Streptomyces vims Attoomi, Streptomyces vims Austintatious, Streptomyces vims Ididsumtinwong, Streptomyces vims PapayaSalad, Gordonia vims Bantam, Mycobacterium vims Barnyard, Mycobacterium vims Konstantine, Mycobacterium vims Predator, Pseudomonas vims B3, Pseudomonas vims JBD67, Pseudomonas vims JD18, Pseudomonas vims PM105, Mycobacterium vims Bemall3, Gordonia vims BetterKatz, Streptomyces vims Bing, Staphylococcus vims 13, Staphylococcus vims 77, Staphylococcus vims 108PVL, Gordonia vims Bowser, Arthrobacter vims Bridgette, Arthrobacter vims Constance, Arthrobacter vims Eileen, Arthrobacter vims Judy, Arthrobacter vims Peas, Gordonia vims Britbrat, Mycobacterium vims Bron, Mycobacterium vims Faith 1, Mycobacterium vims JoeDirt, Mycobacterium vims Rumpelstiltskin, Streptococcus vims 858, Streptococcus vims 2972, Streptococcus vims ALQ132, Streptococcus vims 01205, Streptococcus vims Sfil 1, Pseudomonas vims D3112, Pseudomonas vims DMS3, Pseudomonas vims FHA0480, Pseudomonas vims LPB1, Pseudomonas vims MP22, Pseudomonas vims MP29, Pseudomonas vims MP38, Pseudomonas vims PA1KOR, Cellulophaga vims ST, Bacillus vims 250, Bacillus vims IEBH, Lactococcus vims bIL67, Lactococcus vims c2, Corynebacterium virus C3PO, Corynebacterium virus Darwin, Corynebactenum virus Zion, Lactobacillus virus c5, Lactobacillus virus Ld3, Lactobacillus virus Ldl7, Lactobacillus virus Ld25A, Lactobacillus virus LLKu, Lactobacillus virus phiLdb, Mycobacterium virus Che9c, Mycobacterium virus Sbash, Mycobacterium virus Ardmore, Mycobacterium virus Avani, Mycobacterium virus Boomer, Mycobacterium virus Che8, Mycobacterium vims Che9d, Mycobacterium vims DeadP, Mycobacterium vims Diane, Mycobacterium vims Dorothy, Mycobacterium vims DotProduct, Mycobacterium vims Drago, Mycobacterium vims Fmitloop, Mycobacterium vims GUmbie, Mycobacterium vims Ibhubesi, Mycobacterium vims Llij, Mycobacterium vims Mozy, Mycobacterium vims Mutaformal3, Mycobacterium vims Pacc40, Mycobacterium vims PMC, Mycobacterium vims Ramsey,

Mycobacterium vims RockyHorror, Mycobacterium vims SG4, Mycobacterium vims Shaunal, Mycobacterium vims Shilan, Mycobacterium vims Spartacus, Mycobacterium vims Taj, Mycobacterium vims Tweety, Mycobacterium vims Wee, Mycobacterium vims Yoshi, Salmonella vims Chi, Salmonella vims FSLSP030, Salmonella vims FSLSP088, Salmonella vims iEPS5, Salmonella vims SPN19, Corynebacterium vims PI 201, Clavibacter vims CMP1, Clavibacter vims CN1A, Lactobacillus vims ATCC8014, Lactobacillus vims phiJLl, Pediococcus vims cIPl, Arthrobacter vims Coral, Arthrobacter vims Kepler, Mycobacterium vims Comdog, Mycobacterium vims Firecracker, Rhodobacter vims RcCronus, Gordonia vims DareDevil, Arthrobacter vims Decurro, Stenotrophomonas vims DLP5, Gordonia vims Demosthenes, Gordonia vims Katyusha, Gordonia vims Kvothe, Pseudomonas vims D3, Pseudomonas vims PMG1, Escherichia vims EK99P1, Escherichia vims HK578, Escherichia vims JL1, Escherichia vims SSL2009a, Escherichia vims YD2008s, Shigella vims EP23, Sodalis vims SOI, Microbacterium vims Dismas, Propionibacterium vims B22, Propionibacterium vims Doucette, Propionibacterium vims E6, Propionibacterium vims G4, Microbacterium vims Eden, Enterococcus vims AL2, Enterococcus vims AL3, Enterococcus vims AUEF3, Enterococcus vims EcZZ2, Enterococcus vims EF3, Enterococcus vims EF4, Enterococcus vims EfaCPTl, Enterococcus vims IME196, Enterococcus vims LY0322, Enterococcus vims phiSHEF2, Enterococcus vims phiSHEF4, Enterococcus vims phiSHEF5, Enterococcus vims PMBT2, Enterococcus vims SANTOR1, Edwardsiella vims eiAU, Xanthomonas vims PhiL7, Microbactenum vims Eleri, Gordonia vims Cozz, Gordonia vims Emalyn, Gordonia vims GTE2, Gordonia vims Troje, Gordonia vims Eyre, Gordonia vims Fairfaxidumvirus, Microbacterium vims ISF9, Erwinia vims Eho49, Erwiniavims Eho59, Staphylococcus vims 2638A, Staphylococcus vims QT1, Colwellia vims 9A, Mycobacterium vims Alma, Mycobacterium vims Arturo, Mycobacterium vims Astro, Mycobacterium vims Backyardigan, Mycobacterium vims Benedict, Mycobacterium vims Bethlehem, Mycobacterium vims Billknuckles, Mycobacterium vims BPBiebs31, Mycobacterium vims Bmns, Mycobacterium vims Bxbl, Mycobacterium vims Bxz2, Mycobacterium vims Che 12, Mycobacterium vims Cuco, Mycobacterium vims D29, Mycobacterium vims Doom, Mycobacterium virus Encb, Mycobacterium virus Euphoria, Mycobacterium vims George, Mycobacterium vims Gladiator, Mycobacterium vims Goose, Mycobacterium vims Hammer, Mycobacterium vims Heldan, Mycobacterium vims Jasper, Mycobacterium vims JC27, Mycobacterium vims Jeffabunny, Mycobacterium vims JHC117, Mycobacterium vims KBG, Mycobacterium vims Kssjeb, Mycobacterium vims Kugel, Mycobacterium vims L5, Mycobacterium vims Lesedi, Mycobacterium vims LHTSCC, Mycobacterium vims lockley, Mycobacterium vims Marcell, Mycobacterium vims Microwolf, Mycobacterium vims Mrgordo, Mycobacterium vims Museum, Mycobacterium vims Nepal, Mycobacterium vims Packman, Mycobacterium vims Peaches, Mycobacterium vims Perseus, Mycobacterium vims Pukovnik, Mycobacterium vims Rebeuca, Mycobacterium vims Redrock, Mycobacterium vims Ridgecb, Mycobacterium vims Rockstar, Mycobacterium vims Saintus, Mycobacterium vims Skipole, Mycobacterium vims Solon,

Mycobacterium vims Switzer, Mycobacterium vims SWU1, Mycobacterium vims Tiger, Mycobacterium vims Timshel, Mycobacterium vims Trixie, Mycobacterium vims Turbido, Mycobacterium vims Twister, Mycobacterium vims U2, Mycobacterium vims Violet, Mycobacterium vims Wonder, Mycobacterium vims Gaia, Arthrobacter vims Abidatro, Arthrobacter vims Galaxy, Gordonia vims GAL1, Gordonia vims GMA3, Gordonia vims Gsputl, Gordonia vims GMA7, Gordonia vims GTE7, Gordonia vims Ghobes, Mycobacterium vims Giles, Microbacterium vims OneinaGillian, Gordonia vims GodonK, Microbacterium vims Goodman, Arthrobacter vims Captnmurica, Arthrobacter vims Gordon, Gordonia vims GordTnk2, Proteus vims Isfahan, Gordonia vims Jumbo, Gordonia vims Gustav, Gordonia vims Mahdia, Paenibacillus vims Harrison, Gordonia vims Hedwig, Cellulophaga vims Cbal21, Cellulophaga vims Cbal71, Cellulophaga vims Cbal81, Escherichia vims HK022, Escherichia vims HK75,

Escherichia vims HK97, Escherichia vims HK106, Escherichia vims HK446, Escherichia vims HK542, Escherichia vims HK544, Escherichia vims HK633, Escherichia vims mEp234, Escherichia vims mEpXl, Escherichia vims mEpX2, Streptomyces vims Hiyaa, Salinibacter vims M1EM1, Salinibacter vims M8CR30-2, Listeria vims LP26, Listeria vims LP37, Listeria vims LP110, Listeria vims LP114, Listeria vims P70, Corynebacterium vims phi673, Corynebacterium vims phi674, Microbacterium vims Hamlet, Microbacterium vims Ilzat, Polanbacter vims P12002L, Polaribacter vims P12002S, Nonlabens vims P12024L, Nonlabens vims P12024S, Gordonia vims Jace, Brevibacillus vims Jenst, Corynebacterium vims Juicebox, Salinibacter vims M31CR41-2, Salinibacter vims SRUTV1, Arthrobacter vims Kellezzio, Arthrobacter vims Kitkat, Burkholderia vims KL1, Xanthomonas vims CPI, Microbacterium vims Golden, Microbacterium vims Koji, Arthrobacter vims Bennie, Arthrobacter vims DrRobert, Arthrobacter vims Glenn, Arthrobacter vims HunterDalle, Arthrobacter vims Joann, Arthrobacter vims Korra, Arthrobacter vims Preamble, Arthrobacter vims Pumancara, Arthrobacter vims Wayne, Mycobacterium vims 244, Mycobacterium vims Bask21, Mycobacterium vims CJW1, Mycobacterium virus Eureka, Mycobacterium vims Kostya, Mycobacterium vims Porky, Mycobacterium vims Pumpkin, Mycobacterium vims Sirduracell, Mycobacterium vims Toto, Microbacterium vims Krampus, Salinibacter vims M8CC19, Salinibacter vims M8CRM1, Sphingobium vims Lacusarx, Escherichia vims DE3, Escherichia vims HK629, Escherichia vims HK630, Escherichia vims Lambda, Pseudomonas vims Lana, Arthrobacter vims Laroye, Eggerthella vims PMBT5, Arthobacter vims Liebe, Mycobacterium vims Halo, Mycobacterium vims Liefie, Acinetobacter vims IMEAB3, Acinetobacter vims Loki, Streptomyces vims phiBTl, Streptomyces vims phiC31, Brevibacterium vims LuckyBames, Gordonia vims Lucky 10, Faecalibacterium vims Lugh, Bacillus vims BMBtp2, Bacillus vims TP21, Bacillus vims Mgbhl, Arthrobacter vims Maja, Arthrobacter vims DrManhattan, Mycobacterium vims Ff47, Mycobacterium vims Muddy, Vibrio vims MARIO, Vibrio vims SSP002, Mycobacterium vims Marvin, Mycobacterium vims Mosmoris, Pseudomonas vims PMBT3, Microbacterium vims MementoMori, Microbacterium vims Fireman, Microbacterium vims Metamorphoo, Microbacterium vims RobsFeet, Microbacterium vims Mini, Streptococcus vims 7201, Streptococcus vims DTI, Streptococcus vims phiAbc2, Streptococcus vims Sfil9, Streptococcus vims Sfi21, Gordinia vims Birksandsocks, Gordonia vims Flakey, Gordonia vims Monty, Gordonia vims Stevefrench, Arthrobacter vims Circum, Arthrobacter vims Mudcat, Escherichia vims EC2, Salmonella vims Lumpael, Dinoroseobacter vims D5C, Burkholderia vims BcepNazgul, Microbacterium vims Neferthena, Pseudomonas vims nickie, Pseudomonas vims NP1, Pseudomonas vims PaMx25, Escherichia vims 9g, Escherichia vims JenKl, Escherichia vims JenPl, Escherichia vims JenP2, Salmonella vims SElKor, Salmonella vims 9NA, Salmonella vims SP069, Gordonia vims Nyceirae, Faecalibacterium vims Oengus, Mycobacterium vims Baka, Mycobacterium vims Courthouse, Mycobacterium vims Littlee, Mycobacterium vims Omega, Mycobacterium vims Optimus, Mycobacterium vims Thibault, Gordonia vims BmtonGaster, Gordonia vims OneUp, Gordonia vims Orchid, Thermus vims P23-45, Thermus vims P74-26, Propionibacterium vims ATCC29399BC, Propionibacterium vims ATCC29399BT, Propionibacterium vims Attacne, Propionibacterium vims Keiki, Propionibacterium vims Kubed, Propionibacterium vims Lauchelly, Propionibacterium vims MrAK, Propionibacterium vims Ouroboros, Propionibacterium vims P91, Propionibacterium vims PI 05, Propionibacterium vims PI 44, Propionibacterium vims PI 001, Propionibacterium vims Pl.l, Propionibacterium vims P100A, Propionibacterium vims P100D, Propionibacterium vims P101A, Propionibacterium vims P104A, Propionibacterium vims PA6, Propionibacterium vims Pacnes201215, Propionibacterium vims PAD 20, Propionibacterium vims PAS50, Propionibacterium vims PHL009M11, Propionibacterium vims PHL025M00, Propionibacterium vims PHL037M02, Propionibacterium vims PHL041M10, Propionibacterium vims PHL060L00, Propionibacterium vims PHL067M01, Propionibacterium vims PHL070N00, Propionibacterium vims PHL071N05, Propionibacterium vims PHL082M03, Propionibacterium virus PHL092M00, Propionibacterium virus PHL095N00, Propionibacterium virus PHL111M01, Propionibacterium virus PHL112N00, Propionibacterium virus PHL113M01, Propionibacterium virus PHL114L00, Propionibacterium virus PHL116M00, Propionibacterium virus PHL117M00, Propionibacterium virus PHL117M01, Propionibacterium virus PHL132N00, Propionibacterium virus PHL141N00, Propionibacterium vims PHL151M00, Propionibacterium vims PHL151N00, Propionibacterium vims PHL152M00, Propionibacterium vims PHL163M00, Propionibacterium vims PHL171M01, Propionibacterium vims PHL179M00, Propionibacterium vims PHL194M00, Propionibacterium vims PHL199M00, Propionibacterium vims PHL301M00, Propionibacterium vims PHL308M00, Propionibacterium vims Pirate, Propionibacterium vims Procrassl, Propionibacterium vims SKKY, Propionibacterium vims Solid, Propionibacterium vims Stormbom, Propionibacterium vims Wizzo, Pseudomonas vims PaMx28, Pseudomonas vims PaMx74, Mycobacterium vims Papyms, Mycobacterium vims Send513, Mycobacterium vims Patience, Mycobacterium vims PBI1, Rhodococcus vims Pepy6, Rhodococcus vims Poco6, Staphylococcus vims 11, Staphylococcus vims 29, Staphylococcus vims 37, Staphylococcus vims 53, Staphylococcus vims 55, Staphylococcus vims 69, Staphylococcus vims 71, Staphylococcus vims 80, Staphylococcus vims 85, Staphylococcus vims 88, Staphylococcus vims 92, Staphylococcus vims 96, Staphylococcus vims 187, Staphylococcus vims 52a, Staphylococcus vims 80alpha, Staphylococcus vims CNPH82, Staphylococcus vims EW, Staphylococcus vims IPLA5, Staphylococcus vims IPLA7, Staphylococcus vims IPLA88, Staphylococcus vims PHI 5, Staphylococcus vims phiETA, Staphylococcus vims phiETA2, Staphylococcus vims phiETA3, Staphylococcus vims phiMRl 1, Staphylococcus vims phiMR25, Staphylococcus vims phiNMl, Staphylococcus vims phiNM2, Staphylococcus vims phiNM4, Staphylococcus vims SAP26, Staphylococcus vims X2, Enterococcus vims FL1, Enterococcus vims FL2, Enterococcus vims FL3, Streptomyces vims Picard, Microbacterium vims Pikmin, Corynebacterium vims Poushou, Providencia vims PR1, Listeria vims LP302, Listeria vims PSA, Psimunavims psiM2, Propionibacterium vims PFR1, Microbacterium phage KaiHaiDragon, Microbacterium phage Paschalis, Microbacterium phage Quhwah, Streptomyces vims Darolandstone, Streptomyces vims Raleigh, Escherichia vims N15, Rhodococcus vims RER2, Rhizobium vims P106B, Strepomyces vims Drgrey, Strepomyces vims Rima, Microbacterium vims Hendrix, Gordonia vims Fryberger, Gordoma vims Ronaldo, Aeromonas vims pIS4A, Streptomyces vims Rowa, Gordonia vims Ruthy, Streptomyces vims Jay2Jay, Streptomyces vims Mildred21, Streptomyces vims NootNoot, Streptomyces vims Paradiddles, Streptomyces vims Peebs, Streptomyces vims Samistil2, Pseudomonas vims SMI, Corynebacterium vims SamW, Xylella vims Salvo, Xylella vims Sano, Caulobacter vims Sansa, Enterococcus vims BC611, Enterococcus vims IMEEF1, Enterococcus vims SAP6, Enterococcus vims VD13, Streptococcus vims SPQS1, Salmonella vims Sasha, Corynebacterium vims BFK20, Geobacillus vims Tp84, Streptomyces virus Scapl, Gordonia virus Schnabeltier, Microbacterium vims Schubert, Pseudomonas vims 73, Pseudomonas vims Ab26, Pseudomonas vims Kakheti25, Escherichia vims Cajan, Escherichia vims Seurat, Caulobacter vims Seuss, Staphylococcus vims SEP9, Staphylococcus vims Sextaec, Paenibacillus vims Diva, Paenibacillus vims Hbl0c2, Paenibacillus vims Rani, Paenibacillus vims Shelly, Paenibacillus vims Sitara, Paenibacillus vims Willow, Lactococcus vims 712, Lactococcus vims ASCC191, Lactococcus vims ASCC273, Lactococcus vims ASCC281, Lactococcus vims ASCC465, Lactococcus vims ASCC532, Lactococcus vims Bibb29, Lactococcus vims bIL170, Lactococcus vims CB13, Lactococcus vims CB14, Lactococcus vims CB19, Lactococcus vims CB20, Lactococcus vims jj 50, Lactococcus vims P2, Lactococcus vims P008, Lactococcus vims ski, Lactococcus vims S14, Bacillus vims Slash, Bacillus vims Stahl, Bacillus vims Staley, Bacillus vims Stills, Gordonia vims Bachita, Gordonia vims ClubL, Gordonia vims Smoothie, Arthobacter vims Sonali, Gordonia vims Soups, Gordonia vims Strosahl, Gordonia vims Wait, Gordonia vims Sour, Bacillus vims SPbeta, Microbacterium vims Elyperion, Microbacterium vims Squash, Burkholderia vims phi6442, Burkholderia vims phil026b, Burkholderia vims phiE125, Achromobacter vims 83-24, Achromobacter vims JWX, Arthrobacter vims Tank, Gordonia vims Suzy, Gordonia vims Terapin, Streptomyces vims TGI, Mycobacterium vims Anaya, Mycobacterium vims Angelica, Mycobacterium vims CrimD, Mycobacterium vims Fionnbharth, Mycobacterium vims JAWS, Mycobacterium vims Larva, Mycobacterium vims MacnCheese, Mycobacterium vims Pixie, Mycobacterium vims TM4, Tsukamurella vims ΉN2, Tsukamurella vims TIN3, Tsukamurella vims TIN4, Rhodobacter vims RcSpartan, Rhodobacter vims RcTitan, Mycobacterium vims Tortellini, Staphylococcus vims 47, Staphylococcus vims 3 a, Staphylococcus vims 42e, Staphylococcus vims IPLA35, Staphylococcus vims phi 12, Staphylococcus vims phiSLT, Mycobacterium vims 32HC, Rhodococcus vims Trina, Gordonia vims Trine, Paenibacillus vims Tripp, Flavobacterium vims 1H, Flavobacterium vims 23T, Flavobacterium vims 2A, Flavobacterium vims 6H, Streptomyces vims Lilbooboo, Streptomyces vims Vash, Paenibacillus vims Vegas, Gordonia vims Vendetta, Paracoccus vims Shpa, Pantoea vims Vid5, Acinetobacter vims B1251, Acinetobacter vims R3177, Gordonia vims Brandonkl23, Gordonia vims Lennon, Gordonia vims Vivi2, Bordetella vims CN1, Bordetella vims CN2, Bordetella vims FP1, Bordetella vims MW2, Bacillus vims Wbeta, Rhodococcus vims Weasel, Mycobacterium vims Wildcat, Gordonia vims Billnye, Gordonia vims Twister6, Gordonia vims Wizard, Gordonia vims Hotorobo, Gordonia vims Woes, Streptomyces vims TP1604, Streptomyces vims YDN12, Roseobacter vims RDJLl, Roseobacter vims RDJL2, Xanthomonas vims OP1, Xanthomonas vims Xop411, Xanthomonas vims XplO, Arthobacter vims Yang, Alphaproteobacteria vims phiJIOOl, Pseudomonas vims LK04, Pseudomonas vims M6, Pseudomonas vims MP1412, Pseudomonas vims PAE1, Pseudomonas vims Yua, Gordonia vims Yvonnetastic, Microbacterium vims Zetal847, Rhodococcus vims RGL3, Paenibacillus virus Lily, Vibrio virus CTXphi, Propionibacterium virus B5, Vibrio virus KSF1, Xanthomonas virus Cflc, Vibrio virus fsl, Vibrio virus VGJ, Ralstonia virus RS551, Ralstonia virus RS603, Ralstonia virus RSM1, Ralstonia virus RSM3, Escherichia virus Ifl, Escherichia virus M13, Escherichia virus 122, Salmonella virus IKe, Ralstonia vims PE226, Pseudomonas vims Pfl, Stenotrophomonas vims PSH1, Ralstonia vims RSS1, Vibrio vims fs2, Vibrio vims VFJ, Stenotrophomonas vims SMA6, Stenotrophomonas vims SMA9, Stenotrophomonas vims SMA7, Pseudomonas vims Pf3, Thermus vims OH3, Vibrio vims VfO3K6, Vibrio vims VCY, Vibrio vims VB3, Xanthomonas vims Xfl09, Acholeplasma vims L51, Spiroplasma vims SVTS2, Spiroplasma vims C74, Spiroplasma vims R8A2B, Spiroplasma vims SkVlCR23x, Escherichia vims alpha3, Escherichia vims ID21, Escherichia vims ID32, Escherichia vims ID62, Escherichia vims NC28, Escherichia vims NC29, Escherichia vims NC35, Escherichia vims phiK, Escherichia vims Stl, Escherichia vims WA45, Escherichia vims G4, Escherichia vims ID52, Escherichia vims Talmos, Escherichia vims phiX174, Bdellovibrio vims MAC1, Bdellovibrio vims MFI2K, Chlamydia vims Chpl, Chlamydia vims Chp2, Chlamydia vims CPAR39, Chlamydia vims CPG1, Spiroplasma vims SpV4, Bombyxmori bidensovims, Acerodon celebensis polyomavims 1, Artibeus planirostris polyomavims 2, Artibeus planirostris polyomavims 3, Ateles paniscus polyomavims 1, Cardioderma cor polyomavims 1, Carollia perspicillata polyomavims 1, Chlorocebus pygerythms polyomavims 1, Chlorocebus pygerythms polyomavims 3, Dobsonia moluccensis polyomavims 1, Eidolon helvum polyomavims 1, Gorilla gorilla polyomavims 1, Human polyomavims 5, Human polyomavims 8, Human polyomavims 9, Human polyomavims 13, Human polyomavims 14, Macaca fascicularis polyomavims 1, Mesocricetus auratus polyomavims 1, Minioptems schreibersii polyomavims 1, Minioptems schreibersii polyomavims 2, Molossus molossus polyomavims 1, Mus musculus polyomavims 1, Otomops martiensseni polyomavims 1, Otomops martiensseni polyomavims 2, Pan troglodytes polyomavims 1, Pan troglodytes polyomavims 2, Pan troglodytes polyomavims 3, Pan troglodytes polyomavims 4, Pan troglodytes polyomavims 5, Pan troglodytes polyomavims 6, Pan troglodytes polyomavims 7, Papio cynocephalus polyomavims 1, Piliocolobus badius polyomavims 1, Piliocolobus rufomitratus polyomavims 1, Pongo abelii polyomavims 1, Pongo pygmaeus polyomavims 1, Procyon lotor polyomavims 1, Pteropus vampyrus polyomavims 1, Rattus norvegicus polyomavims 1, Sorex araneus polyomavims 1, Sorex coronatus polyomavims 1, Sorex minutus polyomavims 1, Stumira lilium polyomavims 1, Tupaia belangeri polyomavims 1, Acerodon celebensis polyomavims 2, Artibeus planirostris polyomavims 1, Canis familiaris polyomavims 1, Cebus albifrons polyomavims 1, Cercopithecus erythrotis polyomavims 1, Chlorocebus pygerythms polyomavims 2, Desmodus rotundus polyomavims 1, Dobsonia moluccensis polyomavims 2, Dobsonia moluccensis polyomavims 3, Enhydra lutris polyomavims 1, Equus caballus polyomavims 1, Human polyomavims 1, Human polyomavims 2, Human polyomavims 3, Human polyomavirus 4, Leptonychotes weddellii polyomavirus 1, Loxodonta africana polyomaviras 1, Macaca mulatta polyomavirus 1, Mastomys natalensis polyomavirus 1, Meles meles polyomavirus 1, Microtus arvalis polyomaviras 1, Miniopteras africanus polyomaviras 1, Mus musculus polyomaviras 2, Mus musculus polyomaviras 3, Myodes glareolus polyomaviras 1, Myotis lucif igus polyomaviras 1, Pan troglodytes polyomaviras 8, Papio cynocephalus polyomaviras 2, Pteronotus davyi polyomaviras 1, Pteronotus pamellii polyomaviras 1, Rattus norvegicus polyomaviras 2, Rousettus aegyptiacus polyomaviras 1, Saimiri boliviensis polyomaviras 1, Saimiri sciureus polyomaviras 1, Vicugna pacos polyomaviras 1, Zalophus califomianus polyomaviras 1, Human polyomaviras 6, Human polyomaviras 7, Human polyomaviras 10, Human polyomaviras 11, Anser anser polyomaviras 1, Aves polyomaviras 1, Corvus monedula polyomaviras 1, Cracticus torquatus polyomaviras 1, Erythrara gouldiae polyomaviras 1, Lonchura maj a polyomaviras 1, Pygoscelis adeliae polyomaviras 1, Pyrrhula pyrrhula polyomaviras 1, Serinus canaria polyomaviras 1, Ailuropoda melanoleuca polyomaviras 1, Bos taurus polyomaviras 1, Centropristis striata polyomaviras 1, Delphinus delphis polyomaviras 1, Procyon lotor polyomaviras 2, Rhynchobatus djiddensis polyomaviras 1, Spams aurata polyomaviras 1, Trematomus bemacchii polyomavirus 1, Trematomus pennellii polyomavirus 1, Alphapapillomavirus 1, Alphapapillomaviras 2, Alphapapillomavirus 3, Alphapapillomaviras 4, Alphapapillomaviras 5, Alphapapillomaviras 6, Alphapapillomaviras 7, Alphapapillomaviras 8, Alphapapillomaviras 9, Alphapapillomaviras 10, Alphapapillomaviras 11, Alphapapillomaviras 12, Alphapapillomaviras 13, Alphapapillomaviras 14, Betapapillomavirus 1, Betapapillomaviras 2, Betapapillomaviras 3, Betapapillomaviras 4, Betapapillomavirus 5, Betapapillomaviras 6, Chipapillomaviras 1, Chipapillomaviras 2, Chipapillomavirus 3, Deltapapillomavirus 1, Deltapapillomavirus 2, Deltapapillomavirus 3, Deltapapillomaviras 4, Deltapapillomavirus 5, Deltapapillomavirus 6, Deltapapillomavirus 7, Dyochipapillomaviras 1, Dyodeltapapillomaviras 1, Dyoepsilonpapillomaviras 1, Dyoetapapillomavirus 1, Dyoiotapapillomaviras 1, Dyoiotapapillomaviras 2, Dyokappapapillomaviras 1, Dyokappapapillomavirus 2, Dyokappapapillomaviras 3, Dyokappapapillomaviras 4, Dyokappapapillomaviras 5, Dyolambdapapillomaviras 1, Dyomupapillomavirus 1, Dyonupapillomavirus 1, Dyoomegapapillomavirus 1, Dyoomikronpapillomaviras 1, Dyophipapillomavirus 1, Dyopipapillomaviras 1, Dyopsipapillomaviras 1, Dyorhopapillomaviras 1, Dyosigmapapillomaviras 1, Dyotaupapillomaviras 1, Dyothetapapillomaviras 1, Dyoupsilonpapillomavirus 1, Dyoxipapillomavirus 1, Dyoxipapillomaviras 2, Dyozetapapillomaviras 1, Epsilonpapillomaviras 1, Epsilonpapillomavirus 2, Etapapillomaviras 1, Gammapapillomavirus 1, Gammapapillomaviras 2, Gammapapillomaviras 3, Gammapapillomavirus 4, Gammapapillomaviras 5, Gammapapillomaviras 6, Gammapapillomaviras 7, Gammapapillomaviras 8, Gammapapillomaviras 9, Gammapapillomaviras 10, Gammapapillomaviras 11, Gammapapillomaviras 12, Gammapapillomaviras 13, Gammapapillomaviras 14, Gammapapillomaviras 15, Gammapapillomavirus 16, Gammapapillomavirus 17, Gammapapillomavirus 18, Gammapapillomavirus 19, Gammapapillomavirus 20, Gammapapillomavirus 21, Gammapapillomavirus 22, Gammapapillomavirus 23, Gammapapillomavirus 24, Gammapapillomavirus 25, Gammapapillomavirus 26, Gammapapillomavirus 27, Iotapapillomavirus 1, Iotapapillomavirus 2, Kappapapillomavirus 1, Kappapapillomavirus 2, Lambdapapillomavirus 1, Lambdapapillomavirus 2, Lambdapapillomavirus 3, Lambdapapillomavirus 4, Lambdapapillomavirus 5, Mupapillomavirus 1, Mupapillomavims 2, Mupapillomavirus 3, Nupapillomavirus 1, Omegapapillomavirus 1, Omikronpapillomavims 1, Phipapillomavims 1, Pipapillomavirus 1, Pipapillomavims 2, Psipapillomavirus 1, Psipapillomavims 2, Psipapillomavirus 3, Rhopapillomavirus 1, Rhopapillomavims 2, Sigmapapillomavirus 1, Taupapillomavims 1, Taupapillomavirus 2, Taupapillomavirus 3, Taupapillomavirus 4, Thetapapillomavirus 1, Treisdeltapapillomavims 1, Treisepsilonpapillomavims 1, Treisetapapillomavirus 1, Treisiotapapillomavims 1, Treiskappapapillomavirus 1, Treisthetapapillomavims 1, Treiszetapapillomavirus 1, Upsilonpapillomavirus 1, Upsilonpapillomavims 2, Upsilonpapillomavims 3, Xipapillomavirus 1, Xipapillomavims 2, Xipapillomavims 3, Xipapillomavims 4, Xipapillomavims 5, Zetapapillomavims 1, Alefpapillomavirus 1, Asteroid aquambidensovims 1, Decapod aquambidensovims 1, Blattodean blattambidensovims 1, Hemipteran hemiambidensovims 1, Hemipteran hemiambidensovirus 2, Lepidopteran iteradensovims 1, Lepidopteran iteradensovims 2, Lepidopteran iteradensovims 3, Lepidopteran iteradensovims 4, Lepidopteran iteradensovims 5, Orthopteran miniambidensovirus 1, Blattodean pefuambidensovirus 1, Dipteran protoambidensovirus 1, Lepidopteran protoambidensovims 1, Hemipteran scindoambidensovims 1, Hymenopteran scindoambidensovims 1, Orthopteran scindoambidensovims 1, Dipteran brevihamaparvovirus 1, Dipteran brevihamaparvovirus 2, Carnivore chaphamaparvovims 1, Chiropteran chaphamaparvovims 1, Galliform chaphamaparvovims 1, Galliform chaphamaparvovims 2, Galliform chaphamaparvovims 3, Rodent chaphamaparvovims 1, Rodent chaphamaparvovims 2, Ungulate chaphamaparvovims 1, Decapod hepanhamaparvovims 1, Syngnathid ichthamaparvovims 1, Decapod penstylhamaparvovirus 1, Carnivore amdoparvovims 1, Carnivore amdoparvovims 2, Carnivore amdoparvovims 3, Carnivore amdoparvovims 4, Carnivore amdoparvovims 5, Chiropteran artiparvovims 1, Galliform aveparvovims 1, Gmiform aveparvovims 1, Carnivore bocaparvovims 1, Carnivore bocaparvovims 2, Carnivore bocaparvovims 3, Carnivore bocaparvovims 4, Carnivore bocaparvovims 5, Carnivore bocaparvovims 6, Chiropteran bocaparvovims 1, Chiropteran bocaparvovims 2, Chiropteran bocaparvovims 3, Chiropteran bocaparvovims 4, Lagomorph bocaparvovims 1, Pinniped bocaparvovims 1, Pinniped bocaparvovims 2, Primate bocaparvovims 1, Primate bocaparvovims 2, Rodent bocaparvovims 1, Rodent bocaparvovims 2, Ungulate bocaparvovims 1, Ungulate bocaparvovims 2, Ungulate bocaparvovims 3, Ungulate bocaparvovims 4, Ungulate bocaparvovims 5, Ungulate bocaparvovirus 6, Ungulate bocaparvovirus 7, Ungulate bocaparvovirus 8, Pinniped copiparvovirus 1, Ungulate copiparvovirus 1, Ungulate copiparvovirus 2, Ungulate copiparvovirus 3, Ungulate copiparvovirus 4, Ungulate copiparvovirus 5, Ungulate copiparvovirus 6, Adeno-associated dependoparvovirus A, Adeno-associated dependoparvovirus B, Anseriform dependoparvovirus 1, Avian dependoparvovirus 1, Chiropteran dependoparvovirus 1, Pinniped dependoparvovirus 1, Rodent dependoparvovirus 1, Rodent dependoparvovirus 2, Squamate dependoparvovirus 1, Squamate dependoparvovirus 2, Pinniped erythroparvovirus 1, Primate erythroparvovirus 1, Primate erythroparvovirus 2, Primate erythroparvovirus 3, Primate erythroparvovirus 4, Rodent erythroparvovirus 1, Ungulate erythroparvovirus 1, Primate loriparvovirus 1, Carnivore protoparvovirus, Carnivore protoparvovirus 1, Chiropteran protoparvovirus 1, Eulipotyphla protoparvovirus 1, Primate protoparvovirus 1, Primate protoparvovirus 2, Primate protoparvovirus 3, Primate protoparvovirus 4, Rodent protoparvovirus 1, Rodent protoparvovirus 2, Rodent protoparvovirus 3, Ungulate protoparvovirus 1, Ungulate protoparvovirus 2, Chiropteran tetraparvovirus 1, Primate tetraparvo vims 1, Ungulate tetraparvovirus 1, Ungulate tetraparvovirus 2, Ungulate tetraparvovirus 3, Ungulate tetraparvovirus 4, Chaetoceros diatodnavims 1, Avon-Heathcote Estuary associated kieseladnavims, Chaetoceros protobacilladnavirus 1, Chaetoceros protobacilladnavirus 2, Chaetoceros protobacilladnavirus 3, Chaetoceros protobacilladnavirus 4, Marine protobacilladnavirus 1, Snail associated protobacilladnavirus 1, Snail associated protobacilladnavirus 2, Barbel circovirus, Bat associated circovirus 1, Bat associated circovirus 2, Bat associated circovirus 3, Bat associated circovirus 4, Bat associated circovirus 5, Bat associated circovirus 6, Bat associated circovirus 7, Bat associated circovirus 8, Bat associated circovirus 9, Bat associated circovirus 10, Bat associated circovirus 11, Bat associated circovirus 12, Beak and feather disease vims, Canary circovims, Canine circovims, Chimpanzee associated circovims 1, Civet circovims, Duck circovims, European catfish circovims, Finch circovims, Goose circovims, Gull circovims, Human associated circovims 1, Mink circovims, Mosquito associated circovims 1, Pigeon circovims, Porcine circovims 1, Porcine circovims 2, Porcine circovims 3, Raven circovims, Rodent associated circovims 1, Rodent associated circovims 2, Rodent associated circovims 3, Rodent associated circovims 4, Rodent associated circovims 5, Rodent associated circovims 6, Rodent associated circovims 7, Starling circovims, Swan circovims, Tick associated circovims 1, Tick associated circovims 2, Zebra finch circovims, Ant associated cyclovims 1, Bat associated cyclovims 1, Bat associated cyclovims 2, Bat associated cyclovims 3, Bat associated cyclovims 4, Bat associated cyclovims 5, Bat associated cyclovims 6, Bat associated cyclovims 7, Bat associated cyclovims 8, Bat associated cyclovims 9, Bat associated cyclovims 10, Bat associated cyclovims 11, Bat associated cyclovims 12, Bat associated cyclovims 13, Bat associated cyclovims 14, Bat associated cyclovims 15, Bat associated cyclovims 16, Bovine associated cyclovims 1, Chicken associated cyclovims 1, Chicken associated cyclovirus 2, Chimpanzee associated cyclovirus 1, Cockroach associated cyclovirus 1, Dragonfly associated cyclovirus 1, Dragonfly associated cyclovirus 2, Dragonfly associated cyclovirus 3, Dragonfly associated cyclovirus 4, Dragonfly associated cyclovirus 5, Dragonfly associated cyclovirus 6, Dragonfly associated cyclovirus 7, Dragonfly associated cyclovirus 8, Duck associated cyclovirus 1, Feline associated cyclovirus 1, Goat associated cyclovirus 1, Horse associated cyclovirus 1, Human associated cyclovirus 1, Human associated cyclovirus 2, Human associated cyclovirus 3, Human associated cyclovirus 4, Human associated cyclovirus 5, Human associated cyclovirus 6, Human associated cyclovirus 7, Human associated cyclovirus 8, Human associated cyclovirus 9, Human associated cyclovirus 10, Human associated cyclovirus 11, Human associated cyclovirus 12, Mouse associated cyclovirus 1, Rodent associated cyclovirus 1, Rodent associated cyclovirus 2, Spider associated cyclovirus 1, Squirrel associated cyclovirus 1, Bovine associated bovismacovirus 1, Bovine associated bovismacovirus 2, Dragonfly associated bovismacovirus 1, Bovine associated cosmacovirus 1, Dragonfly associated dragsmacovirus 1, Bovine associated drosmacovirus 1, Camel associated drosmacovirus 1, Camel associated drosmacovirus2, Bovine associated huchismacovirus 1, Bovine associated huchismacovims 2, Chicken associated huchismacovirus 1, Chicken associated huchismacovirus 2, Human associated huchismacovirus 1, Human associated huchismacovims 2, Human associated huchismacovims 3, Bovine associated porprismacovims 1, Camel associated porprismacovims 1, Camel associated porprismacovims 2, Camel associated porprismacovims 3, Camel associated porprismacovims 4, Chimpanzee associated porprismacovims 1, Chimpanzee associated porprismacovims 2, Gorilla associated porprismacovims 1, Howler monkey associated porprismacovims 1, Human associated porprismacovims 1, Human associated porprismacovims 2, Lemur associated porprismacovims 1, Porcine associated porprismacovims 1, Porcine associated porprismacovims 2, Porcine associated porprismacovims 3, Porcine associated porprismacovims 4, Porcine associated porprismacovims 5, Porcine associated porprismacovims 6, Porcine associated porprismacovims 7, Porcine associated porprismacovims 8, Porcine associated porprismacovims 9, Porcine associated porprismacovims 10, Rat associated porprismacovims 1, Sheep associated porprismacovims 1, Sheep associated porprismacovims 2, Sheep associated porprismacovims 3, Turkey associated porprismacovims 1, Abaca bunchy top vims, Banana bunchy top vims, Cardamom bushy dwarf vims, Black medic leaf roll vims, Faba bean necrotic stunt vims, Faba bean necrotic yellows vims, Faba bean yellow leaf vims, Milk vetch dwarf vims, Pea necrotic yellow dwarf vims, Pea yellow stunt vims, Subterranean clover stunt vims, Coconut foliar decay vims, Brisavims, Yientovims, Beet curly top Iran vims, Exomis microphylla latent vims, Spinach curly top Arizona vims, Abutilon golden mosaic vims, Abutilon mosaic Bolivia vims, Abutilon mosaic Brazil vims, Abutilon mosaic vims, African cassava mosaic Burkina Faso vims, African cassava mosaic vims, Ageratum enation vims, Ageratum leaf curl Sichuan vims, Ageratum leaf curl virus, Ageratum yellow vein Hualian virus, Ageratum yellow vein Sri Lanka virus, Ageratum yellow vein virus, Allamanda leaf curl virus, Allamanda leaf mottle distortion virus, Altemanthera yellow vein virus, Andrographis yellow vein leaf curl virus, Asystasia mosaic Madagascar virus, Bean calico mosaic virus, Bean chlorosis virus, Bean dwarf mosaic virus, Bean golden mosaic virus, Bean golden yellow mosaic virus, Bean leaf crumple virus, Bean white chlorosis mosaic virus, Bean yellow mosaic Mexico virus, Bhendi yellow vein Bhubhaneswar vims, Bhendi yellow vein Haryana vims, Bhendi yellow vein mosaic Delhi vims, Bhendi yellow vein mosaic vims, Bitter gourd yellow mosaic vims, Blainvillea yellow spot vims, Blechum interveinal chlorosis vims, Blechum yellow vein vims, Boerhavia yellow spot vims, Cabbage leaf curl Jamaica vims, Cabbage leaf curl vims, Capraria yellow spot vims, Cassava mosaic Madagascar vims, Catharanthus yellow mosaic vims, Centrosema yellow spot vims, Chayote yellow mosaic vims, Chenopodium leaf curl vims, Chilli leaf curl Ahmedabad vims, Chilli leaf curl Bhavanisagar vims, Chilli leaf curl Gonda vims, Chilli leaf curl India vims, Chilli leaf curl Kanpur vims, Chilli leaf curl Sri Lanka vims, Chilli leaf curl Vellanad vims, Chilli leaf curl vims, Chino del tomate Amazonas vims, Chino del tomate vims, Cleome golden mosaic vims, Cleome leaf cmmple vims, Clerodendron golden mosaic vims, Clerodendron yellow mosaic vims, Clerodendmm golden mosaic China vims, Clerodendmm golden mosaic Jiangsu vims, Cnidoscolus mosaic leaf deformation vims, Coccinia mosaic Tamil Nadu vims, Common bean mottle vims, Common bean severe mosaic vims, Corchoms golden mosaic vims, Corchoms yellow spot vims, Corchorus yellow vein mosaic vims, Corchoms yellow vein vims, Cotton chlorotic spot vims, Cotton leaf cmmple vims, Cotton leaf curl Alabad vims, Cotton leaf curl Bangalore vims, Cotton leaf curl Barasat vims, Cotton leaf curl Gezira vims, Cotton leaf curl Kokhran vims, Cotton leaf curl Multan vims, Cotton yellow mosaic vims, Cowpea bright yellow mosaic vims, Cowpea golden mosaic vims, Crassocephalum yellow vein vims, Croton golden mosaic vims, Croton yellow vein mosaic vims, Cucurbit leaf cmmple vims, Dalechampia chlorotic mosaic vims, Datura leaf curl vims, Datura leaf distortion vims, Deinbollia mosaic vims, Desmodium leaf distortion vims, Desmodium mottle vims, Dicliptera yellow mottle Cuba vims, Dicliptera yellow mottle vims, Dolichos yellow mosaic vims, Duranta leaf curl vims, East African cassava mosaic Cameroon vims, East African cassava mosaic Kenya vims, East African cassava mosaic Malawi vims, East African cassava mosaic vims, East African cassava mosaic Zanzibar vims, Eclipta yellow vein vims, Emilia yellow vein Fujian vims, Emilia yellow vein Thailand vims, Emilia yellow vein vims, Erectites yellow mosaic vims, Eupatorium yellow vein mosaic vims, Eupatorium yellow vein vims, Euphorbia leaf curl Guangxi vims, Euphorbia leaf curl vims, Euphorbia mosaic Pern vims, Euphorbia mosaic vims, Euphorbia yellow leaf curl vims, Euphorbia yellow mosaic vims, French bean leaf curl vims, Hedyotis uncinella yellow mosaic vims, Hemidesmus yellow mosaic vims, Hibiscus golden mosaic vims, Hollyhock leaf curl vims, Hollyhock yellow vein mosaic vims, Hollyhock yellow vein vims, Honeysuckle yellow vein vims, Horsegram yellow mosaic vims, Indian cassava mosaic vims, Jacquemontia mosaic Yucatan vims, Jacquemontia yellow mosaic vims, Jacquemontia yellow vein vims, Jatropha leaf curl Gujarat vims, Jatropha leaf curl vims, Jatropha leaf yellow mosaic vims, Jatropha mosaic India vims, Jatropha mosaic Nigeria vims, Jatropha mosaic vims, Jatropha yellow mosaic vims, Kudzu mosaic vims, Leonums mosaic vims, Lindemia anagallis yellow vein vims, Lisianthus enation leaf curl vims, Ludwigia yellow vein Vietnam vims, Ludwigia yellow vein vims, Luffa yellow mosaic vims, Lycianthes yellow mosaic vims, Macroptilium bright mosaic vims, Macroptilium common mosaic vims, Macroptilium golden mosaic vims, Macroptilium mosaic Puerto Rico vims, Macroptilium yellow mosaic Florida vims, Macroptilium yellow mosaic vims, Macroptilium yellow spot vims, Macroptilium yellow vein vims, Malvastmm bright yellow mosaic vims, Malvastmm leaf curl Philippines vims, Malvastmm leaf curl vims, Malvastmm yellow mosaic Helshire vims, Malvastmm yellow mosaic Jamaica vims, Malvastmm yellow mosaic vims, Malvastmm yellow vein Cambodia vims, Malvastmm yellow vein Honghe vims, Malvastmm yellow vein Lahore vims, Malvastmm yellow vein vims, Malvastmm yellow vein Yunnan vims, Melochia mosaic vims, Melochia yellow mosaic vims, Melon chlorotic leaf curl vims, Melon chlorotic mosaic vims, Melon yellow mosaic vims, Merremia mosaic Puerto Rico vims, Merremia mosaic vims, Mesta yellow vein mosaic Bahraich vims, Mimosa yellow leaf curl vims, Mirabilis leaf curl vims, Mungbean yellow mosaic India vims, Mungbean yellow mosaic vims, Okra enation leaf curl vims, Okra leaf curl Oman vims, Okra mottle vims, Okra yellow crinkle vims,

Okra yellow mosaic Mexico vims, Oxalis yellow vein vims, Papaya leaf cmmple vims, Papaya leaf curl China vims, Papaya leaf curl Guandong vims, Papaya leaf curl vims, Passionfmit leaf curl vims, Passionfmit leaf distortion vims, Passionfmit severe leaf distortion vims, Pavonia mosaic vims, Pavonia yellow mosaic vims, Pea leaf distortion vims, Pedilanthus leaf curl vims, Pepper golden mosaic vims, Pepper huasteco yellow vein vims, Pepper leaf curl Bangladesh vims, Pepper leaf curl Lahore vims, Pepper leaf curl vims, Pepper leaf curl Yunnan vims, Pepper leafroll vims, Pepper yellow leaf curl Aceh vims, Pepper yellow leaf curl Indonesia vims, Pepper yellow leaf curl Indonesia vims 2, Pepper yellow leaf curl Thailand vims, Pepper yellow leaf curl vims, Pepper yellow vein Mali vims, Potato yellow mosaic Panama vims, Potato yellow mosaic vims, Pouzolzia golden mosaic vims, Pouzolzia mosaic Guangdong vims, Pouzolzia yellow mosaic vims, Premna leaf curl vims, Pumpkin yellow mosaic vims, Radish leaf curl vims, Ramie mosaic Yunnan vims, Rhynchosia golden mosaic Havana vims, Rhynchosia golden mosaic Sinaloa vims, Rhynchosia golden mosaic vims, Rhynchosia mild mosaic vims,

Rhynchosia mgose golden mosaic vims, Rhynchosia yellow mosaic India vims, Rhynchosia yellow mosaic vims, Rose leaf curl vims, Sauropus leaf curl vims, Senecio yellow mosaic vims, Senna leaf curl vims, Sida angular mosaic vims, Sida bright yellow mosaic vims, Sida chlorotic mottle vims, Sida chlorotic vein vims, Sida ciliaris golden mosaic vims, Sida common mosaic vims, Sida golden mosaic Braco virus, Sida golden mosaic Brazil virus, Sida golden mosaic Buckup vims, Sida golden mosaic Costa Rica vims, Sida golden mosaic Florida vims, Sida golden mosaic Lara vims, Sida golden mosaic vims, Sida golden mottle vims, Sida golden yellow spot vims, Sida golden yellow vein vims, Sida leaf curl vims, Sida micrantha mosaic vims, Sida mosaic Alagoas vims, Sida mosaic Bolivia vims 1, Sida mosaic Bolivia vims 2, Sida mosaic Sinaloa vims, Sida mottle Alagoas vims, Sida mottle vims, Sida yellow blotch vims, Sida yellow leaf curl vims, Sida yellow mosaic Alagoas vims, Sida yellow mosaic China vims, Sida yellow mosaic vims, Sida yellow mosaic Yucatan vims, Sida yellow mottle vims, Sida yellow net vims, Sida yellow vein Vietnam vims, Sida yellow vein vims, Sidastmm golden leaf spot vims, Siegesbeckia yellow vein Guangxi vims, Siegesbeckia yellow vein vims, Solanum mosaic Bolivia vims, South African cassava mosaic vims, Soybean blistering mosaic vims, Soybean chlorotic blotch vims, Soybean mild mottle vims, Spilanthes yellow vein vims, Spinach yellow vein vims, Squash leaf curl China vims, Squash leaf curl Philippines vims, Squash leaf curl vims, Squash leaf curl Yunnan vims, Squash mild leaf curl vims, Sri Lankan cassava mosaic vims, Stachytarpheta leaf curl vims, Sunn hemp leaf distortion vims, Sweet potato golden vein Korea vims, Sweet potato leaf curl Canary vims, Sweet potato leaf curl China vims, Sweet potato leaf curl Georgia vims, Sweet potato leaf curl Guangxi vims, Sweet potato leaf curl Henan vims, Sweet potato leaf curl Hubei vims, Sweet potato leaf curl Sao Paulo vims, Sweet potato leaf curl Shandong vims, Sweet potato leaf curl Sichuan vims 1, Sweet potato leaf curl Sichuan vims 2, Sweet potato leaf curl South Carolina vims, Sweet potato leaf curl vims, Sweet potato mosaic vims, Synedrella yellow vein clearing vims, Telfairia golden mosaic vims, Tobacco curly shoot vims, Tobacco leaf curl Comoros vims, Tobacco leaf curl Cuba vims, Tobacco leaf curl Dominican Republic vims, Tobacco leaf curl Pusa vims, Tobacco leaf curl Thailand vims, Tobacco leaf curl Yunnan vims, Tobacco leaf curl Zimbabwe vims, Tobacco leaf mgose vims, Tobacco mottle leaf curl vims, Tobacco yellow crinkle vims, Tomato bright yellow mosaic vims, Tomato bright yellow mottle vims, Tomato chino La Paz vims, Tomato chlorotic leaf curl vims, Tomato chlorotic leaf distortion vims, Tomato chlorotic mottle Guyane vims, Tomato chlorotic mottle vims, Tomato common mosaic vims, Tomato curly stunt vims, Tomato dwarf leaf vims, Tomato enation leaf curl vims, Tomato golden leaf distortion vims, Tomato golden leaf spot vims, Tomato golden mosaic vims, Tomato golden mottle vims, Tomato golden vein vims, Tomato mterveinal chlorosis vims, Tomato latent vims, Tomato leaf curl Anjouan vims, Tomato leaf curl Amsha vims, Tomato leaf curl Bangalore vims, Tomato leaf curl Bangladesh vims, Tomato leaf curl Burkina Faso vims, Tomato leaf curl Cebu vims, Tomato leaf curl China vims, Tomato leaf curl Comoros vims, Tomato leaf curl Diana vims, Tomato leaf curl Ghana vims, Tomato leaf curl Guangdong vims, Tomato leaf curl Guangxi vims, Tomato leaf curl Gujarat vims, Tomato leaf curl Hainan vims, Tomato leaf curl Hanoi vims, Tomato leaf curl Hsinchu vims, Tomato leaf curl Iran vims, Tomato leaf curl Japan vims, Tomato leaf curl Java vims, Tomato leaf curl Joydebpur virus, Tomato leaf curl Karnataka virus, Tomato leaf curl Karnataka virus 2, Tomato leaf curl Karnataka virus 3, Tomato leaf curl Kerala virus, Tomato leaf curl Laos virus, Tomato leaf curl Liwa vims, Tomato leaf curl Madagascar vims, Tomato leaf curl Mahe vims, Tomato leaf curl Malaysia vims, Tomato leaf curl Mali vims, Tomato leaf curl Mindanao vims, Tomato leaf curl Moheli vims, Tomato leaf curl Namakely vims, Tomato leaf curl New Delhi vims, Tomato leaf curl New Delhi vims 2, Tomato leaf curl New Delhi vims 4, Tomato leaf curl New Delhi vims 5, Tomato leaf curl Nigeria vims, Tomato leaf curl Palampur vims, Tomato leaf curl Patna vims, Tomato leaf curl Philippines vims, Tomato leaf curl Pune vims, Tomato leaf curl purple vein vims, Tomato leaf curl Rajasthan vims, Tomato leaf curl Seychelles vims, Tomato leaf curl Sinaloa vims, Tomato leaf curl Sri Lanka vims, Tomato leaf curl Sudan vims, Tomato leaf curl Sulawesi vims, Tomato leaf curl Taiwan vims, Tomato leaf curl Tanzania vims, Tomato leaf curl Toliara vims, Tomato leaf curl Uganda vims, Tomato leaf curl Vietnam vims, Tomato leaf curl vims, Tomato leaf deformation vims, Tomato leaf distortion vims, Tomato mild mosaic vims, Tomato mild yellow leaf curl Aragua vims, Tomato mosaic Havana vims, Tomato mottle leaf curl vims, Tomato mottle Taino vims, Tomato mottle vims, Tomato mottle wrinkle vims, Tomato mgose mosaic vims, Tomato mgose yellow leaf curl vims, Tomato severe leaf curl Kalakada vims, Tomato severe leaf curl vims, Tomato severe mgose vims, Tomato twisted leaf vims, Tomato wrinkled mosaic vims, Tomato yellow leaf curl Axarquia vims, Tomato yellow leaf curl China vims, Tomato yellow leaf curl Guangdong vims, Tomato yellow leaf curl Indonesia vims, Tomato yellow leaf curl Kanchanaburi vims, Tomato yellow leaf curl Malaga vims, Tomato yellow leaf curl Mali vims, Tomato yellow leaf curl Sardinia vims, Tomato yellow leaf curl Shuangbai vims, Tomato yellow leaf curl Thailand vims, Tomato yellow leaf curl Vietnam vims, Tomato yellow leaf curl vims, Tomato yellow leaf curl Yunnan vims, Tomato yellow leaf distortion vims, Tomato yellow margin leaf curl vims, Tomato yellow mottle vims, Tomato yellow spot vims, Tomato yellow vein streak vims, Triumfetta yellow mosaic vims, Velvet bean golden mosaic vims, Velvet bean severe mosaic vims, Vemonia crinkle vims, Vemonia yellow vein Fujian vims, Vemonia yellow vein vims, Vigna yellow mosaic vims, Vinca leaf curl vims, Watermelon chlorotic stunt vims, West African Asystasia vims 1, West African Asystasia vims 2, West African Asystasia vims 3, Whitefly-associated begomovims 1, Whitefly-associated begomovims 2, Whitefly- associated begomovims 3, Whitefly-associated begomovims 4, Whitefly-associated begomovims 6, Whitefly-associated begomovims 7, Wissadula golden mosaic vims, Wissadula yellow mosaic vims, Alfalfa leaf curl vims, Euphorbia caput-medusae latent vims, French bean severe leaf curl vims, Plantago lanceolata latent vims, Beet curly top vims, Horseradish curly top vims, Spinach severe curly top vims, Eragrostis curvula streak vims, Grapevine red blotch vims, Pmnus latent vims, Wild Vitis latent vims, Axonopus compressus streak vims, Bromus catharticus striate mosaic vims, Chickpea chlorosis Australia vims, Chickpea chlorosis vims, Chickpea chlorotic dwarf vims, Chickpea redleaf vims, Chickpea yellow dwarf virus, Chickpea yellows virus, Chloris striate mosaic virus, Digitaria ciliaris striate mosaic vims, Digitaria didactyla striate mosaic vims, Digitaria streak vims, Dragonfly-associated mastrevims, Eragrostis minor streak vims, Eragrostis streak vims, Maize streak dwarfing vims, Maize streak Reunion vims, Maize streak vims, Maize striate mosaic vims, Miscanthus streak vims, Oat dwarf vims, Panicum streak vims, Paspalum dilatatum striate mosaic vims, Paspalum striate mosaic vims, Rice latent vims 1, Rice latent vims 2, Sacchamm streak vims, Sporobolus striate mosaic vims 1, Sporobolus striate mosaic vims 2, Sugarcane chlorotic streak vims, Sugarcane streak Egypt vims, Sugarcane streak Reunion vims, Sugarcane streak vims, Sugarcane striate vims, Sugarcane white streak vims, Sweet potato symptomless vims 1, Switchgrass mosaic-associated vims, Tobacco yellow dwarf vims, Urochloa streak vims, Wheat dwarf India vims, Wheat dwarf vims, Tomato pseudo-curly top vims, Sesame curly top vims, Turnip curly top vims, Turnip leaf roll vims, Citms chlorotic dwarf associated vims, Mulberry mosaic dwarf associated vims, Blackbird associated gemycircularvims 1, Bovine associated gemycircularvirus 1, Bromus associated gemycircularvims 1, Cassava associated gemycircularvims 1, Chickadee associated gemycircularvims 1, Chicken associated gemycircularvims 1, Chicken associated gemycircularvims 2, Dragonfly associated gemycircularvims 1, Equine associated gemycircularvims 1, Fur seal associated gemycircularvims 1, Gerygone associated gemycircularvims 1, Gerygone associated gemycircularvims 2, Gerygone associated gemycircularvims 3, Hypericum associated gemycircularvims 1, Lama associated gemycircularvims 1, Mallard associated gemycircularvims 1, Minioptems associated gemycircularvims 1, Mongoose associated gemycircularvims 1, Mosquito associated gemycircularvims 1, Odonata associated gemycircularvims 1, Odonata associated gemycircularvims 2, Poaceae associated gemycircularvims 1, Porcine associated gemycircularvims 1, Porcine associated gemycircularvims 2, Pteropus associated gemycircularvims 1, Pteropus associated gemycircularvims 2, Pteropus associated gemycircularvims 3, Pteropus associated gemycircularvims 4, Pteropus associated gemycircularvims 5, Pteropus associated gemycircularvims 6, Pteropus associated gemycircularvims 7, Pteropus associated gemycircularvims 8, Pteropus associated gemycircularvims 9, Pteropus associated gemycircularvims 10, Rat associated gemycircularvims 1, Sclerotinia gemycircularvims 1, Sewage derived gemycircularvims 1, Sewage derived gemycircularvims 2, Sewage derived gemycircularvims 3, Sewage derived gemycircularvims 4, Sewage derived gemycircularvims 5, Sheep associated gemycircularvims 1,

Soybean associated gemycircularvims 1, Dragonfly associated gemyduguivims 1, Canine associated gemygorvims 1, Mallard associated gemygorvims 1, Pteropus associated gemygorvirus 1, Sewage derived gemygorvims 1, Starling associated gemygorvims 1, Badger associated gemykibivims 1, Black robin associated gemykibivims 1, Blackbird associated gemykibivims 1, Bovine associated gemykibivims 1, Dragonfly associated gemykibivims 1, Human associated gemykibivims 1, Human associated gemykibivims 2, Human associated gemykibivims 3, Human associated gemykibivims 4, Human associated gemykibivirus 5, Mongoose associated gemykibivirus 1, Pteropus associated gemykibivirus 1, Rhinolophus associated gemykibivims 1, Rhinolophus associated gemykibivims 2, Sewage derived gemykibivirus 1, Sewage derived gemykibivims 2, Pteropus associated gemykolovirus 1, Pteropus associated gemykolovirus 2, Bovine associated gemykrogvirus 1, Caribou associated gemykrogvirus 1, Sewage derived gemykrogvirus 1, Rabbit associated gemykroznavirus 1, Ostrich associated gemytondvirus 1, Human associated gemyvongvirus 1, Alphapleolipovirus HHPV1, Alphapleolipovirus HHPY2, Alphapleolipovims HRPV1, Alphapleolipovims HRPV2, Alphapleolipovirus HRPV6, Betapleolipovirus HGPY1, Betapleolipovirus HHPV3, Betapleolipovims HHPV4, Betapleolipovims HRPV3, Betapleolipovims HRPV9, Betapleolipovims HRPV10, Betapleolipovims HRPV11, Betapleolipovims HRPV12, Betapleolipovims SNJ2, Gammapleolipovirus His2, Amasya cherry disease associated chrysovims, Anthurium mosaic-associated chrysovims, Aspergillus fumigatus chrysovims, Brassica campestris chrysovims, Colletotrichum gloeosporioides chrysovims, Cryphonectria nitschkei chrysovims 1, Fusarium oxysporum chrysovims 1, Helminthosporium victoriae vims 145S, Isariajavanica chrysovims, Macrophomina phaseolina chrysovims, Penicillium brevicompactum vims, Penicillium chrysogenum vims, Penicillium cyaneofulvum vims, Persea americana chrysovims, Raphanus sativus chrysovims, Shuangao insect- associated chrysovims, Verticillium dahliae chrysovims 1, Altemaria altemata chrysovims, Botryosphaeria dothidea chrysovims, Colletotrichum fmcticola chrysovims 1, Fusarium gramineamm chrysovims, Fusarium oxyspomm chrysovims 2, Magnaporthe oryzae chrysovims, Penicillium janczewskii chrysovims 1, Penicillium janczewskii chrysovims 2, Rosellinia necatrix megabimavims 1, Rosellinia necatrix quadrivims 1, Giardia lamblia vims, Leishmania RNA vims 1, Leishmania RNA vims 2, Saccharomyces cerevisiae vims L-A, Saccharomyces cerevisiae vims LBCLa, Scheffersomyces segobiensis vims L, Tuber aestivum vims 1, Ustilago maydis vims HI, Xanthophyllomyces dendrorhous vims L1A, Xanthophyllomyces dendrorhous vims LIB, Trichomonas vaginalis vims 1, Trichomonas vaginalis vims 2, Trichomonas vaginalis vims 3, Trichomonas vaginalis vims 4, Aspergillus foetidus slow vims 1, Beauveria bassiana victorivims 1, Chalara elegans RNA Vims 1, Coniothyrium minitans RNA vims, Epichloe festucae vims 1, Gremmeniella abietina RNA vims LI, Helicobasidium mompa totivims 1-17, Helminthosporium victoriae vims 190S, Magnaporthe oryzae vims 1, Magnaporthe oryzae vims 2, Rosellinia necatrix victorivims 1, Sphaeropsis sapmea RNA vims 1, Sphaeropsis sapmeaRNA vims 2, Tolypocladium cylindrosporum vims 1, Eriocheir sinensis reovims, Micromonas pusilla reovims, African horse sickness vims, Bluetongue vims, Changuinola vims, Chenuda vims, Chobar Gorge vims, Corriparta vims, Epizootic hemorrhagic disease vims, Equine encephalosis vims, Eubenangee vims, Great Island vims, Ieri vims, Lebombo vims, Omngo vims, Palyam vims, Pemvian horse sickness vims, St Croix River vims, Umatilla vims, Wad Medani vims, Wallal vims, Warrego vims, Wongorr vims, Yunnan orbivirus, Rice dwarf virus, Rice gall dwarf virus, Wound tumor virus, Rotavirus A, Rotavirus B, Rotavirus C, Rotavirus D, Rotavirus F, Rotavirus G, Rotavirus H, Rotavirus I, Rotavirus J, Banna virus, Kadipiro virus, Liao ning virus, Aquareovirus A, Aquareovirus B, Aquareovirus C, Aquareovirus D, Aquareovirus E, Aquareovirus F, Aquareovirus G, Colorado tick fever coltivirus, Eyach coltivirus,

Kundal coltivirus, Tai Forest coltivirus, Tarumizu coltivirus, Cypovirus 1, Cypovirus 2, Cypovirus 3, Cypovirus 4, Cypovirus 5, Cypovirus 6, Cypovirus 7, Cypovirus 8, Cypovirus 9, Cypovirus 10,

Cypovirus 11, Cypovirus 12, Cypovirus 13, Cypovirus 14, Cypovirus 15, Cypovirus 16, Aedes pseudoscutellaris reovirus, Fiji disease virus, Garlic dwarf virus, Maize rough dwarf virus, Mai de Rio Cuarto virus, Nilaparvata lugens reovirus, Oat sterile dwarf virus, Pangola stunt virus, Rice black streaked dwarf virus, Southern rice black-streaked dwarf virus, Idnoreovirus 1, Idnoreovirus 2, Idnoreovirus 3, Idnoreovirus 4, Idnoreovirus 5, Mycoreovirus 1, Mycoreovirus 2, Mycoreovirus 3, Avian orthoreovirus, Baboon orthoreovirus, Broome orthoreovirus, Mahlapitsi orthoreovirus, Mammalian orthoreovirus, Nelson Bay orthoreovirus, Neoavian orthoreovirus, Piscine orthoreovirus, Reptilian orthoreovirus, Testudine orthoreovirus, Echinochloa ragged stunt virus, Rice ragged stunt vims, Pseudomonas vims phi6, Pseudomonas vims phi8, Pseudomonas vims phi 12, Pseudomonas vims phi 13 , Pseudomonas vims phi2954, Pseudomonas vims phiNN, Pseudomonas vims phiYY, Antheraea eucalypti vims, Damatrima vims, Dasychira pudibunda vims, Nudaurelia capensis beta vims, Philosamia cynthia x ricini vims, Pseudoplusia includens vims, Trichoplusia ni vims, Dendrolimus punctatus vims, Helicoverpa armigera stunt vims, Nudaurelia capensis omega vims, Beet necrotic yellow vein vims, Beet soil-bome mosaic vims, Burdock mottle vims, Rice stripe necrosis vims, Orthohepevims A, Orthohepevims B, Orthohepevirus C, Orthohepevims D, Piscihepevims A, Rubella vims, Alfalfa mosaic vims, Amazon lily mild mottle vims, Pelargonium zonate spot vims, Broad bean mottle vims, Brome mosaic vims, Cassia yellow blotch vims, Cowpea chlorotic mottle vims, Melandrium yellow fleck vims, Spring beauty latent vims, Cucumber mosaic vims, Gayfeather mild mottle vims, Peanut stunt vims, Tomato aspermy vims, Ageratum latent vims, American plum line pattern vims, Apple mosaic vims, Asparagus vims 2, Blackberry chlorotic ringspot vims, Blueberry shock vims, Citms leaf mgose vims, Citms variegation vims, Elm mottle vims, Fragaria chiloensis latent vims, Humulus japonicus latent vims, Lilac leaf chlorosis vims, Lilac ring mottle vims, Parietana mottle vims, Privet ringspot vims, Pmne dwarf vims, Pmnus necrotic ringspot vims, Spinach latent vims, Strawberry necrotic shock vims, Tobacco streak vims, Tomato necrotic streak vims, Tulare apple mosaic vims, Olive latent vims 2, Air potato ampelovims 1, Blackberry vein banding -associated vims, Grapevine leafroll-associated vims 1,

Grapevine leafroll-associated vims 3, Grapevine leafroll-associated vims 4, Grapevine leafroll-associated vims 13, Little cherry vims 2, Pineapple mealybug wilt-associated vims 1, Pineapple mealybug wilt- associated vims 2, Pineapple mealybug wilt-associated vims 3, Pistachio ampelovims A, Plum bark necrosis stem pitting -associated vims, Arracacha vims 1, Beet yellow stunt vims, Beet yellows vims, Blackcurrant closterovims 1, Burdock yellows vims, Carnation necrotic fleck vims, Carrot yellow leaf vims, Citms tristeza vims, Grapevine leafroll-associated vims 2, Mint vims 1, Raspberry leaf mottle vims, Rehmannia vims 1, Rose leaf rosette-associated vims, Strawberry chlorotic fleck-associated vims, Tobacco vims 1, Wheat yellow leaf vims, Abutilon yellows vims, Bean yellow disorder vims, Beet pseudoyellows vims, Blackberry yellow vein-associated vims, Cucurbit yellow stunting disorder vims, Diodia vein chlorosis vims, Lettuce chlorosis vims, Lettuce infectious yellows vims, Potato yellow vein vims, Strawberry pallidosis-associated vims, Sweet potato chlorotic stunt vims, Tetterwort vein chlorosis vims, Tomato chlorosis vims, Tomato infectious chlorosis vims, Arecapalm velarivims 1, Cordyline vims 1, Cordyline vims 2, Cordyline vims 3, Cordyline vims 4, Grapevine leafroll-associated vims 7, Little cherry vims 1, Actinidia vims 1, Alligatorweed stunting vims, Blueberry vims A, Megakepasma mosaic vims, Mint vein banding-associated vims, Olive leaf yellowing-associated vims, Persimmon vims B, Agaricus bispoms alphaendomavims 1, Basella alba alphaendomavirus 1, Bell pepper alphaendomavirus, Cluster bean alphaendomavims 1, Cucumis melo alphaendomavims, Erysiphe cichoraceamm alphaendomavims, Grapevine endophyte alphaendomavims, Helianthus annuus alphaendomavims, Helicobasidium mompa alphaendomavims 1, Hordeum vulgare alphaendomavims, Hot pepper alphaendomavims, Lagenaria siceraria alphaendomavims, Oryza mfipogon alphaendomavims, Oryza sativa alphaendomavims, Persea americana alphaendomavims 1, Phaseolus vulgaris alphaendomavims 1, Phaseolus vulgaris alphaendomavims 2, Phaseolus vulgaris alphaendomavims 3, Phytophthora alphaendomavims 1, Rhizoctonia cerealis alphaendomavims 1, Rhizoctonia solani alphaendomavims 2, Vicia faba alphaendomavims, Winged bean alphaendomavims 1, Yerba mate alphaendomavims, Altemaria brassicicola betaendomavims 1, Botrytis cinerea betaendomavims 1, Gremmeniella abietina betaendomavims 1, Rosellinia necatrix betaendomavims 1, Sclerotinia minor betaendomavims 1, Sclerotinia sclerotiomm betaendomavims 1, Tuber aestivum betaendomavims, Blueberry necrotic ring blotch vims, Tea plant necrotic ring blotch vims, Citms leprosis vims C, Citms leprosis vims C2, Hibiscus green spot vims 2, Privet idaeovims, Raspberry bushy dwarf vims, Japanese holly fem mottle pteridovirus, Maize associated ptendovims, Aura vims, Barmah Forest vims, Bebaru vims, Cabassou vims, Chikungunya vims, Eastern equine encephalitis vims, Eilat vims, Everglades vims, Fort Morgan vims, Getah vims, Highlands J vims, Madariaga vims, Mayaro vims, Middelburg vims, Mosso das Pedras vims, Mucambo vims, Ndumu vims, Onyong-nyong vims, Pixuna vims, Rio Negro vims, Ross River vims, Salmon pancreas disease vims, Semliki Forest vims, Sindbis vims, Southern elephant seal vims, Tonate vims, Trocara vims, Una vims, Venezuelan equine encephalitis vims, Western equine encephalitis vims, Whataroa vims, Chinese wheat mosaic vims, Japanese soil-borne wheat mosaic vims, Oat golden stripe vims, Soil-bome cereal mosaic vims, Soil- borne wheat mosaic virus, Sorghum chlorotic spot virus, Drakaea vims A, Gentian ovary ringspot vims, Anthoxanthum latent blanching vims, Barley stripe mosaic vims, Lychnis ringspot vims, Poa semilatent vims, Indian peanut clump vims, Peanut clump vims, Beet soil-home vims, Beet vims Q, Broad bean necrosis vims, Colombian potato soil-home vims, Potato mop-top vims, Bell pepper mottle vims, Bmgmansia mild mottle vims, Cactus mild mottle vims, Clitoria yellow mottle vims, Cucumber fmit mottle mosaic vims, Cucumber green mottle mosaic vims, Cucumber mottle vims, Frangipani mosaic vims, Hibiscus latent Fort Pierce vims, Hibiscus latent Singapore vims, Kyuri green mottle mosaic vims, Maracuj a mosaic vims, Obuda pepper vims, Odontoglossum ringspot vims, Opuntia chlorotic ringspot vims, Paprika mild mottle vims, Passion f it mosaic vims, Pepper mild mottle vims, Plumeria mosaic vims, Rattail cactus necrosis-associated vims, Rehmannia mosaic vims, Ribgrass mosaic vims, Streptocarpus flower break vims, Sunn-hemp mosaic vims, Tobacco latent vims, Tobacco mild green mosaic vims, Tobacco mosaic vims, Tomato brown mgose fmit vims, Tomato mosaic vims, Tomato mottle mosaic vims, Tropical soda apple mosaic vims, Turnip vein-clearing vims, Ullucus mild mottle vims, Wasabi mottle vims, Yellow tailflower mild mottle vims, Youcai mosaic vims, Zucchini green mottle mosaic vims, Pea early-browning vims, Pepper ringspot vims, Tobacco rattle vims, Alfalfa vims S, Arachis pintoi vims, Blackberry vims E, Garlic mite-bome filamentous vims, Garlic vims A, Garlic vims B, Garlic vims C, Garlic vims D, Garlic vims E, Garlic vims X, Shallot vims X, Vanilla latent vims, Botrytis vims X, Lolium latent vims, Citms yellow vein clearing vims, Indian citms ringspot vims, Donkey orchid symptomless vims, Actinidia vims X, Allium vims X, Alstroemeria vims X,

Altemanthera mosaic vims, Asparagus vims 3, Bamboo mosaic vims, Cactus vims X, Cassava common mosaic vims, Cassava vims X, Clover yellow mosaic vims, Cymbidium mosaic vims, Foxtail mosaic vims, Hosta vims X, Hydrangea ringspot vims, Lagenaria mild mosaic vims, Lettuce vims X, Lily vims X, Malva mosaic vims, Mint vims X, Narcissus mosaic vims, Nerine vims X, Opuntia vims X, Papaya mosaic vims, Pepino mosaic vims, Phaius vims X, Pitaya vims X, Plantago asiatica mosaic vims,

Plantain vims X, Potato aucuba mosaic vims, Potato vims X, Schlumbergera vims X, Strawberry mild yellow edge vims, Tamus red mosaic vims, Tulip vims X, Vanilla vims X, White clover mosaic vims, Yam vims X, Zygocactus vims X, Sclerotinia sclerotiomm debilitation-associated RNA vims, Aconitum latent vims, American hop latent vims, Atractylodes mottle vims, Blueberry scorch vims, Butterbur mosaic vims, Cactus vims 2, Caper latent vims, Carnation latent vims, Chrysanthemum vims B, Cole latent vims, Coleus vein necrosis vims, Cowpea mild mottle vims, Cucumber vein-clearing vims, Daphne vims S, Gaillardia latent vims, Garlic common latent vims, Helemum vims S, Helleboms mosaic vims, Helleboms net necrosis vims, Hippeastmm latent vims, Hop latent vims, Hop mosaic vims, Hydrangea chlorotic mottle vims, Kalanchoe latent vims, Ligustmm necrotic ringspot vims, Ligustmm vims A, Lily symptomless vims, Melon yellowing-associated vims, Mirabilis jalapa mottle vims, Narcissus common latent virus, Nerine latent virus, Passiflora latent virus, Pea streak virus, Phlox virus B, Phlox virus M, Phlox virus S, Poplar mosaic virus, Potato latent virus, Potato virus H, Potato vims M, Potato vims P, Potato vims S, Red clover vein mosaic vims, Sambucus vims C, Sambucus vims D, Sambucus vims E, Shallot latent vims, Sint-Jan onion latent vims, Strawberry pseudo mild yellow edge vims, Sweet potato C6 vims, Sweet potato chlorotic fleck vims, Verbena latent vims, Yam latent vims, Apple stem pitting vims, Apricot latent vims, Asian pmnus vims 1, Asian pmnus vims 2, Grapevine mpestris stem pitting- associated vims, Grapevine vims T, Peach chlorotic mottle vims, Rubus canadensis vims 1, African oil palm ringspot vims, Cherry green ring mottle vims, Cherry necrotic msty mottle vims, Cherry rusty mottle associated vims, Cherry twisted leaf associated vims, Banana mild mosaic vims, Banana vims X, Sugarcane striate mosaic-associated vims, Apple stem grooving vims, Cherry vims A, Currant vims A, Mume vims A, Carrot Ch vims 1, Carrot Ch vims 2, Citms leaf blotch vims, Diuris vims A, Diuris vims B, Hardenbergia vims A, Actinidia seed home latent vims, Apricot vein clearing associated vims, Caucasus pmnus vims, Ribes americanum vims A, Potato vims T, Pmnus vims T, Apple chlorotic leaf spot vims, Apricot pseudo-chlorotic leaf spot vims, Cherry mottle leaf vims, Grapevine berry inner necrosis vims, Grapevine Pinot gris vims, Peach mosaic vims, Phlomis mottle vims, Actinidia vims A, Actinidia vims B, Arracacha vims V, Blackberry vims A, Grapevine vims A, Grapevine vims B, Grapevine vims D, Grapevine vims E, Grapevine vims F, Grapevine vims G, Grapevine vims H, Grapevine vims I, Grapevine vims J, Heracleum latent vims, Mint vims 2, Watermelon vims A, Fusarium deltaflexivims 1, Sclerotinia deltaflexivims 1, Soybean-associated deltaflexivims 1, Botrytis vims F, Grapevine fleck vims, Bermuda grass etched-line vims, Blackberry vims S, Citms sudden death- associated vims, Grapevine asteroid mosaic associated vims, Grapevine Syrah vims 1, Maize rayado fino vims, Nectarine marafivims M, Oat blue dwarf vims, Olive latent vims 3, Peach marafivims D, Anagyris vein yellowing vims, Andean potato latent vims, Andean potato mild mosaic vims, Belladonna mottle vims, Cacao yellow mosaic vims, Calopogonium yellow vein vims, Chayote mosaic vims, Chiltepin yellow mosaic vims, Clitoria yellow vein vims, Desmodium yellow mottle vims, Dulcamara mottle vims, Eggplant mosaic vims, Erysimum latent vims, Kennedya yellow mosaic vims, Melon mgose mosaic vims, Nemesia ring necrosis vims, Okra mosaic vims, Ononis yellow mosaic vims, Passion fmit yellow mosaic vims, Peanut yellow mosaic vims, Petunia vein banding vims, Physalis mottle vims, Plantago mottle vims, Scrophularia mottle vims, Tomato blistering mosaic tymovims, Turnip yellow mosaic vims, Voandzeia necrotic mosaic vims, Wild cucumber mosaic vims, Bombyx mori latent vims, Poinsettia mosaic vims, Apoi vims, Aroa vims, Bagaza vims, Banzi vims, Bouboui vims, Bukalasa bat vims, Cacipacore vims, Carey Island vims, Cowbone Ridge vims, Dakar bat vims, Dengue vims, Edge Hill vims, Entebbe bat vims, Gadgets Gully vims, Ilheus vims, Israel turkey meningoencephalomyelitis vims, Japanese encephalitis vims, Jugra vims, Jutiapa vims, Kadam vims, Kedougou vims, Kokobera vims, Koutango vims, Kyasanur Forest disease virus, Langat virus, Loupmg ill virus, Meaban virus, Modoc virus, Montana myotis leukoencephalitis virus, Murray Valley encephalitis virus, Ntaya virus, Omsk hemorrhagic fever virus, Phnom Penh bat virus, Powassan virus, Rio Bravo virus, Royal Farm virus, Saboya vims, Saint Louis encephalitis vims, Sal Vieja vims, San Perlita vims, Saumarez Reef vims,

Sepik vims, Tembusu vims, Tick-bome encephalitis vims, Tyuleniy vims, Uganda S vims, Usutu vims, Wesselsbron vims, West Nile vims, Yaounde vims, Yellow fever vims, Yokose vims, Zika vims, Hepacivims A, Hepacivims B, Hepacivims C, Hepacivims D, Flepacivims E, Hepacivims F, Hepacivims G, Hepacivims H, Hepacivims I, Hepacivims J, Hepacivims K, Hepacivims L, Hepacivims M, Hepacivims N, Pegivims A, Pegivims B, Pegivims C, Pegivims D, Pegivims E, Pegivims F, Pegivims G, Pegivims H, Pegivims I, Pegivims J, Pegivims K, Pestivims A, Pestivims B, Pestivims C, Pestivims D, Pestivims E, Pestivims F, Pestivims G, Pestivims H, Pestivims I, Pestivims J, Pestivims K, Black beetle vims, Boolarra vims, Flock House vims, Nodamura vims, Pariacoto vims, Barfin flounder nervous necrosis vims, Redspotted grouper nervous necrosis vims, Striped jack nervous necrosis vims, Tiger puffer nervous necrosis vims, Lake Sinai vims 1, Lake Sinai vims 2, Providence vims, Alfalfa enamovims 1, Birdsfoot trefoil enamovims 1, Citms vein enation vims, Grapevine enamovirus 1, Pea enation mosaic vims 1, Apple associated luteovims, Apple luteovims 1, Barley yellow dwarf vims kerll, Barley yellow dwarf vims kerlll, Barley yellow dwarf vims MAV, Barley yellow dwarf vims PAS, Barley yellow dwarf vims PAV, Bean leafroll vims, Cherry associated luteovims, Nectarine stem pitting associated vims, Red clover associated luteovims, Rose spring dwarf-associated vims, Soybean dwarf vims, Beet chlorosis vims, Beet mild yellowing vims, Beet western yellows vims, Carrot red leaf vims, Cereal yellow dwarf vims RPS, Cereal yellow dwarf vims RPY, Chickpea chlorotic stunt vims, Cotton leafroll dwarf vims, Cucurbit aphid-bome yellows vims, Faba bean polerovims 1, Maize yellow dwarf vims RMV, Maize yellow mosaic vims, Melon aphid-bome yellows vims, Pepo aphid-bome yellows vims, Pepper vein yellows vims 1, Pepper vein yellows vims 2, Pepper vein yellows vims 3, Pepper vein yellows vims 4, Pepper vein yellows vims 5, Pepper vein yellows vims 6, Potato leafroll vims, Pumpkin polerovims, Suakwa aphid-bome yellows vims, Sugarcane yellow leaf vims, Tobacco vein distorting vims, Turnip yellows vims, Barley yellow dwarf vims GPV, Barley yellow dwarf vims SGV, Chickpea stunt disease associated vims, Groundnut rosette assistor vims, Indonesian soybean dwarf vims, Sweet potato leaf speckling vims, Tobacco necrotic dwarf vims, Carrot mottle mimic vims, Carrot mottle vims, Ethiopian tobacco bushy top vims, Groundnut rosette vims, Lettuce speckles mottle vims, Opium poppy mosaic vims, Pea enation mosaic vims 2, Tobacco bushy top vims, Tobacco mottle vims, Angelonia flower break vims, Calibrachoa mottle vims, Carnation mottle vims, Honeysuckle ringspot vims, Nootka lupine vein clearing vims, Pelargonium flower break vims, Saguaro cactus vims, Olive latent vims 1, Olive mild mosaic vims, Potato necrosis vims, Tobacco necrosis vims A, Cucumber leaf spot vims, Johnsongrass chlorotic stripe mosaic virus, Maize white line mosaic virus, Pothos latent vims, Yam spherical vims, Oat chlorotic stunt vims, Cardamine chlorotic fleck vims, Hibiscus chlorotic ringspot vims, Japanese iris necrotic ring vims, Turnip crinkle vims, Beet black scorch vims, Leek white stripe vims, Tobacco necrosis vims D, Galinsoga mosaic vims, Cowpea mottle vims, Melon necrotic spot vims, Pea stem necrosis vims, Soybean yellow mottle mosaic vims, Furcraea necrotic streak vims, Maize chlorotic mottle vims, Cocksfoot mild mosaic vims, Panicum mosaic vims, Thin paspalum asymptomatic vims, Clematis chlorotic mottle vims, Elderberry latent vims, Pelargonium chlorotic ring pattern vims, Pelargonium line pattern vims, Pelargonium ringspot vims, Rosa mgosa leaf distortion vims, Artichoke mottled crinkle vims, Carnation Italian ringspot vims, Cucumber Bulgarian latent vims, Cucumber necrosis vims, Cymbidium ringspot vims, Eggplant mottled crinkle vims, Grapevine Algerian latent vims, Havel River vims, Lato River vims, Limonium flower distortion vims, Moroccan pepper vims, Neckar River vims, Pelargonium leaf curl vims, Pelargonium necrotic spot vims, Petunia asteroid mosaic vims, Sitke waterborne vims, Tomato bushy stunt vims, Maize necrotic streak vims, Ahlum waterborne vims, Bean mild mosaic vims, Chenopodium necrosis vims, Cucumber soil-bome vims, Trailing lespedeza vims 1, Weddel waterborne vims, Carnation ringspot vims, Red clover necrotic mosaic vims, Sweet clover necrotic mosaic vims, Escherichia vims FI, Escherichia vims Qbeta, Escherichia vims BZ13, Escherichia vims MS2, Saccharomyces 20S RNA namavims, Saccharomyces 23S RNA namavims, Cryphonectria mitovims 1, Ophiostoma mitovims 4, Ophiostoma mitovims 5, Ophiostoma mitovims 6, Ophiostoma mitovims 3a, Botrytis botoulivims, Sclerotinia botoulivims 2, Magnaporthe magoulivims 1, Rhizoctonia magoulivims 1, Cassava vims C, Epims cherry vims, Ourmia melon vims, Sclerotinia scleroulivims 1, Soybean scleroulivims 1, Soybean scleroulivims 2, Beihai yingvims, Charybdis yingvims, Hubei yingvims, Sanxia yingvims, Shahe yingvims, Wenzhou yingvims, Wuhan yingvims, Xinzhou yingvims, Blueberry mosaic associated ophiovims, Citrus psorosis ophiovims,

Freesia sneak ophiovims, Lettuce ring necrosis ophiovims, Mirafiori lettuce big-vein ophiovims, Ranunculus white mottle ophiovims, Tulip mild mottle mosaic ophiovims, Argas mivims, Barnacle mivims, Beetle mivims, Bole mivims, Bmnnich mivims, Changping mivims, Charybdis mivims, Cockroach mivims, Crab mivims, Crustacean mivims, Dermacentor mivims, Hermit mivims, Hippoboscid mivims, Hubei mivims, Hubei odonate mivims, Imjin mivims, Lacewing mivims, Lishi mivims, Lonestar mivims, Louse fly mivims, Mosquito mivims, Myriapod mivims, Odonate mivims, Sanxia mivims, Shayang mivims, Suffolk mivims, Taiyuan mivims, Wenlmg mivims, Wuhan mivims, Xinzhou mivims, Barnacle hexartovims, Caligid hexartovims, Beihai peropuvims, Hubei peropuvims, Odonate peropuvims, Pillworm peropuvims, Pteromalus puparum peropuvims, Woodlouse peropuvims, Queensland carbovims, Southwest carbovims, Sharpbelly culterviras, Elapid 1 orthobomavirus, Mammalian 1 orthobomavirus, Mammalian 2 orthobomavirus, Passeriform 1 orthobomavirus, Passeriform 2 orthobomavirus, Psitaciform 1 orthobomavirus, Psittaciform 2 orthobomaviras, Waterbird 1 orthobomavirus, Lloviu cuevavirus, Mengla dianlovims, Bombali ebolavirus, Bundibugyo ebolavims, Reston ebolavims, Sudan ebolavims, Tai Forest ebolavims, Zaire ebolavims, Marburg marburgvims, Xilang striavims, Huangjiao thamnovims, Gerrid arlivims, Hubei arlivims, Lishi arliviras, Odonate arbvims, Tacheng arlivims, Wuchang arlivims, Hubei hubramonavims, Lentinula hubramonavims, Dadou sclerotimonavims, Drop sclerotimonavims, Glycine sclerotimonavims, Hubei sclerotimonavims, Illinois sclerotimonavims, Phyllosphere sclerotimonavims, Sclerotinia sclerotimonavims, Beihai berhavims, Echinoderm berhavims, Sipunculid berhavims, Beihai cmstavims, Wenling cmstavims, Wenzhou cmstavims, Midway nyavims, Nyamanini nyavims, Sierra Nevada nyavims, Orinoco orinovims, Soybean cyst nematode socyvims, Tapeworm tapwovims, Avian metaavulavims 2, Avian metaavulavims 5, Avian metaavulavims 6, Avian metaavulavims 7, Avian metaavulavims 8, Avian metaavulavims 10, Avian metaavulavims 11, Avian metaavulavims 14, Avian metaavulavims 15, Avian metaavulavims 20, Avian orthoavulavims 1, Avian orthoavulavims 9, Avian orthoavulavims 12, Avian orthoavulavims 13, Avian orthoavulavims 16, Avian orthoavulavims 17, Avian orthoavulavims 18, Avian orthoavulavims 19, Avian orthoavulavims 21, Avian orthovulavims 21, Avian paraavulavims 3, Avian paraavulavims 4, Synodus synodonvims, Oncorhynchus aquaparamyxovims, Salmo aquaparamyxovims, Reptilian ferlavims, Cedar henipavims, Ghanaian bat henipavims, Hendra henipavims, Mojiang henipavims, Nipah henipavims, Beilong jeilongvims, Jun jeilongvims,

Lophuromys jeilongvims 1, Lophuromys jeilongvims 2, Miniopteran jeilongvims, Myodes jeilongvims, Tailam jeilongvims, Canine morbillivims, Cetacean morbillivims, Feline morbillivirus, Measles morbillivims, Phocine morbillivims, Rinderpest morbillivims, Small ruminant morbillivims, Mossman narmovirus, Myodes narmovirus, Nariva narmovirus, Tupaia narmovirus, Bovine respirovims 3, Caprine respirovims 3, Human respirovims 1, Human respirovims 3, Murine respirovims, Porcine respirovims 1, Squirrel respirovims, Salem salemvims, Human orthombulavims 2, Human orthombulavims 4, Mammalian orthombulavims 5, Mammalian orthombulavims 6, Mapuera orthombulavims, Mumps orthombulavims, Porcine orthombulavims, Simian orthombulavims, Achimota parambulavims 1, Achimota parambulavims 2, Hervey parambulavims, Menangle parambulavims, Sosuga parambulavims, Teviot parambulavims, Tioman parambulavims, Tuhoko parambulavims 1, Tuhoko parambulavims 2, Tuhoko parambulavims 3, Cynoglossus cynoglossusvims, Hoplichthys hoplichthysvims, Scoliodon scoliodonvims, Avian metapneumovirus, Human metapneumovims, Bovine orthopneumovirus, Human orthopneumovims, Murine orthopneumovirus, Arboretum almendravims, Balsa almendravims, Coot Bay almendravims, Menghai almendravims, Puerto Almendras almendravims, Rio Chico almendravims, Xingshan alphanemrhavims, Xinzhou alphanemrhavims, Eggplant mottled dwarf alphanucleorhabdovims, Maize Iranian mosaic alphanucleorhabdovims, Maize mosaic alphanucleorhabdovirus, Morogoro maize-associated alphanucleorhabdovirus, Physostegia chlorotic mottle alphanucleorhabdovirus, Potato yellow dwarf alphanucleorhabdovirus, Rice yellow stunt alphanucleorhabdovirus, Taro vein chlorosis alphanucleorhabdovirus, Wheat yellow striate alphanucleorhabdovirus, Aruac arurhavirus, Inhangapi arurhavirus, Santabarbara arurhavirus, Xiburema arurhavirus, Bahia barhavirus, Muir barhavirus, Alfalfa betanucleorhabdovirus, Blackcurrant betanucleorhabdovims, Datura yellow vein betanucleorhabdovirus, Sonchus yellow net betanucleorhabdovirus, Sowthistle yellow vein betanucleorhabdovirus, Trefoil betanucleorhabdovirus, Caligus caligrhavirus, Lepeophtheirus caligrhavirus, Salmonlouse caligrhavims, Curionopolis curiovirus, Iriri curiovirus, Itacaiunas curiovims, Rochambeau curiovims, Alfalfa dwarf cytorhabdovirus, Barley yellow striate mosaic cytorhabdovirus, Broccoli necrotic yellows cytorhabdovirus, Cabbage cytorhabdovirus, Colocasia bobone disease-associated cytorhabdovirus, Festuca leaf streak cytorhabdovirus, Lettuce necrotic yellows cytorhabdovirus, Lettuce yellow mottle cytorhabdovirus, Maize yellow striate cytorhabdovirus, Maize-associated cytorhabdovirus, Northern cereal mosaic cytorhabdovirus, Papaya cytorhabdovirus, Persimmon cytorhabdovirus, Raspberry vein chlorosis cytorhabdovirus, Rice stripe mosaic cytorhabdovirus, Sonchus cytorhabdovirus 1, Strawberry crinkle cytorhabdovirus, Tomato yellow mottle -associated cytorhabdovirus, Wheat American striate mosaic cytorhabdovirus, Wuhan 4 insect cytorhabdovirus, Wuhan 5 insect cytorhabdovirus, Wuhan 6 insect cytorhabdovirus, Yerba mate chlorosis-associated cytorhabdovirus, Citrus chlorotic spot dichorhavirus, Citrus leprosis N dichorhavirus, Clerodendrum chlorotic spot dichorhavirus, Coffee ringspot dichorhavirus, Orchid fleck dichorhavirus, Adelaide River ephemerovirus, Berrimah ephemerovirus, Bovine fever ephemerovirus, Kimberley ephemerovirus, Koolpinyah ephemerovirus, Kotonkan ephemerovirus, Obodhiang ephemerovirus, Yata ephemerovirus, Maize fine streak gammanucleorhabdovirus, Flanders hapavirus, Gray Lodge hapavirus, Hart Park hapavirus, Holmes hapavirus, Joinjakaka hapavirus, Kamese hapavirus, La Joya hapavirus, Landjia hapavirus, Manitoba hapavirus, Marco hapavirus, Mosqueiro hapavirus, Mossuril hapavirus, Ngaingan hapavirus, Ord River hapavirus, Parry Creek hapavirus, Wongabel hapavirus, Barur ledantevirus, Fikirini ledantevirus, Fukuoka ledantevirus, Kanyawara ledantevirus, Kern Canyon ledantevirus, Keuraliba ledantevirus, Kolente ledantevirus, Kumasi ledantevirus, Le Dantec ledantevirus, Mount Elgon bat ledantevirus, Nishimuro ledantevirus, Nkolbisson ledantevirus, Oita ledantevirus, Vaprio ledantevirus, Wuhan ledantevirus, Yongjia ledantevirus, Lonestar zarhavirus, Aravan lyssavirus, Australian bat lyssavirus, Bokeloh bat lyssavirus, Duvenhage lyssavirus, European bat 1 lyssavirus, European bat 2 lyssavirus, Gannoruwa bat lyssavirus, Ikoma lyssavirus, Irkut lyssavirus, Khujand lyssavirus, Lagos bat lyssavirus, Lleida bat lyssavirus, Mokola lyssavirus, Rabies lyssavirus, Shimoni bat lyssavirus, Taiwan bat lyssavirus, West Caucasian bat lyssavirus, Moussa mousrhavirus, Hirame novirhabdovirus, Piscine novirhabdovirus, Salmonid novirhabdovirus, Snakehead novirhabdovirus, Culex ohlsrhavirus, Northcreek ohlsrhavirus, Ohlsdorf ohlsrhavirus, Riverside ohlsrhavirus, Tongilchon ohlsrhavirus, Anguillid perhabdovirus, Perch perhabdovirus, Sea trout perhabdovirus, Connecticut sawgrhavirus, Island sawgrhavirus, Minto sawgrhavirus, Sawgrass sawgrhavirus, Drosophila affinis sigmavirus, Drosophila ananassae sigmavirus, Drosophila immigrans sigmavirus, Drosophila melanogaster sigmavirus, Drosophila obscura sigmavirus, Drosophila tristis sigmavirus, Muscina stabulans sigmavims, Carp sprivivirus, Pike fry sprivivirus, Almpiwar sripuvirus, Chaco sripuvirus, Charleville sripuvirus, Cuiaba sripuvirus, Hainan sripuvirus, Niakha sripuvirus, Sena Madureira sripuvirus, Sripur sripuvirus, Garba sunrhavirus, Harrison sunrhavirus, Kwatta sunrhavirus, Oakvale sunrhavirus, Sunguru sunrhavirus, Walkabout sunrhavirus, Bas-Congo tibrovirus, Beatrice Hill tibrovirus, Coastal Plains tibrovirus, Ekpoma 1 tibrovirus, Ekpoma 2 tibrovirus, Sweetwater Branch tibrovirus, Tibrogargan tibrovirus, Durham tupavirus, Klamath tupavirus, Tupaia tupavirus, Lettuce big-vein associated varicosavirus, Alagoas vesiculovims, American bat vesiculovirus, Carajas vesiculovirus, Chandipura vesiculovirus, Cocal vesiculovirus, Indiana vesiculovims, Isfahan vesiculovims, Jurona vesiculovims, Malpais Spring vesiculovims, Maraba vesiculovims, Morreton vesiculovims, New Jersey vesiculovims, Perinet vesiculovims, Piry vesiculovims, Radi vesiculovims, Yug Bogdanovac vesiculovims, Zahedan zarhavims, Reptile sunshinevirus 1, Bolahun anphevims, Dipteran anphevims, Drosophilid anphevims, Odonate anphevims, Orthopteran anphevims, Shuangao anphevims, Xincheng anphevims, Beihai yuyuevims, Shahe yuyuevims, Hairy antennavims, Striated antennavims, Haartman hartmanivirus, Muikkunen hartmanivims, Schoolhouse hartmanivirus, Zurich hartmanivirus, Allpahuayo mammarenavims, Alxa mammarenavims, Argentinian mammarenavirus, Bear Canyon mammarenavirus, Brazilian mammarenavims, Cali mammarenavims, Chapare mammarenavims, Chevrier mammarenavims, Cupixi mammarenavims, Flexal mammarenavims, Gairo mammarenavims, Guanarito mammarenavims, Ippy mammarenavims, Lassa mammarenavims, Latino mammarenavims, Loei River mammarenavims, Lujo mammarenavims, Luna mammarenavims, Lunk mammarenavims, Lymphocytic choriomeningitis mammarenavims, Machupo mammarenavims, Mariental mammarenavims, Merino Walk mammarenavims, Mobala mammarenavims, Mopeia mammarenavims, Okahandja mammarenavims, Ohveros mammarenavims, Paraguayan mammarenavims, Pirital mammarenavims, Planalto mammarenavims, Ryukyu mammarenavims, Serra do Navio mammarenavims, Solwezi mammarenavims, Souris mammarenavims, Tacaribe mammarenavims, Tamiami mammarenavims, Wenzhou mammarenavims, Whitewater Arroyo mammarenavims, Xapuri mammarenavims, California reptarenavims, Giessen reptarenavims, Golden reptarenavims, Ordinary reptarenavims, Rotterdam reptarenavims, Crustacean lincmvims, Actinidia chlorotic ringspot-associated emaravims, Blackberry leaf mottle associated emaravims, European mountain ash ringspot-associated emaravims, Fig mosaic emaravirus, High Plains wheat mosaic emaravirus, Pigeonpea sterility mosaic emaravirus 1, Pigeonpea sterility mosaic emaravirus 2, Pistacia emaravirus B, Raspberry leaf blotch emaravirus, Redbud yellow ringspot-associated emaravirus, Rose rosette emaravirus, Batfish actinovirus, Goosefish actinovirus, Spikefish actinovirus, Hagfish agnathovirus, Bmo loanvirus, Longquan loanvims, Laibin mobatvirus, Nova mobatvims, Quezon mobatvirus, Andes orthohantavirus, Asama orthohantavirus, Asikkala orthohantavirus, Bayou orthohantavirus, Black Creek Canal orthohantavirus, Bowe orthohantavirus, Bruges orthohantavirus, Cano Delgadito orthohantavirus, Cao Bang orthohantavirus, Choclo orthohantavirus, Dabieshan orthohantavirus, Dobrava-Belgrade orthohantavirus, El Moro Canyon orthohantavirus, Fugong orthohantavirus, Fusong orthohantavirus, Hantaan orthohantavirus, Jeju orthohantavirus, Kenkeme orthohantavirus, Khabarovsk orthohantavirus, Laguna Negra orthohantavirus, Luxi orthohantavirus, Maporal orthohantavirus, Montano orthohantavirus, Necocli orthohantavirus, Oxbow orthohantavirus, Prospect Hill orthohantavirus, Puumala orthohantavirus, Rockport orthohantavirus, Sangassou orthohantavirus, Seewis orhtohantavirus, Seoul orthohantavirus, Sin Nombre orthohantavirus, Thailand orthohantavirus, Tigray orthohantavirus, Tula orthohantavirus, Yakeshi orthohantavirus, Imjin thottimvirus, Thottopalayam thottimvirus, Gecko reptillovirus, Leptomonas shilevirus, Myriapod hubavirus, Artashat orthonairovirus, Chim orthonairovirus, Crimean-Congo hemorrhagic fever orthonairovims, Dera Ghazi Khan orthonairovirus, Dugbe orthonairovirus, Estero Real orthonairovirus, Hazara orthonairovims, Hughes orthonairovims, Kasokero orthonairovims, Keterah orthonairovims, Nairobi sheep disease orthonairovims, Qalyub orthonairovims, Sakhalin orthonairovims, Tamdy orthonairovims, Thiafora orthonairovims, Spider shaspivims, Strider striwavims, Herbert herbevims, Kibale herbevims, Tai herbevims, Acara orthobunyavims, Aino orthobunyavirus, Akabane orthobunyavims, Alajuela orthobunyavims, Anadyr orthobunyavims, Anhembi orthobunyavims, Anopheles A orthobunyavims, Anopheles B orthobunyavims, Bakau orthobunyavims, Batai orthobunyavims, Batama orthobunyavims, Bellavista orthobunyavims, Benevides orthobunyavims, Bertioga orthobunyavims, Bimiti orthobunyavims, Birao orthobunyavims, Botambi orthobunyavims, Bozo orthobunyavims, Bunyamwera orthobunyavims, Bushbush orthobunyavims, Buttonwillow orthobunyavims, Bwamba orthobunyavims, Cache Valley orthobunyavims, Cachoeira Porteira orthobunyavims, California encephalitis orthobunyavims, Capim orthobunyavims, Carapam orthobunyavims, Cat Que orthobunyavims, Catu orthobunyavims, Enseada orthobunyavims, Faceys paddock orthobunyavims, Fort Sherman orthobunyavims, Gamboa orthobunyavims, Guajara orthobunyavims, Guama orthobunyavims, Guaroa orthobunyavims, Iaco orthobunyavims, Ilesha orthobunyavims, Ingwavuma orthobunyavims, Jamestown Canyon orthobunyavims, Jatobal orthobunyavims, Kaeng Khoi orthobunyavims, Kairi orthobunyavims, Keystone orthobunyavims, Koongol orthobunyavims, La Crosse orthobunyavims, Leanyer orthobunyavims, Lumbo orthbunyavims, Macaua orthobunyavirus, Madrid orthobunyavirus, Maguari orthobimyavirus, Main Drain orthobunyavirus, Manzanilla orthobunyavirus, Marituba orthobunyavirus, Melao orthobunyavirus, Mermet orthobunyavirus, Minatitlan orthobunyavirus, MPoko orthobunyavirus, Nyando orthobunyavirus, Olifantsvlei orthobunyavirus, Oriboca orthobunyavirus, Oropouche orthobunyavirus, Patois orthobunyavirus, Peaton orthobunyavirus, Potosi orthobunyavirus, Sabo orthobunyavirus, San Angelo orthobunyavirus, Sango orthobunyavirus, Schmallenberg orthobunyavirus, Serra do Navio orthobunyavirus, Shuni orthobunyavirus, Simbu orthobunyavirus, Snowshoe hare orthobunyavirus, Sororoca orthobunyavirus, Tacaiuma orthobunyavirus, Tahyna orthobunyavirus, Tataguine orthobunyavirus, Tensaw orthobunyavirus, Tete orthobunyavirus, Thimiri orthobunyavirus, Timboteua orthobunyavirus, Trivittatus orthobimyavirus, Turlock orthobunyavirus, Utinga orthobunyavirus, Witwatersrand orthobunyavirus, Wolkberg orthobunyavirus, Wyeomyia orthobunyavirus, Zegla orthobunyavirus, Caimito pacuvirus, Chilibre pacuvirus, Pacui pacuvirus, Rio Preto da Eva pacuvirus, Tapirape pacuvirus, Insect shangavirus, Ferak feravirus, Jonchet jonvirus, Anopheles orthophasmavirus, Culex orthophasmavirus, Ganda orthophasmavirus, Kigluaik phantom orthophasmavirus, Odonate orthophasmavirus, Qingling orthophasmavirus, Wuchang cockroach orthophasmavirus 1, Wuhan mosquito orthophasmavirus 1, Wuhan mosquito orthophasmavirus 2, Sanxia sawastrivirus, Insect wuhivirus, Bhanja bandavirus, Dabie bandavirus, Guertu bandavirus, Heartland bandavirus, Hunter Island bandavirus, Kismaayo bandavirus, Lone Star bandavirus, Dipteran beidivirus, Citrus coguvirus,

Coguvirus eburi, Entoleuca entovirus, Cumuto goukovirus, Gouleako goukovirus, Yichang insect goukovirus, Horsefly horwuvirus, Dipteran hudivirus, Lepidopteran hudovims, Blackleg ixovirus,

Norway ixovirus, Scapularis ixovirus, Laurel Lake laulavirus, Lentinula lentinuvirus, Mothra mobuvirus, Badu phasivims, Dipteran phasivims, Fly phasivirus, Phasi Charoen-like phasivirus, Wutai mosquito phasivirus, Adana phlebovims, Aguacate phlebovirus, Alcube phlebovirus, Alenquer phlebovirus, Ambe phlebovims, Anhanga phlebovirus, Arumowot phlebovims, Buenaventura phlebovims, Bujam phlebovims, Cacao phlebovims, Campana phlebovims, Candiru phlebovims, Chagres phlebovims, Code phlebovims, Dashli phlebovims, Durania phlebovims, Echarate phlebovims, Frijoles phlebovims, Gabek phlebovims, Gordil phlebovims, Icoaraci phlebovims, Itaituba phlebovims, Itaporanga phlebovims, Ixcanal phlebovims, Karimabad phlebovims, La Gloria phlebovims, Lara phlebovims, Leticia phlebovims, Maldonado phlebovims, Massilia phlebovims, Medjerda phlebovims, Mona Grita phlebovims, Mukawa phlebovims, Munguba phlebovims, Naples phlebovims, Nique phlebovims, Ntepes phlebovims, Odrenisrou phlebovims, Oriximma phlebovims, Pena Blanca phlebovims, Punique phlebovims, Punta Toro phlebovims, Rift Valley fever phlebovims, Rio Grande phlebovims, Saint Floris phlebovims, Salanga phlebovims, Salehabad phlebovims, Salobo phlabovims, Sicilian phlebovims, Tapara phlebovims, Tehran phlebovims, Tico phebovims, Toros phlebovims, Toscana phlebovims, Tres Almendras phlebovirus, Turuna phlebovirus, Uriurana phleboviras, Urucuri phlebovirus, Viola phlebovirus, Zerdali phlebovirus, Pidgey pidchovirus, Apple rubodvirus 1, Apple rubodvirus 2, Echinochloahoja blanca tenuivirus, Iranian wheat stripe tenuivirus, Maize stripe tenuivirus, Melon tenuivirus, Rice grassy stunt tenuivirus, Rice hoja blanca tenuivirus, Rice stripe tenuivirus, Urochloa hoja blanca tenuivirus, American dog uukuvirus, Dabieshan uukuvirus, Grand Arbaud uukuvirus, Huangpi uukuvirus, Kabuto mountain uukuvirus, Kaisodi uukuvirus, Lihan uukuvirus, Murre uukuvirus, Pacific coast uukuvirus, Precarious Point uukuvirus, Rukutama uukuvirus, Schmidt uukuvirus, Silverwater uukuvirus, Tacheng uukuvirus, Uukuniemi uukuvirus, Yongjia uukuvirus. Zaliv Terpeniya uukuvims, Shrimp wenrivirus, Alstroemeria necrotic streak orthotospovirus, Alstroemeria yellow spot orthotospovirus, Bean necrotic mosaic orthotospovirus, Calla lily chlorotic spot orthotospovirus, Capsicum chlorosis orthotospovirus, Chrysanthemum stem necrosis orthotospovirus, Groundnut bud necrosis orthotospovirus, Groundnut chlorotic fan spot orthotospovirus, Groundnut ringspot orthotospovirus, Groundnut yellow spot orthotospovirus, Hippeastrum chlorotic ringspot orthotospovirus, Impatiens necrotic spot orthotospovirus, Iris yellow spot orthotospovirus, Melon severe mosaic orthotospovirus, Melon yellow spot orthotospovirus, Mulberry vein banding associated orthotospovirus, Pepper chlorotic spot orthotospovirus, Polygonum ringspot orthotospovirus, Soybean vein necrosis orthotospovirus, Tomato chlorotic spot orthotospovirus, Tomato spotted wilt orthotospovirus, Tomato yellow ring orthotospovirus, Tomato zonate spot orthotospovirus, Watermelon bud necrosis orthotospovirus, Watermelon silver mottle orthotospovirus, Zucchini lethal chlorosis orthotospovirus, Millipede wumivirus, Tilapia tilapinevirus, Influenza A virus, Influenza B virus, Influenza D virus, Influenza C virus, Salmon isavirus, Johnston Atoll quaranjavirus, Quaranfil quaranjavirus, Dhori thogotovirus, Thogoto thogotovirus, Allium cepa amalgavirus 1, Allium cepa amalgavirus 2, Blueberry latent virus, Rhododendron virus A, Southern tomato vims, Spinach amalgavirus 1, Vicia cryptic vims M, Zoostera marina amalgavirus 1, Zoostera marina amalgavims 2, Zygosaccharomyces bailii vims Z, Cryphonectria hypo vims 1, Cryphonectria hypovims 2, Cryphonectria hypovims 3, Cryphonectria hypovims 4, Beet cryptic vims 1, Carrot cryptic vims, Cherry chlorotic rusty spot associated partitivims, Chondrostereum purpureum cryptic vims 1, Flammulina velutipes browning vims, Helicobasidium mompa partitivims V70, Heterobasidion partitivims 1, Heterobasidion partitivims 3, Heterobasidion partitivims 12, Heterobasidion partitivims 13, Heterobasidion partitivims 15, Rosellinia necatrix partitivims 2, Vicia cryptic vims, White clover cryptic vims 1, Atkinsonella hypoxylon vims, Cannabis cryptic vims, Ceratocystis resinifera vims 1, Crimson clover cryptic vims 2, Dill cryptic vims 2,

Fusarium poae vims 1, Heterobasidion partitivims 2, Heterobasidion partitivims 7, Heterobasidion partitivims 8, Heterobasidion partitivims P, Hop trefoil cryptic vims 2, Pleurotus ostreatus vims 1, Primula malacoides vims 1 , Red clover cryptic vims 2, Rhizoctonia solani vims 717, Rosellinia necatrix virus 1, White clover cryptic virus 2, Cryptosporidium parvum virus 1, Beet cryptic virus 2, Beet cryptic virus 3, Fig cryptic virus, Pepper cryptic virus 1, Pepper cryptic virus 2, Aspergillus ochraceous virus, Discula destructiva virus 1, Discula destructiva virus 2, Fusarium solani virus 1, Gremmeniella abietina RNA virus MSI, Ophiostoma partitivirus 1, Penicillium stoloniferum virus F, Penicillium stoloniferum virus S, Agaricus bisporus virus 4, Alfalfa cryptic virus 1, Carnation cryptic virus 1, Carrot temperate virus 1, Carrot temperate vims 2, Carrot temperate vims 3, Carrot temperate vims 4, Gaeumannomyces graminis vims 0196A, Gaeumannomyces graminis vims T1A, Hop trefoil cryptic vims 1, Hop trefoil cryptic vims 3, Radish yellow edge vims, Ryegrass cryptic vims, Spinach temperate vims, White clover cryptic vims 3, Beihai picobimavims, Equine picobimavims, Human picobimavims, Aplysia abyssovims 1, Muarterivims afrigant, Alphaarterivims equid, Lambdaarterivirus afriporav, Deltaarterivims hemfev, Epsilonarterivirus hemcep, Epsilonarterivims safriver, Epsilonarterivims zamalb, Etaarterivims ugarco 1, Iotaarterivims debrazmo, Iotaarterivims kibreg 1, Iotaarterivims pejah, Thetaarterivirus kafuba, Thetaarterivirus mikelba 1, Zetaarterivims ugarco 1, Betaarterivims suid 2, Betaarterivims chinrav 1, Betaarterivirus ninrav, Betaarterivims sheoin, Betaarterivims suid 1, Betaarterivims timiclar, Gammaarterivims lacdeh, Nuaiterivims guemel, Kappaarterivims wobum, Chinturpovims 1, Ptyasnivims 1, Oligodon snake nidovims 1, Microhyla letovims 1, Bat coronavirus CDPHE15, Bat coronavims HKU10, Rhinolophus fermmequinum alphacoronavims HuB-2013, Human coronavims 229E, Lucheng Rn rat coronavims, Mink coronavims 1, Minioptems bat coronavims 1, Minioptems bat coronavims HKU8, Myotis ricketti alphacoronavims Sax-2011, Nyctalus velutinus alphacoronavims SC-2013, Pipistrellus kuhlii coronavims 3398, Porcine epidemic diarrhea vims, Scotophilus bat coronavims 512, Rhinolophus bat coronavims HKU2, Human coronavims NL63, NL63-related bat coronavims strain BtKYNL63-9b, Sorex araneus coronavims T14, Suncus murinus coronavims X74, Alphacoronavims 1, Betacoronavims 1, China Rattus coronavims HKU24, Human coronavims HKU 1, Murine coronavims, Myodes coronavims 2JL14, Bat Hp-betacoronavims Zhejiang2013, Hedgehog coronavims 1, Middle East respiratory syndrome -related coronavims, Pipistrellus bat coronavims HKU5, Tylonycteris bat coronavims HKU4, Eidolon bat coronavims C704, Rousettus bat coronavims GCCDC1, Rousettus bat coronavims HKU9. Severe acute respiratory syndrome-related coronavims, Wigeon coronavims HKU20, Bulbul coronavims HKU11, Common moorhen coronavims HKU21, Coronavims HKU 15, Munia coronavims HKU13, White-eye coronavims HKU16, Night heron coronavims HKU19, Goose coronavims CB17, Beluga whale coronavims SW1, Avian coronavims, Avian coronavims 9203, Duck coronavims 2714, Turrinivims 1, Botrylloides leachii nidovims, Alphamesonivirus 4, Alphamesonivims 8, Alphamesonivims 5, Alphamesonivims 7, Alphamesonivims 2, Alphamesonivims 3,

Alphamesonivims 9, Alphamesonivims 1, Alphamesonivims 10, Alphamesonivims 6, Planidovims 1, Nangarvims 1, Halfbeak nidovims 1, Charybnivims 1, Decronivims 1, Paguronivims 1, Gill-associated virus, Okavirus 1, Yellow head virus, White bream virus, Fathead minnow nidovirus 1, Chinook salmon nidovirus 1, Bovine nidovirus 1, Hebius tobanivirus 1, Infratovirus 1, Lycodon tobanivirus 1, Ball python nidovirus 1, Morelia tobanivirus 1, Berisnavirus 1, Shingleback nidovirus 1, Sectovirus 1, Bovine torovirus, Equine torovirus, Porcine torovirus, Bavaria virus, European brown hare syndrome vims, Rabbit hemorrhagic disease vims, Minovims A, Nacovims A, Newbury 1 vims, Norwalk vims,

Recovims A, Nordland vims, Sapporo vims, Saint Valerien vims, Feline calicivims, Vesicular exanthema of swine vims, Acute bee paralysis vims, Israeli acute paralysis vims, Kashmir bee vims, Mud crab vims, Solenopsis invicta vims 1, Taura syndrome vims, Aphid lethal paralysis vims, Cricket paralysis vims, Drosophila C vims, Rhopalosiphum padi vims, Black queen cell vims, Flimetobi P vims, Homalodisca coagulata vims 1, Plautia stall intestine vims, Triatoma vims, Antheraea pemyi iflavirus, Brevicoryne brassicae vims, Deformed wing vims, Dinocampus coccinellae paralysis vims, Ectropis obliqua vims, Infectious flacherie vims, Lygus lineolaris vims 1, Lymantria dispar iflavirus 1, Nilaparvata lugens honeydew vims 1, Perina nuda vims, Sacbrood vims, Slow bee paralysis vims, Spodoptera exigua iflavirus 1, Spodoptera exigua iflavirus 2, Varroa destmctor vims 1, Chaetoceros socialis forma radians RNA vims 1, Chaetoceros tenuissimus RNA vims 01, Rhizosolenia setigera RNA vims 01, Astamavirus, Aurantiochytrium single-stranded RNA vims 01, Jericamavims B, Sanfamavirus 1, Sanfamavirus 2, Sanfamavims 3, Heterosigma akashiwo RNA vims, Britamavirus 1, Britamavims 4, Palmamavims 128, Palmamavims 473, Britamavims 2, Britamavims 3, Chaetamavims 2, Chaetenuissamavims II, Jericamavims A, Palmamavims 156, Aalivims A, Ailurivims A, Ampivims A, Anativims A, Anativims B, Bovine rhinitis A vims, Bovine rhinitis B vims, Equine rhinitis A vims, Foot-and-mouth disease vims, Aquamavirus A, Avihepatovims A, Avisivims A, Avisivims B, Avisivims C, Boosepivims A, Boosepivims B, Boosepivims C, Bopivims A, Cardiovims A, Cardiovims B, Cardiovims C, Cardiovims

D, Cardiovims E, Cardiovims F, Cosavims A, Cosavims B, Cosavims D, Cosavims E, Cosavims F, Crahelivims A, Crohivims A, Crohivims B, Cadicivims A, Cadiciviras B, Diresapivims A, Diresapivims B, Enterovims A, Enterovirus B, Enterovims C, Enterovims D, Enterovims E, Enterovims F, Enterovims G, Enterovims H, Enterovims I, Enterovims J, Enterovims K, Enterovims L, Rhinovims A, Rhinovims B, Rhinovims C, Erbovims A, Felipivims A, Fipivims A, Fipivims B, Fipivims C, Fipivims D, Fipivims

E, Gallivims A, Gmhelivims A, Gmsopivims A, Gmsopivims B, Harkavims A, Hemipivims A, Hepatovims A, Hepatovims B, Hepatovims C, Hepatovims D, Hepatovims E, Hepatovims F,

Hepatovims G, Hepatovims H, Hepatovims I, Hunnivims A, Aichivims A, Aichivims B, Aichivims C, Aichivims D, Aichivims E, Aichivims F, Kunsagivims A, Kunsagivims B, Kunsagivims C, Limnipivims A, Limnipivims B, Limnipivims C, Livupivims A, Ludopivims A, Malagasivims A, Malagasivims B, Megrivims A, Megrivims B, Megrivims C, Megrivims D, Megrivims E, Mischivims A, Mischivims B, Mischivims C, Mischivims D, Mosavims A, Mosavims B, Mupivims A, Myrropivims A, Orivims A, Oscivirus A, Parabovirus A, Parabovirus B, Parabovirus C, Parechovirus A, Parechoviras B, Parechovirus C, Parechovirus D, Parechovirus E, Parechovirus F, Pasivirus A, Passerivirus A, Passerivirus B, Pemapivirus A, Poecivirus A, Potamipivirus A, Potamipivirus B, Rabovirus A, Rabovirus B, Rabovirus C, Rabovirus D, Rafivirus A, Rafivirus B, Rafivirus C, Rohelivirus A, Rosavirus A, Rosavirus B, Rosavirus C, Sakobuvirus A, Salivirus A, Sapelovirus A, Sapelovirus B, Senecavirus A, Shanbavirus A, Sicinivirus A, Symapivirus A, Teschovirus A, Teschovirus B, Torchivirus A, Tottorivirus A, Tremovirus A, Tremovirus B, Tropivirus A, Chironomus riparius vims 1, Hubei chipolycivirus, Hubei hupolycivims, Formica exsecta vims 3, Lasius neglectus vims 1, Lasius neglectus vims 2, Lasius niger vims 1, Linepithema humile vims 2, Monomorium pharaonis vims 1, Monomorium pharaonis vims 2, Myrmica scabrinodis vims 1, Shuangao insect vims 8, Solenopsis invicta vims 2, Solenopsis invicta vims 4, Andean potato mottle vims, Bean pod mottle vims, Bean mgose mosaic vims, Broad bean stain vims, Broad bean tme mosaic vims, Cowpea mosaic vims, Cowpea severe mosaic vims, Glycine mosaic vims, Pea green mottle vims, Pea mild mosaic vims, Quail pea mosaic vims, Radish mosaic vims, Red clover mottle vims, Squash mosaic vims, Ullucus vims C, Broad bean wilt vims 1, Broad bean wilt vims 2, Cucurbit mild mosaic vims, Gentian mosaic vims, Grapevine fabavims, Lamium mild mosaic vims, Pmnus vims F, Aeonium ringspot vims, Apricot latent ringspot vims, Arabis mosaic vims, Arracacha vims A, Artichoke Aegean ringspot vims, Artichoke Italian latent vims, Artichoke yellow ringspot vims, Beet ringspot vims, Blackcurrant reversion vims, Blueberry latent spherical vims, Blueberry leaf mottle vims, Cassava American latent vims, Cassava green mottle vims, Cherry leaf roll vims, Chicory yellow mottle vims, Cocoa necrosis vims, Crimson clover latent vims, Cycas necrotic stunt vims, Grapevine Anatolian ringspot vims, Grapevine Bulgarian latent vims, Grapevine chrome mosaic vims, Grapevine deformation vims, Grapevine fanleaf vims, Grapevine Tunisian ringspot vims, Hibiscus latent ringspot vims, Lucerne Australian latent vims, Melon mild mottle vims, Mulberry mosaic leaf roll associated vims, Mulberry ringspot vims, Myrobalan latent ringspot vims, Olive latent ringspot vims, Peach rosette mosaic vims, Potato black ringspot vims, Potato vims B, Potato vims U, Raspberry ringspot vims, Soybean latent spherical vims, Tobacco ringspot vims, Tomato black ring vims, Tomato ringspot vims, Apple latent spherical vims, Arracacha vims B, Cherry rasp leaf vims, Currant latent vims, Stocky pmne vims, Chocolate lily vims A, Dioscorea mosaic associated vims, Satsuma dwarf vims, Black raspberry necrosis vims, Strawberry mottle vims, Carrot necrotic dieback vims, Dandelion yellow mosaic vims, Parsnip yellow fleck vims, Carrot torradovims 1, Lettuce necrotic leaf curl vims, Motherwort yellow mottle vims, Squash chlorotic leaf spot vims, Tomato marchitez vims, Tomato tornado vims, Anthriscus yellows vims, Bellflower vein chlorosis vims, Maize chlorotic dwarf vims, Rice tungro spherical vims, Strawberry latent ringspot vims, Solenopsis invicta vims 3, Nylanderia fulva vims 1, Heterocapsa circularisquama RNA vims 01, Mushroom bacilliform vims, Poinsettia latent vims, Artemisia vims A, Blueberry shoestring virus, Cocksfoot mottle virus, Cymbidium chlorotic mosaic virus, Imperata yellow mottle virus, Lucerne transient streak virus, Papaya lethal yellowing virus, Rice yellow mottle virus, Rottboellia yellow mottle virus, Ryegrass mottle virus, Sesbania mosaic virus, Solanum nodiflorum mottle vims, Southern bean mosaic vims, Southern cowpea mosaic vims, Sowbane mosaic vims,

Soybean yellow common mosaic vims, Subterranean clover mottle vims, Turnip rosette vims, Velvet tobacco mottle vims, Areca palm necrotic ringspot vims, Areca palm necrotic spindle-spot vims, Bellflower veinal mottle vims, Blackberry vims Y, Barley mild mosaic vims, Barley yellow mosaic vims, Oat mosaic vims, Rice necrosis mosaic vims, Wheat spindle streak mosaic vims, Wheat yellow mosaic vims, Celery latent vims, Cassava brown streak vims, Coccinia mottle vims, Cucumber vein yellowing vims, Squash vein yellowing vims, Sweet potato mild mottle vims, Tomato mild mottle vims, Ugandan cassava brown streak vims, Alpinia mosaic vims, Alpinia oxyphylla mosaic vims, Artichoke latent vims, Broad-leafed dock vims A, Cardamom mosaic vims, Chinese yam necrotic mosaic vims, Maclura mosaic vims, Narcissus latent vims, Yam chlorotic mosaic vims, Yam chlorotic necrosis vims, Caladenia vims A, Sugarcane streak mosaic vims, Triticum mosaic vims, African eggplant mosaic vims, Algerian watermelon mosaic vims, Alstroemeria mosaic vims, Altemanthera mild mosaic vims, Amaranthus leaf mottle vims, Amazon lily mosaic vims, Angelica vims Y, Apium vims Y, Araujia mosaic vims, Arracacha mottle vims, Asparagus vims 1, Banana bract mosaic vims, Barbacena vims Y, Basella mgose mosaic vims, Bean common mosaic necrosis vims, Bean common mosaic vims, Bean yellow mosaic vims, Beet mosaic vims, Bidens mosaic vims, Bidens mottle vims, Blue squill vims A, Bmgmansia mosaic vims, Bmgmansia suaveolens mottle vims, Butterfly flower mosaic vims, Calanthe mild mosaic vims, Calla lily latent vims, Callistephus mottle vims, Canna yellow streak vims, Carnation vein mottle vims, Carrot thin leaf vims, Carrot vims Y, Catharanthus mosaic vims, Celery mosaic vims, Ceratobium mosaic vims, Chilli ringspot vims, Chilli veinal mottle vims, Chinese artichoke mosaic vims, Clitoria vims Y, Clover yellow vein vims, Cocksfoot streak vims, Colombian datura vims, Commelina mosaic vims, Cowpea aphid-bome mosaic vims, Cucurbit vein banding vims, Cypripedium vims Y, Cyrtanthus elatus vims A, Daphne mosaic vims, Daphne vims Y, Dasheen mosaic vims, Datura shoestring vims, Dendrobium chlorotic mosaic vims, Dioscorea mosaic vims, Diuris vims Y, Donkey orchid vims A, East Asian Passiflora distortion vims, East Asian Passiflora vims, Endive necrotic mosaic vims, Euphorbia ringspot vims, Freesia mosaic vims, Fritillary vims Y, Gloriosa stripe mosaic vims, Gomphocarpus mosaic vims, Habenaria mosaic vims, Flardenbergia mosaic vims, Henbane mosaic vims, Hibbertia vims Y, Hippeastmm mosaic vims, Hyacinth mosaic vims, Impatiens flower break vims, Iris fiilva mosaic vims, Iris mild mosaic vims, Ins severe mosaic vims, Japanese yam mosaic vims, Jasmine vims T, Johnsongrass mosaic vims, Kalanchoe mosaic vims, Keunjorong mosaic vims, Konjac mosaic vims,

Leek yellow stripe vims, Lettuce Italian necrotic vims, Lettuce mosaic vims, Lily mottle vims, Lily vims Y, Lupinus mosaic virus, Lycoris mild mottle virus, Maize dwarf mosaic vims, Malva vein clearing vims, Mashua vims Y, Meadow saffron breaking vims, Mediterranean mda vims, Moroccan watermelon mosaic vims, Narcissus degeneration vims, Narcissus late season yellows vims, Narcissus yellow stripe vims, Nerine yellow stripe vims, Nothoscordum mosaic vims, Onion yellow dwarf vims, Omithogalum mosaic vims, Omithogalum vims 2, Omithogalum vims 3, Panax vims Y, Papaya leaf distortion mosaic vims, Papaya ringspot vims, Paris mosaic necrosis vims, Parsnip mosaic vims, Passiflora chlorosis vims, Passion fruit woodiness vims, Pea seed-borne mosaic vims, Peanut mottle vims, Pecan mosaic-associated vims, Pennisetum mosaic vims, Pepper mottle vims, Pepper severe mosaic vims, Pepper veinal mottle vims, Pepper yellow mosaic vims, Pern tomato mosaic vims, Pfaffia mosaic vims, Platycodon mild mottle vims, Pleione vims Y, Plum pox vims, Pokeweed mosaic vims, Potato vims A, Potato vims V, Potato vims Y, Potato yellow blotch vims, Ranunculus leaf distortion vims, Ranunculus mild mosaic vims, Ranunculus mosaic vims, Rhopalanthe vims Y, Saffron latent vims, Sarcochilus vims Y, Scallion mosaic vims, Shallot yellow stripe vims, Sorghum mosaic vims, Soybean mosaic vims, Spiranthes mosaic vims 3, Sudan watermelon mosaic vims, Sugarcane mosaic vims, Sunflower chlorotic mottle vims, Sunflower mild mosaic vims, Sunflower mosaic vims, Sunflower ring blotch vims, Sweet potato feathery mottle vims, Sweet potato latent vims, Sweet potato mild speckling vims, Sweet potato vims 2, Sweet potato vims C, Sweet potato vims G, Tamarillo leaf malformation vims, Telfairia mosaic vims, Telosma mosaic vims, Thunberg fritillary mosaic vims, Tobacco etch vims, Tobacco mosqueado vims, Tobacco vein banding mosaic vims, Tobacco vein mottling vims, Tomato necrotic stunt vims, Tradescantia mild mosaic vims, Tuberose mild mosaic vims, Tuberose mild mottle vims, Tulip breaking vims, Tulip mosaic vims, Turnip mosaic vims, Twisted-stalk chlorotic streak vims, Vallota mosaic vims, Vanilla distortion mosaic vims, Verbena vims Y, Watermelon leaf mottle vims, Watermelon mosaic vims, Wild melon banding vims, Wild onion symptomless vims, Wild potato mosaic vims, Wild tomato mosaic vims, Wisteria vein mosaic vims, Yam mild mosaic vims, Yam mosaic vims, Yambean mosaic vims, Zantedeschia mild mosaic vims, Zea mosaic vims, Zucchini shoestring vims, Zucchini tigre mosaic vims, Zucchini yellow fleck vims, Zucchini yellow mosaic vims, Passiflora edulis symptomless vims, Rose yellow mosaic vims, Agropyron mosaic vims, Hordeum mosaic vims, Ryegrass mosaic vims, Brome streak mosaic vims, Oat necrotic mottle vims, Tall oatgrass mosaic vims, Wheat eqlid mosaic vims, Wheat streak mosaic vims, Yellow oat grass mosaic vims, Common reed chlorotic stripe vims, Longan witches broom-associated vims, Spartma mottle vims, Avastrovims 1, Avastrovims 2, Avastrovims 3, Mamastrovims 1, Mamastrovims 2, Mamastrovims 3, Mamastrovims 4, Mamastrovims 5, Mamastrovims 6, Mamastrovims 7, Mamastrovims 8, Mamastrovims 9, Mamastrovims 10, Mamastrovims 11, Mamastrovims 12, Mamastrovims 13, Mamastrovims 14, Mamastrovims 15, Mamastrovims 16, Mamastrovims 17, Mamastrovims 18, Mamastrovims 19, Infectious pancreatic necrosis virus, Tellina virus, Yellowtail ascites virus, Infectious bursal disease virus, Blotched snakehead virus, Lates calcarifer bimavirus, Drosophina B bimavirus, Drosophila X virus, Mosquito X virus, Rotifer bimavirus, Tellina virus 1, Euprostema elaeasa virus, Thosea asigna virus, Botrytis porri botybimavirus 1, Duck hepatitis B virus, Heron hepatitis B virus, Parrot hepatitis B virus, Tibetan frog hepatitis B virus, Blue gill hepatitis B virus, Capuchin monkey hepatitis B vims, Chinese shrew hepatitis B vims, Domestic cat hepatitis B vims, Ground squirrel hepatitis vims, Hepatitis B vims, Long-fingered bat hepatitis B vims, Pomona bat hepatitis B vims, Roundleaf bat hepatitis B vims, Tai Forest hepatitis B vims, Tent making bat hepatitis B vims, Woodchuck hepatitis vims, Woolly monkey hepatitis B vims, White sucker hepatitis B vims, Anopheles gambiae Moose vims, Antheraea semotivims Tamy, Ascaris lumbricoides Tas vims, Bombyx mori Pao vims, Caenorhabditis elegans Cerl3 vims, Drosophila melanogaster Bel vims, Drosophila melanogaster Roo vims, Drosophila semotivims Max, Drosophila simulans Ninja vims, Schistosoma semotivims Sinbad, Takifiigu mbripes Suzu vims, Aglaonema bacilliform vims, Banana streak GF vims, Banana streak IM vims, Banana streak MY vims, Banana streak OL vims, Banana streak UA vims, Banana streak UI vims, Banana streak UL vims, Banana streak UM vims, Banana streak VN vims, Birch leaf roll-associated vims, Blackberry vims F, Bougainvillea chlorotic vein banding vims, Cacao bacilliform Sri Lanka vims, Cacao mild mosaic vims, Cacao swollen shoot CD vims, Cacao swollen shoot CE vims, Cacao swollen shoot Ghana M vims, Cacao swollen shoot Ghana N vims, Cacao swollen shoot Ghana Q vims, Cacao swollen shoot Togo A vims, Cacao swollen shoot Togo B vims, Cacao yellow vein banding vims, Canna yellow mottle associated vims, Canna yellow mottle vims,

Citms yellow mosaic vims, Codonopsis vein clearing vims, Commelina yellow mottle vims, Dioscorea bacilliform AL vims, Dioscorea bacilliform AL vims 2, Dioscorea bacilliform ES vims, Dioscorea bacilliform RT vims 1, Dioscorea bacilliform RT vims 2, Dioscorea bacilliform SN vims, Dioscorea bacilliform TR vims, Fig badnavims 1, Gooseberry vein banding associated vims, Grapevine badnavims 1, Grapevine Roditis leaf discoloration-associated vims, Grapevine vein clearing vims, Jujube mosaic- associated vims, Kalanchoe top-spotting vims, Mulberry badnavims 1, Pagoda yellow mosaic associated vims, Pineapple bacilliform CO vims, Pineapple bacilliform ER vims, Piper yellow mottle vims, Rubus yellow net vims, Schefflera ringspot vims, Spiraea yellow leafspot vims, Sugarcane bacilliform Guadeloupe A vims, Sugarcane bacilliform Guadeloupe D vims, Sugarcane bacilliform IM vims, Sugarcane bacilliform MO vims, Sweet potato pakakuy vims, Taro bacilliform CH vims, Taro bacilliform vims, Wisteria badnavims 1, Yacon necrotic mottle vims, Angelica bushy stunt vims, Atractylodes mild mottle vims, Carnation etched ring vims, Cauliflower mosaic vims, Dahlia mosaic vims, Figwort mosaic vims, Horseradish latent vims, Lamium leaf distortion vims, Mirabilis mosaic vims, Rudbeckia flower distortion vims, Soybean Putnam vims, Strawberry vein banding vims, Thistle mottle vims, Cassava vein mosaic vims, Sweet potato collusive vims, Dioscorea nummularia associated virus, Petunia vein clearing virus, Rose yellow vein virus, Sweet potato vein clearing virus, Tobacco vein clearing virus, Blueberry red ringspot virus, Cestrum yellow leaf curling virus, Peanut chlorotic streak virus, Soybean chlorotic mottle vims, Rice tungro bacilliform vims, Blueberry fruit drop associated vims, Ceratitis capitata Yoyo vims, Drosophila ananassae Tom vims, Drosophila melanogaster 17-6 vims, Drosophila melanogaster 297 vims, Drosophila melanogaster Gypsy vims, Drosophila melanogaster Idefix vims, Drosophila melanogaster Tirant vims, Drosophila melanogaster Zam vims, Drosophila virilis Tvl vims, Trichoplusia ni TED vims, Arabidopsis thaliana Athila vims, Arabidopsis thaliana Tat4 vims, Bombyx mori Mag vims, Caenorhabditis elegans Cerl vims, Cladosporium ftilvum T-l vims, Dictyostelium discoideum Skipper vims, Drosophila buzzatii Osvaldo vims, Drosophila melanogaster 412 vims, Drosophila melanogaster Blastopia vims, Drosophila melanogaster Mdgl vims, Drosophila melanogaster Mdg3 vims, Drosophila melanogaster Micropia vims, Drosophila virilis Ulysses vims, Fusarium oxysporum Skippy vims, Lilium henryi Dell vims, Saccharomyces cerevisiae Ty3 vims, Schizosaccharomyces pombe Tfl vims, Schizosaccharomyces pombe Tf2 vims, Takifugu mbripes Sushi vims, Tribolium castaneum Woot vims, Tripneustis gratilla SURL vims, Aedes aegypti Mosqcopia vims, Candida albicans Tca2 vims, Candida albicans Tca5 vims, Drosophila melanogaster 1731 vims, Drosophila melanogaster copia vims, Saccharomyces cerevisiae Ty5 vims, Volvox carteri Lueckenbuesser vims, Volvox carteri Osser vims, Arabidopsis thaliana Aril vims, Arabidopsis thaliana AtREl vims, Arabidopsis thaliana evelknievel vims, Arabidopsis thaliana Tal vims, Brassica oleracea Melmoth vims, Cajanus cajan Panzee vims, Glycine max Tgmr vims, Hordeum vulgare BARE-1 vims, Nicotiana tabacum Tntl vims, Nicotiana tabacum Ttol vims, Oryza australiensis RIREl vims, Oryza longistaminata Retrofit vims, Physamm polycephalum Tpl vims, Saccharomyces cerevisiae Tyl vims, Saccharomyces cerevisiae Ty2 vims, Saccharomyces cerevisiae Ty4 vims, Solanum tuberosum Tstl vims, Triticum aestivum WIS2 vims, Zea mays Hopscotch vims, Zea mays Sto4 vims, Arabidopsis thaliana Endovir vims, Glycine max SIREl vims, Lycopersicon esculentum ToRTLl vims, Zea mays Opie2 vims, Zea mays Prem2 vims, Phaseolus vulgaris Tpv2-6 vims, Avian carcinoma Mill Hill vims 2, Avian leukosis vims, Avian myeloblastosis vims, Avian myelocytomatosis vims 29, Avian sarcoma vims CT10, Fujmami sarcoma vims, Rous sarcoma vims, UR2 sarcoma vims, Y73 sarcoma vims, Jaagsiekte sheep retrovims, Langur vims, Mason-Pfizer monkey vims, Mouse mammary tumor vims, Squirrel monkey retrovims, Bovine leukemia vims, Primate T-lymphotropic vims 1, Primate T-lymphotropic vims 2, Primate T-lymphotropic vims 3, Walleye dermal sarcoma vims, Walleye epidermal hyperplasia vims 1, Walleye epidermal hyperplasia vims 2, Chick syncytial vims, Feline leukemia vims, Finkel- Biskis-Jmkins murine sarcoma vims, Gardner- Amstein feline sarcoma vims, Gibbon ape leukemia vims, Guinea pig type-C oncovims, Hardy-Zuckerman feline sarcoma vims, Harvey murine sarcoma vims, Kirsten murine sarcoma vims, Koala retrovims, Moloney murine sarcoma vims, Murine leukemia vims, Porcine type-C oncovirus, Reticuloendotheliosis virus, Snyder-Theilen feline sarcoma virus, Trager duck spleen necrosis virus, Viper retrovirus, Woolly monkey sarcoma virus, Bovine immunodeficiency virus, Caprine arthritis encephalitis virus, Equine infectious anemia virus, Feline immunodeficiency vims, Human immunodeficiency vims 1, Human immunodeficiency vims 2, Jembrana disease vims, Puma lentivims, Simian immunodeficiency vims, Visna-maedi vims, Bovine foamy vims, Equine foamy vims, Feline foamy vims, Brown greater galago prosimian foamy vims, Bornean orangutan simian foamy vims, Central chimpanzee simian foamy vims, Cynomolgus macaque simian foamy vims, Eastern chimpanzee simian foamy vims, Grivet simian foamy vims, Guenon simian foamy vims, Japanese macaque simian foamy vims, Rhesus macaque simian foamy vims, Spider monkey simian foamy vims, Squirrel monkey simian foamy vims, Taiwanese macaque simian foamy vims, Western chimpanzee simian foamy vims, Western lowland gorilla simian foamy vims, White -tufted-ear marmoset simian foamy vims, Yellow breasted capuchin simian foamy vims, Aspergillus fiimigatus polymycovims 1, Aspergillus spelaeus polymycovims 1, Beauveria bassiana polymycovims 1, Botryoshaeria dothidea polymycovims 1, Cladosporium cladosporioides polymycovims 1, Colletotrichum camelliae polymycovims 1, Fusarium redolens polymycovims 1, Magnaporthe oryzae polymycovims 1, Penicillium digitatum polymycovims 1, Penicillum brevicompactum polymycovims 1, Macrobrachium satellite vims 1, Tobacco albetovims 1, Tobacco albetovims 2, Tobacco albetovims 3, Maize aumaivims 1, Panicum papanivims 1, Tobacco virtovims 1, Acanthocystis turfacea chlorella vims 1, Hydra viridis Chlorella vims 1, Paramecium bursaria Chlorella vims 1, Paramecium bursaria Chlorella vims Al, Paramecium bursaria Chlorella vims ALIA, Paramecium bursaria Chlorella vims AL2A, Paramecium bursaria Chlorella vims BJ2C, Paramecium bursaria Chlorella vims CA4A, Paramecium bursaria Chlorella vims CA4B, Paramecium bursaria Chlorella vims IL3A, Paramecium bursaria Chlorella vims NCI A, Paramecium bursaria Chlorella vims NE8A, Paramecium bursaria Chlorella vims NY2A, Paramecium bursaria Chlorella vims NYsl, Paramecium bursaria Chlorella vims SCI A, Paramecium bursaria Chlorella vims XY6E, Paramecium bursaria Chlorella vims XZ3A, Paramecium bursaria Chlorella vims XZ4A, Paramecium bursaria Chlorella vims XZ4C, Emiliania huxleyi vims 86, Ectocarpus fasciculatus vims a, Ectocarpus siliculosus vims 1, Ectocarpus siliculosus vims a, Feldmannia irregularis vims a, Feldmannia species vims, Feldmannia species vims a, Hincksia hmckiae vims a, Myriotrichia clavaeformis vims a, Pilayella littoralis vims 1, Micromonas pusilla vims SP1, Ostreococcus tauri vims OtV5, Chrysochromulina brevifilum vims PW1, Heterosigma akashiwo vims 01, Cafeteria roenbergensis vims, Acanthamoeba polyphaga mimivims, Heliothis virescens ascovims 3a, Spodoptera fmgiperda ascovims la, Trichoplusia ni ascovims 2a, Diadromus pulchellus toursvims, Lymphocystis disease vims 1, Lymphocystis disease vims 2, Lymphocystis disease vims 3, Infectious spleen and kidney necrosis vims, Scale drop disease vims, Ambystoma tigrinum vims, Common midwife toad vims, Epizootic haematopoietic necrosis vims, Frog virus 3, Santee-Cooper ranavirus, Singapore grouper iridovirus, Anopheles minimus iridovirus, Invertebrate iridescent virus 3, Invertebrate iridescent virus 9, Invertebrate iridescent virus 22,

Invertebrate iridescent virus 25, Decapod iridescent virus 1, Invertebrate iridescent vims 6, Invertebrate iridescent vims 31, Marseillevims marseillevirus, Senegalvims marseillevirus, Lausannevims, Tunisvims, African swine fever vims, Canarypox vims, Flamingopox vims, Fowlpox vims, Juncopox vims, Mynahpox vims, Penguinpox vims, Pigeonpox vims, Psittacinepox vims, Quailpox vims, Sparrowpox vims, Starlingpox vims, Turkeypox vims, Goatpox vims, Lumpy skin disease vims, Sheeppox vims, Murmansk microtuspox vims, Yokapox vims, Mule deerpox vims, Nile crocodilepox vims, Hare fibroma vims, Myxoma vims, Rabbit fibroma vims, Squirrel fibroma vims, Eastern kangaroopox vims, Western kangaroopox vims, Molluscum contagiosum vims, Sea otterpox vims, Abatino macacapox vims, Akhmeta vims, Camelpox vims, Cowpox vims, Ectromelia vims, Monkeypox vims, Raccoonpox vims, Skunkpox vims, Taterapox vims, Vaccinia vims, Variola vims, Volepox vims, Cotia vims, Bovine papular stomatitis vims, Grey sealpox vims, Orf vims, Pseudocowpox vims, Red deerpox vims, Pteropox vims, Salmon gillpox vims, Squirrelpox vims, Swinepox vims, Eptesipox vims, Tanapox vims, Yaba monkey tumor vims, Anomala cuprea entomopoxvims, Aphodius tasmaniae entomopoxvims, Demodema bonariensis entomopoxvims, Dermolepida albohirtum entomopoxvims, Figulus sublaevis entomopoxvims, Geotmpes sylvaticus entomopoxvims, Melolontha melolontha entomopoxvims, Acrobasis zelleri entomopoxvims, Adoxophyes honmai entomopoxvims, Amsacta moorei entomopoxvims, Arphia conspersa entomopoxvims, Choristoneura biennis entomopoxvims, Choristoneura conflicta entomopoxvims, Choristoneura diversuma entomopoxvims, Choristoneura fumiferana entomopoxvims, Choristoneura rosaceana entomopoxvims, Chorizagrotis auxiliaris entomopoxvims, Heliothis armigera entomopoxvims, Locusta migratoria entomopoxvims, Mythimna separata entomopoxvims, Oedaleus senegalensis entomopoxvims, Operophtera brumata entomopoxvims, Schistocerca gregaria entomopoxvims, Melanoplus sanguinipes entomopoxvims, Aedes aegypti entomopoxvims, Camptochironomus tentans entomopoxvims, Chironomus attenuatus entomopoxvims, Chironomus luridus entomopoxvims, Chironomus plumosus entomopoxvims, Goeldichironomus holoprasinus entomopoxvims, Diachasmimorpha entomopoxvims, Cafeteriavims-dependent mavims, Mimivims-dependent vims Sputnik, Mimivims-dependent vims Zamilon, Sulfolobus turreted icosahedral vims 1, Sulfolobus turreted icosahedral vims 2, Pseudomonas vims PR4, Pseudomonas vims PRDl, Bacillus vims AP50, Bacillus vims Bam35, Bacillus vims GIL16, Bacillus vims Wipl, Gluconobacter vims GC1, Bovine atadenovims D, Deer atadenovims A, Duck atadenovims A, Lizard atadenovims A, Ovine atadenovims D, Possum atadenovims A, Psittacine atadenovims A, Snake atadenovims A, Duck aviadenovims B, Falcon aviadenovims A, Fowl aviadenovims A, Fowl aviadenovims B, Fowl aviadenovims C, Fowl aviadenovims D, Fowl aviadenovims E, Goose aviadenovims A, Pigeon aviadenovirus A, Pigeon aviadenovirus B, Psitacme aviadenovirus B, Psitacine aviadenoviras C, Turkey aviadenovirus B, Turkey aviadenovirus C, Turkey aviadenovirus D, Sturgeon ichtadenovirus A, Bat mastadenovirus A, Bat mastadenovirus B, Bat mastadenovirus C, Bat mastadenovirus D, Bat mastadenovirus E, Bat mastadenovirus F, Bat mastadenovirus G, Bat mastadenovirus H, Bat mastadenovirus I, Bat mastadenovirus J, Bovine mastadenovirus A, Bovine mastadenovirus B, Bovine mastadenovirus C, Canine mastadenovirus A, Deer mastadenovirus B, Dolphin mastadenovirus A, Dolphin mastadenovirus B, Equine mastadenovirus A, Equine mastadenovirus B, Human mastadenovirus A, Human mastadenovirus B, Human mastadenovirus C, Human mastadenovirus D, Human mastadenovirus E, Human mastadenovirus F, Human mastadenovirus G, Murine mastadenovirus A, Murine mastadenovirus B, Murine mastadenovirus C, Ovine mastadenovirus A, Ovine mastadenovirus B, Ovine mastadenovirus C, Platyrrhini mastadenovirus A, Polar bear mastadenovirus A, Porcine mastadenovirus A, Porcine mastadenovirus B, Porcine mastadenovirus C, Sea lion mastadenovirus A, Simian mastadenovirus A, Simian mastadenovirus B, Simian mastadenovirus C, Simian mastadenovirus D, Simian mastadenovirus E, Simian mastadenovirus F, Simian mastadenovirus G, Simian mastadenovirus H, Simian mastadenovirus I, Skunk mastadenovirus A, Squirrel mastadenovirus A, Tree shrew mastadenovirus A, Frog siadenovirus A, Great tit siadenovirus A, Penguin siadenovirus A, Raptor siadenovirus A, Skua siadenovirus A, Turkey siadenovirus A, Pseudoalteromonas virus Cr39582, Pseudoalteromonas virus PM2, Haloarcula hispanica icosahedral virus 2, Haloarcula hispanica virus PHI, Haloarcula hispanica virus SHI, Haloarcula virus HCIVl, Natrinema virus SNJ1, Thermus virus IN93, Thermus virus P23-77, Alphalipothrixvirus SBFV2, Alphalipothrixvirus SFV1, Acidianus filamentous virus 3, Acidianus filamentous virus 6, Acidianus filamentous virus 7, Acidianus filamentous virus 8, Acidianus filamentous virus 9, Sulfolobus islandicus filamentous virus, Acidianus filamentous virus 2, Deltalipothrixvirus SBFV3, Acidianus filamentous virus 1, Acidianus rod-shaped virus 1, Sulfolobus islandicus rod-shaped vims 1, Sulfolobus islandicus rod-shaped vims 2, Ageratum yellow vein Singapore alphasatellite, Cotton leaf curl Saudi Arabia alphasatellite, Ash gourd yellow vein mosaic alphasatellite, Capsicum India alphasatellite, Cleome leaf crumple alphasatellite, Croton yellow vein mosaic alphasatellite, Euphorbia yellow mosaic alphasatellite, Melon chlorotic mosaic alphasatellite, Sida Cuba alphasatellite, Tomato leaf curl New Delhi alphasatellite, Tomato leaf curl Vimdhunagar alphasatellite, Tomato yellow spot alphasatellite, Whitefly associated Guatemala alphasatellite 2, Whitefly associated Puerto Rico alphasatellite 1, Ageratum enation alphasatellite, Ageratum yellow vein alphasatellite, Ageratum yellow vein China alphasatellite, Ageratum yellow vein India alphasatellite, Bhendi yellow vein alphasatellite, Cassava mosaic Madagascar alphasatellite, Chilli leaf curl alphasatellite, Cotton leaf curl Egypt alphasatellite, Cotton leaf curl Gezira alphasatellite, Cotton leaf curl Lucknow alphasatellite, Cotton leaf curl Multan alphasatellite, Gossypium darwinii symptomless alphasatellite, Malvastmm yellow mosaic alphasatellite, Malvastrum yellow mosaic Cameroon alphasatellite, Pedilanthus leaf curl alphasatellite, Sida leaf curl alphasatellite, Sida yellow vein Vietnam alphasatellite, Sunflower leaf curl Karnataka alphasatellite, Synedrella leaf curl alphasatellite, Tobacco curly shoot alphasatellite, Tomato leaf curl Buea alphasatellite, Tomato leaf curl Cameroon alphasatellite, Tomato leaf curl Pakistan alphasatellite, Tomato yellow leaf curl China alphasatellite, Tomato yellow leaf curl Thailand alphasatellite, Tomato yellow leaf curl Yunnan alphasatellite, Eclipta yellow vein alphasatellite, Gossypium mustelinum symptomless alphasatellite, Hollyhock yellow vein alphasatellite, Mesta yellow vein mosaic alphasatellite, Okra enation leaf curl alphasatellite, Okra yellow crinkle Cameroon alphasatellite, Vemonia yellow vein Fujian alphasatellite, Dragonfly associated alphasatellite, Whitefly associated Guatemala alphasatellite 1, Banana bunchy top alphasatellite 1, Banana bunchy top alphasatellite 2, Banana bunchy top alphasatellite 3, Cardamom bushy dwarf alphasatellite, Milk vetch dwarf alphasatellite 2, Pea necrotic yellow dwarf alphasatellite 2, Sophora yellow stunt alphasatellite 4, Sophora yellow stunt alphasatellite 5, Subterranean clover stunt alphasatellite 2, Faba bean necrotic yellows alphasatellite 2, Milk vetch dwarf alphasatellite 3, Faba bean necrotic stunt alphasatellite, Milk vetch dwarf alphasatellite 1, Pea necrotic yellow dwarf alphasatellite 1, Sophora yellow stunt alphasatellite 2, Cow vetch latent alphasatellite, Sophora yellow stunt alphasatellite 3, Faba bean necrotic yellows alphasatellite 1, Faba bean necrotic yellows alphasatellite 3, Sophora yellow stunt alphasatellite 1, Subterranean clover stunt alphasatellite 1, Coconut foliar decay alphasatellite, Acidianus bottle-shaped virus, Torque teno vims 1, Torque teno vims 2, Torque teno vims 3, Torque teno vims 4, Torque teno vims 5, Torque teno vims 6, Torque teno vims 7, Torque teno vims 8, Torque teno vims 9, Torque teno vims 10, Torque teno vims 11, Torque teno vims 12, Torque teno vims 13, Torque teno vims 14, Torque teno vims 15, Torque teno vims 16, Torque teno vims 17, Torque teno vims 18, Torque teno vims 19, Torque teno vims 20, Torque teno vims 21, Torque teno vims 22, Torque teno vims 23, Torque teno vims 24, Torque teno vims 25, Torque teno vims 26, Torque teno vims 27, Torque teno vims 28, Torque teno vims 29, Torque teno mini vims 1, Torque teno mini vims 2, Torque teno mini vims 3, Torque teno mini vims 4, Torque teno mini vims 5, Torque teno mini vims 6, Torque teno mini vims 7, Torque teno mini vims 8, Torque teno mini vims 9, Torque teno mini vims 10, Torque teno mini vims 11, Torque teno mini vims 12, Torque teno tupaia vims, Torque teno tamarin vims, Torque teno felis vims, Torque teno felis vims 2, Torque teno midi vims 1, Torque teno midi vims 2, Torque teno midi vims 3, Torque teno midi vims 4, Torque teno midi vims 5, Torque teno midi vims 6, Torque teno midi vims 7, Torque teno midi vims 8, Torque teno midi vims 9, Torque teno midi vims 10, Torque teno midi vims 11, Torque teno midi vims 12, Torque teno midi vims 13, Torque teno midi vims 14, Torque teno midi vims 15, Chicken anemia vims, Torque teno sus vims la, Torque teno sus vims lb, Torque teno sus vims k2a, Torque teno sus vims k2b, Torque teno seal vims 1, Torque teno seal vims 2, Torque teno seal vims 3, Torque teno seal virus 8, Torque teno seal virus 9, Torque teno zalophus virus 1, Torque teno equus virus 1, Torque teno seal virus 4, Torque teno seal virus 5, Torque teno canis virus, Torque teno douroucouli virus, Avocado sunblotch viroid, Eggplant latent viroid, Apple hammerhead viroid, Chrysanthemum chlorotic mottle viroid, Peach latent mosaic viroid, Adoxophyes honmai nucleopolyhedrovirus, Agrotis ipsilon multiple nucleopolyhedrovirus, Agrotis segetum nucleopolyhedrovirus A, Agrotis segetum nucleopolyhedrovirus B, Antheraea pemyi nucleopolyhedrovirus, Anticarsia gemmatalis multiple nucleopolyhedrovirus, Autographa califomica multiple nucleopolyhedrovirus, Bombyx mori nucleopolyhedrovirus, Buzura suppressaria nucleopolyhedrovirus, Catopsilia pomona nucleopolyhedrovirus, Choristoneura fumiferana DEF multiple nucleopolyhedrovirus, Choristoneura fumiferana multiple nucleopolyhedrovirus, Choristoneura murinana nucleopolyhedrovirus, Choristoneura rosaceana nucleopolyhedrovirus, Chrysodeixis chalcites nucleopolyhedrovirus, Chrysodeixis includens nucleopolyhedrovirus, Clanis bilineata nucleopolyhedrovirus, Condylorrhiza vestigialis nucleopolyhedrovirus, Cryptophlebia peltastica nucleopolyhedrovirus, Cyclophragma undans nucleopolyhedrovirus, Ectropis obliqua nucleopolyhedrovirus, Epiphyas postvittana nucleopolyhedrovims, Euproctis pseudoconspersa nucleopolyhedrovirus, Helicoverpa armigera nucleopolyhedrovirus, Hemileuca species nucleopolyhedrovirus, Hyphantria cunea nucleopolyhedrovirus, Hyposidra talaca nucleopolyhedrovims, Lambdina fiscellaria nucleopolyhedrovims, Leucania separata nucleopolyhedrovims, Lonomia obliqua nucleopolyhedrovims, Lymantria dispar multiple nucleopolyhedrovims, Lymantria xylina nucleopolyhedrovims, Mamestra brassicae multiple nucleopolyhedrovims, Mamestra configurata nucleopolyhedrovims A, Mamestra configurata nucleopolyhedrovims B, Mamca vitrata nucleopolyhedrovims, Mythimna unipuncta nucleopolyhedrovims A, Mythimna unipuncta nucleopolyhedrovims B, Operophtera bmmata nucleopolyhedrovims, Orgyia leucostigma nucleopolyhedrovims, Orgyia pseudotsugata multiple nucleopolyhedrovims, Oxyplax ochracea nucleopolyhedrovims, Peridroma saucia nucleopolyhedrovims, Perigonia lusca nucleopolyhedrovims, Spodoptera eridania nucleopolyhedrovims, Spodoptera exempta nucleopolyhedrovims, Spodoptera exigua multiple nucleopolyhedrovims, Spodoptera fmgiperda multiple nucleopolyhedrovims, Spodoptera littoralis nucleopolyhedrovims, Spodoptera litura nucleopolyhedrovims, Sucrajujuba nucleopolyhedrovims, Thysanoplusia orichalcea nucleopolyhedrovims, Trichoplusia m single nucleopolyhedrovims, Urbanus proteus nucleopolyhedrovims, Wiseana signata nucleopolyhedrovims, Adoxophyes orana granulovims, Agrotis segetum granulovims, Artogeia rapae granulovims, Choristoneura fumiferana granulovims, Clostera anachoreta granulovims, Clostera anastomosis granulovims A, Clostera anastomosis granulovims B, Cnaphalocrocis medinalis granulovims, Cryptophlebia leucotreta granulovims, Cydia pomonella granulovims, Diatraea saccharalis granulovims, Epinotia aporema granulovims, Erinnyis ello granulovirus, Harrisma brillians granulovirus, Helicoverpa armigera granulovirus, Lacanobia oleracea granulovirus, Mocis latipes granulovirus, Mythimna unipuncta granulovirus A, Mythimna unipuncta granulovirus B, Phthorimaea operculella granulovirus, Plodia interpunctella granulovirus, Plutella xylostella granulovirus, Spodoptera frugiperda granulovirus, Spodoptera litura granulovirus, Trichoplusia ni granulovirus, Xestia c-nigrum granulovirus, Culex nigripalpus nucleopolyhedrovirus, Neodiprion lecontei nucleopolyhedrovirus, Neodiprion sertifer nucleopolyhedrovirus, Acidianus two-tailed virus, Aeropyrum pemix bacilliform virus 1, Flavobacterium virus FLiP, Sulfolobus spindle-shaped virus 1, Sulfolobus spindle-shaped virus 2, Sulfolobus spindle-shaped virus 4, Sulfolobus spindle-shaped virus 5, Sulfolobus spindle-shaped virus 7, Sulfolobus spindle-shaped virus 8, Sulfolobus spindle-shaped virus 9, Acidianus spindle-shaped virus 1, Sulfolobus spindle-shaped virus 6, Pyrobaculum spherical virus, Thermoproteus tenax spherical virus 1, Sulfolobus newzealandicus droplet-shaped virus, Aeropyrum pemix ovoid vims 1, Salterprovirus His 1 , Glossina hytrosavims, Musca hytrosavims, White spot syndrome vims, Gryllus bimaculatus nudivims, Oryctes rhinoceros nudivims, Fleliothis zea nudivims, Sulfolobus ellipsoid vims 1, Acholeplasma vims L2, Apanteles crassicomis bracovims, Apanteles fumiferanae bracovims, Ascogaster argentifrons bracovims, Ascogaster quadridentata bracovims, Cardiochiles nigriceps bracovims, Chelonus altitudinis bracovims, Chelonus blackbumi bracovims, Chelonus inanitus bracovims, Chelonus insularis bracovims, Chelonus near curvimaculatus bracovims, Chelonus texanus bracovims, Cotesia congregata bracovims, Cotesia flavipes bracovims, Cotesia glomerata bracovims, Cotesia hyphantriae bracovims, Cotesia kariyai bracovims, Cotesia marginiventris bracovims, Cotesia melanoscela bracovims, Cotesia mbecula bracovims, Cotesia schaeferi bracovims, Diolcogaster facetosa bracovims, Glyptapanteles flavicoxis bracovims, Glyptapanteles indiensis bracovims, Glyptapanteles liparidis bracovims, Hypomicrogaster canadensis bracovims,

Hypomicrogaster ectdytolophae bracovims, Microplitis croceipes bracovims, Microplitis demolitor bracovims, Phanerotoma flavitestacea bracovims, Pholetesor omigis bracovims, Protapanteles paleacritae bracovims, Tranosema rostrale bracovims, Campoletis aprilis ichnovims, Campoletis flavicincta ichnovims, Campoletis sonorensis ichnovims, Casinaria arjuna ichnovims, Casinaria forcipata ichnovims, Casmaria infesta ichnovims, Diadegma acronyctae ichnovims, Diadegma intermptum ichnovims, Diadegma terebrans ichnovims, Enytus montanus ichnovims, Eriboms terebrans ichnovims, Glypta fumiferanae ichnovims, Elyposoter annulipes ichnovims, Elyposoter exiguae ichnovims, Elyposoter fugitivus ichnovims, Elyposoter lymantriae ichnovims, Hyposoter pilosulus ichnovims, Elyposoter rivalis ichnovims, Olesicampe benefactor ichnovims, Olesicampe geniculatae ichnovims, Synetaeris tenuifemur ichnovims, Alphaportoglobovims SPV2, Sulfolobus alphaportoglobovims 1, Apple dimple fruit viroid. Apple scar skin viroid, Australian grapevine viroid, Citms bent leaf viroid, Citms dwarfing viroid, Citrus viroid V, Citms viroid VI, Grapevine yellow speckle viroid 1, Grapevine yellow speckle viroid 2, Pear blister canker viroid, Citrus bark cracking viroid, Coconut cadang-cadang viroid, Coconut tinangaj a viroid, Hop latent viroid, Coleus blumei viroid 1, Coleus blumei viroid 2, Coleus blumei viroid 3, Dahlia latent viroid, Hop stunt viroid, Chrysanthemum stunt viroid, Citrus exocortis viroid, Columnea latent viroid, Iresine viroid 1, Pepper chat fruit viroid, Potato spindle tuber viroid, Tomato apical stunt viroid, Tomato chlorotic dwarf viroid, Tomato planta macho viroid, Aeropyrum coil-shaped virus, Nitmarvirus NSV1, Ageratum leaf curl Buea betasatellite, Ageratum leaf curl Cameroon betasatellite, Ageratum yellow leaf curl betasatellite, Ageratum yellow vein betasatellite, Ageratum yellow vein India betasatellite, Ageratum yellow vein Sri Lanka betasatellite, Altemanthera yellow vein betasatellite, Andrographis yellow vein leaf curl betasatellite, Bhendi yellow vein mosaic betasatellite, Cardiospermum yellow leaf curl betasatellite, Chili leaf curl betasatellite, Chili leaf curl Jaunpur betasatellite, Chili leaf curl Sri Lanka betasatellite, Cotton leaf curl Gezira betasatellite, Cotton leaf curl Multan betasatellite, Croton yellow vein mosaic betasatellite, Eupatorium yellow vein betasatellite, Eupatorium yellow vein mosaic betasatellite, French bean leaf curl betasatellite, Hedyotis yellow mosaic betasatellite,

Honeysuckle yellow vein betasatellite, Honeysuckle yellow vein mosaic betasatellite, Malvastrum leaf curl betasatellite, Malvastrum leaf curl Guangdong betasatellite, Mirabilis leaf curl betasatellite, Momordica yellow mosaic betasatellite, Mungbean yellow mosaic betasatellite, Okra leaf curl Oman betasatellite, Papaya leaf curl betasatellite, Papaya leaf curl China betasatellite, Papaya leaf curl India betasatellite, Rhynchosia yellow mosaic betasatellite, Rose leaf curl betasatellite, Siegesbeckia yellow vein betasatellite, Tobacco curly shoot betasatellite, Tobacco leaf curl betasatellite, Tobacco leaf curl Japan betasatellite, Tobacco leaf curl Patna betasatellite, Tomato leaf curl Bangalore betasatellite, Tomato leaf curl Bangladesh betasatellite, Tomato leaf curl betasatellite, Tomato leaf curl China betasatellite, Tomato leaf curl Gandhinagar betasatellite, Tomato leaf curl Java betasatellite, Tomato leaf curl Joydebpur betasatellite, Tomato leaf curl Laguna betasatellite, Tomato leaf curl Laos betasatellite,

Tomato leaf curl Malaysia betasatellite, Tomato leaf curl Nepal betasatellite, Tomato leaf curl Patna betasatellite, Tomato leaf curl Philippine betasatellite, Tomato leaf curl Sri Lanka betasatellite, Tomato leaf curl Yemen betasatellite, Tomato yellow leaf curl China betasatellite, Tomato yellow leaf curl Rajasthan betasatellite, Tomato yellow leaf curl Shandong betasatellite, Tomato yellow leaf curl Thailand betasatellite, Tomato yellow leaf curl Vietnam betasatellite, Tomato yellow leaf curl Yunnan betasatellite, Vemonia yellow vein betasatellite, Vemoma yellow vein Fujian betasatellite, Croton yellow vein deltasatellite, Malvastrum leaf curl deltasatellite, Sida golden yellow vein deltasatellite 1, Sida golden yellow vein deltasatellite 2, Sida golden yellow vein deltasatellite 3, Sweet potato leaf curl deltasatellite 1, Sweet potato leaf curl deltasatellite 2, Sweet potato leaf curl deltasatellite 3, Tomato leaf curl deltasatellite, Tomato yellow leaf distortion deltasatellite 1, Tomato yellow leaf distortion deltasatellite 2, Pyrobaculum filamentous vims 1, Thermoproteus tenax vims 1, Hepatitis delta vims, Heterocapsa circularisquama DNA virus 01, and Rhizidiomyces virus. Other viruses include the ICTV Master species list (https://talk.ictvQn¾lne org/fsla¾/TU¾ster-speci¾s-lists/us s¾/9601). which is incorporated by reference herein.

In one embodiment, the virus is a coronoavirus. In one embodiment, the virus is SARS-CoV-2. In one embodiment, the virus in an influenza vims. In one embodiment, In one embodiment, the vims in an influenza A vims, an influenza B vims, an influenza C vims, or an influeza D vims.

Amino Acid and Nucleic Acid Sequences

Table 1 provides a summary of the amino acid and nucleic acid sequences.

Table 1.

EXPERIMENTAL EXAMPLES

The invention is further described in detail by reference to the following experimental examples. These examples are provided for purposes of illustration only and are not intended to be limiting unless otherwise specified. Thus, the invention should in no way be construed as being limited to the following examples, but rather, should be construed to encompass any and all variations which become evident as a result of the teaching provided herein.

Without further description, it is believed that one of ordinary skill in the art can, using the preceding description and the following illustrative examples, make and utilize the present invention and practice the claimed methods. The following working examples therefore, specifically point out certain embodiments of the present invention, and are not to be construed as limiting in any way the remainder of the disclosure.

Example 1: Targeted Destruction of Coronavirus RNA by CRISPR-Casl3 Delivered with Integration Deficient Lentiviral Vectors

The data presented herein demonstrate the efficacy of using RNA-targeting CRISPR-Casl3 platforms as an approach to 1) identify effective CRISPR-guide RNAs targeting essential and conserved coronavirus RNA sequences, 2) identify the most robust guide-RNA and CRISPR-Casl3 platforms for robust coronavirus RNA cleavage, and 3), harness non-integrating lentiviral vectors pseudotyped with coronavirus Spike protein. These experiments represent a major first step toward the development of a novel targeted therapeutic for treating coronavirus infections. Notably, the rapid programmability and delivery of this approach could be adapted to target diverse coronavirus strains or other infectious RNA viruses, such as influenza.

Coronavirus lifecycle

Coronavirus genomes are encoded by a large (~30kb), single-stranded mRNA, which is capped and polyadenylated, allowing for translation by host proteins. Coronavirus genomes replicate entirely through RNA intermediates, generating both full-length genomic mRNA and nested subgenomic mRNAs, allowing for expression of numerous viral proteins. Targeting

As a result of coronavirus replication and transcription, 5’ sequences (Leader) and 3’ sequences (S2M or Nucleocapsid ORF) are common to genomic and all subgenomic RNAs (Figure 1). These sequences provide the opportunity for design of guide-RNAs which have the capacity for broad efficacy. Tiling CRISPR RNAs (crRNAs) are tested in cell-based luciferase reporter assays using a luciferase reporter mRNA containing coronavirus target sequences in 5’ UTR or 3TJTR regions.

Cleavage

RNA cleavage efficacy and specificity of coronavirus target sequences are determined in the above assays utilizing novel CRISPR-Casl3 systems (eraseR platforms), with enhanced guide-RNA expression constructs and/or CRISPR arrays (Figure 2).

Delivery

Lentiviral vectors are enveloped and can be pseudotyped with different viral envelope proteins to alter viral tropism (Figure 3). The efficacy and stability of lentiviral vectors pseudotyped with coronavirus envelope spike protein to transduce ACE2-expressing cell types is determined. Nonintegrating, 3rd generation lentiviral vectors, produced using catalytically inactive Integrase, offer a safe and transient expression approach for viral RNA clearance, without permanent expression.

Lentiviral constructs encoding CRISPR-Casl3 components can be packaged into non-integrating lentiviral particles pseudotyped with viral envelope proteins. For example, the lentiviral particle can be pseudotyped with the Spike glycoprotein from SARS-CoV-2 coronavirus, which provides specificity for entry into ACE2 receptor expressing cells. (Figure 4B). This allows for specific targeting of ‘coronavirus- targeted’ cell types. Post-transduction, the processing and formation of non-integrating lentiviral episomes allows for transient expression of CRISPR-Casl3 components for acute targeted degradation of CoV genomic and subgenomic viral mRNAs (Figure 4C).

A Luciferase reporter containing the SARS-2-CoV S2M sequence was used. (Figure 7A). Seven crRNAs were designed targeting the CoV leader sequence. (Figure 7B). Cell-based luciferase assays demonstrate robust knockdown of CoV Leader Luc reporter activity in cells with crRNAs targeting SARS- CoV-2 leader sequence (crRNAs A through G) or Luciferase coding sequence (Luc), relative to a non targeting crRNA (Figure 7C).

Additionally, a Luciferase reporter containing the SARS-2-CoV S2M sequence was used. (Figure 8A). Six crRNAs were designed targeting the SARS-2-CoV S2M sequence. (Figure 8B). Cell-based luciferase assays demonstrate robust knockdown of CoV S2M Luc reporter activity in cells with crRNAs targeting SARS-CoV-2 S2M sequence (crRNAs A through F) or Luciferase coding sequence (Luc), relative to a non-targeting crRNA (Figure 8C).

Example 2: One-step Directional Assembly of CRISPR-Casl3 crRNA Arrays

The data provided herein demonstrates the design and validation of an approach to generate crRNA arrays by direct ligation of multiple annealed oligo pairs containing nucleotide substitutions within DR sequences (Figure 9D). This rapid assembly approach was used to efficiently generate tandem ordered arrays for 3 spacer sequences, which notably, do not contain poly T stretches within the DR sequence, thereby promoting full-length array transcription. Given other potential nucleotide substitutions in these positions, arrays of up to 7 crRNAs lacking a DR T stretch could be assembled in a single-step, or arrays up to 8 crRNAs if a DR T stretch is included (Figure 9E).

CRISPR-Casl3 guide RNAs occur naturally in bacterial species in tandem arrays, which are subsequently processed into single guides by Cas 13 -mediated cleavage (Figure 9A). This cleavage activity is separable from target RNA cleavage activity, thus ‘catalytically dead’ (dCasl3) retains this crRNA processing ability. Many CRISPR-Casl3 direct repeats contain poly T sequences of 4-5 nucleotides which have the potential to inhibit single or tandem full-length crRNA expression from commonly used Pol III promoters, such as hU6, in mammalian cells (Figure 9B). Crystallography studies have revealed that the poly T stretches occur in the loop region of the direct repeat (DR), and that at least one T nucleotide projects into space, suggesting it doesn’t play an important role in CRISPR-Casl3 binding or cleavage. As shown herein, mutation of two positions within this T stretch, T17C or T18C, does not inhibit dCasl3 or Casl3-mediated activity. Thus, these changes can be harnessed to generate diversity within the DR sequence to allow for multiplex, directional cloning.

Mammalian guide-RNA expression cassettes are generally created by cloning annealed oligonucleotides comprising the spacer sequence into a cassette comprised of a mammalian Pol III promoter, a Direct Repeat and a terminator of 6 or more Ts (Figure 9C). Commonly, multiple guide- RNAs are expressed by adding addition Pol III promoter cassettes, however this can significantly increase the complexity and size of the vector. Generation of tandem crRNA arrays would significantly decrease the size requirements of the vector; however, nucleotide synthesis of long arrays is prohibited due to size and the repeat nature of DR sequences.

Example 3: Enhanced Knockdown of SARS-CoV-2 Viral Sequences with a CRISPR crRNA Array

Example 4 demonstrates the design and validation of CRISPR guide-RNAs capable of robust knockdown of a luciferase reporter encoding SARS-CoV-2 viral sequences. Example 5 demonstrates the development of a cloning strategy for the directional assembly of tandem crRNA arrays, which take advantage of base substitutions in non-essential residues within the loop region of Casl3b Direct Repeat (Figure 9E and Figure 10A). The data presented herein demonstrates that all possible base mutations within these two loop residues (T17 and T18) do not negatively affect guide RNA targeting and knockdown of a luciferase reporter mRNA for two independent guide RNAs targeting luciferase coding sequence (Luc-a and Luc-b) (Figure 10B).

Lentiviral gene transfer vectors encoding CRISPR-Casl3 with single ortnple crRNA arrays targeting SARS-CoV-2 viral sequences were developed. (Figure 11 A). A luciferase reporter was constructed containing Leader and N protein SARS-CoV-2 viral target sequences, encoded in both the 5’ and 3 ’ UTR regions of a Luciferase reporter mRNA (Figure 1 IB). The data presented herein shows that expression of multiple guide-RNAs from a single promoter, encoded in a lentiviral transfer vector, results in greater luciferase activity knockdown compared with expression of a single guide RNA (Figure 11C). These results demonstrate greater efficacy for using multiple guide-RNAs targeting a single viral genome, with the added benefit that multiple guide RNAs may further prevent viral ‘escape,’ which may occur through random mutagenesis or by therapeutic selection.

Additionally, the CRISPR-Casl3 expression cassette encoding the tripe guide array is small enough to be packaged within an AAV vector, which may be a useful alternative viral gene therapy delivery method (Figure 12).

Example 4: Targeting Influenza Virus Subtypes with CRISPR-Casl3

Examples 4 and 6 demonstrate that CRISPR-Casl3 can efficiently knockdown the expression of a luciferase reporter encoding coronavirus SARS-CoV-2 viral sequences. Based on the replication characteristics, single guide RNAs can be designed to target all coronavirus genomic and subgenomic RNAs. Additionally, expression of multiple guide RNAs in an array, expressed from a single promoter, resulted in enhanced viral reporter knockdown.

Similar to coronavirus, Influenza viruses are enveloped, RNA viruses which infect both animals and humans and have significant potential for becoming global pandemics. In contrast to coronavirus, influenza virus is composed of 8 independent viral RNA segments, which localize and replicate within the vertebrate nucleus (Figure 13 A). Viral RNA (vRNA) segments encode at least 10 proteins, which encode viral replication enzymes, structural proteins and envelope glycoproteins required for host cell binding and fusion. The multi-segment viral RNA genome allows for rapid mutation and viral selection; as viral segments can be readily switched between viral subtypes within infected cells. This has led to a diverse number of Influenza subtypes, which are categorized by envelope proteins Hemagglutinin (HA) and Neuraminidase (NA). These features present a unique challenge for the targeted degradation of Influenza viral RNA by CRISPR-Casl3.

The data presented herein presents the design of crRNAs which could target the 4 major Influenza A viral subtypes which have cause significant human disease in the recent past, and retain significant potential for becoming global pandemics (H1N 1, H2N2, H3N2 and H7N9). Using multiple sequence alignment of viral protein coding sequences across these four subtypes, conserved segments were identified for five of the 8 viral segments (Table 2). Large conserved viral sequences across subtypes for HA and NA genes were not identified, consistent with their rapid evolution which enables evasion to host immunity. For these five regions, guide RNAs were designed to target either the negative- sense viral RNA (vRNA) or positive-sense viral protein coding mRNA. Guide-RNA arrays were designed to express all five crRNAs from a single Pol III promoter.

Encoding CRISPR guide arrays and Casl3 expression cassettes within a lentiviral gene transfer vector (or alternative gene therapy vector, such as AAV), would allow for the generation of a single particle for delivery and expression of CRISPR-Casl3 components to vertebrate cells (Figure 14). Pseudotyping lentiviral vectors with NA and HA envelope proteins could be utilized to target specific cell types infected by Influenza vims, such as airway epithelia.

Table 2. Sequence alignment and identification of conserved coding sequences among Influenza A Segments from H1N1, H2N2, H3N2, H7N9.

The disclosures of each and every patent, patent application, and publication cited herein are hereby incorporated herein by reference in their entirety. While this invention has been disclosed with reference to specific embodiments, it is apparent that other embodiments and variations of this invention may be devised by others skilled in the art without departing from the true spirit and scope of the invention. The appended claims are intended to be construed to include all such embodiments and equivalent variations.

Claims

CLAIMS What is claimed is:

1. A tandem array comprising at least two CRISPR RNA (crRNA), wherein each crRNA comprises a guide sequence and a direct repeat (DR) sequence.

2. The tandem array of claim 1, wherein each guide sequence in the tandem array is different.

3. The tandem array of claim 1 or claim 2, wherein each DR sequence in the tandem array is different.

4. The tandem array of any of claims 1-3, wherein each DR sequence comprises a nucleotide mutation within the loop region of the DR sequence.

5. The tandem array of any of claims 1-4, wherein each DR sequence comprises a T17 or T18 nucleotide mutation.

6. The tandem array of any of claims 1-5, wherein each crRNA comprises a DR sequence independently selected from SEQ ID NOs: 265-274.

7. The tandem array of any of claims 1-6, DR sequence is 3’ from the guide sequence.

8. The tandem array of any of claims 1-7, wherein each guide sequence is independently substantially complementary to a Coronavirus genomic mRNA sequence or a Coronavirus subgenomic mRNA sequence.

9. The tandem array of claim 8, wherein each guide sequence is substantially complementary to a Coronavirus leader sequence, Coronavirus S sequence, Coronavirus E sequence, Coronavirus M sequence, N sequence, or Coronavirus S2M sequence.

10. The tandem array of claim 8 or 9, wherein each guide sequence is independently substantially complementary to a sequence at least 80% homologous to a sequence selected from SEQ ID NOs: 168-174, 176-181, 186, and 187.

11. The tandem array of any of claims 8-10, wherein each guide sequence comprises a sequence at least 80% homologous to a sequence selected from SEQ ID NOs: 189-224.

12. The tandem array of any of claims 8-11, wherein the tandem array comprises a sequence at least 80% homologous to SEQ ID NO:275.

13. The tandem array of any of claims 1-7, wherein each guide sequence is independently substantially complementary to an influenza virus genomic RNA sequence or an influenza virus subgenomic RNA sequence.

14. The tandem array of claim 13, wherein each guide sequence is substantially complementary to an influenza virus PB2 sequence, influenza virus PB1 sequence, influenza virus PA sequence, influenza virus NP sequence, or influenza virus M sequence.

15. The tandem array of claim 13 or 14, wherein each guide sequence is independently substantially complementary to a sequence at least 80% homologous to a sequence selected from SEQ ID NOs: 225-244.

16. The tandem array of any of claims 13-15, wherein each guide sequence comprises a sequence at least 80% homologous to a sequence selected from SEQ ID NOs: 245-249.

17. The tandem array of any of claims 8-11, wherein the tandem array comprises a sequence at least 80% homologous to a sequence selected from SEQ ID NO:276-279.

18. A composition comprising a tandem array of any of claims 1-17.

19. The composition of claim 18, composition further comprises a Cas protein.

20. The composition of claim 19, wherein the Cas protein is Casl3

21. The composition of claim 18 or claim 19, wherein the Cas protein comprises a sequence at least 80% identical to a sequence selected from SEQ ID NOs: 1-47.

22. The composition of any of claims 18-21, wherein the Cas protein further comprises a localization signal or export signal

23. The composition of claim 22, wherein the Cas protein comprises an NES, wherein the NES comprises a sequence at least 80% identical to SEQ ID NO:58-59.

24. The composition of claim 22, wherein the Cas protein comprises a nuclear localization signal (NLS), wherein the NLS comprises a sequence at least 80% identical to SEQ ID NO: 50-57 and 323-935.

25. The composition of claim 22, wherein the Cas protein comprises a localization signal, wherein the localization signal comprises a sequence at least 80% identical to SEQ ID NO: 60- 66

26. A method of generating a tandem array comprising at least two CRISPR RNA (crRNA), wherein each crRNA comprises a guide sequence and a direct repeat (DR) sequence, the method comprising: ligating at least two the crRNA sequences, wherein each crRNA sequence comprises a unique DR sequence, wherein the ligation generates the tandem array.

27. A method of decreasing the number of two or more unique target RNA in a subject, the method comprising administering to the subject a tandem array of any of claims 1-17 and a Cas protein or nucleic acid encoding a Cas protein; or administering a composition of any of claims 18- 25.

28. The method of claim 27, wherein the tandem array comprises at least two unique crRNA sequences which are substantially complementary to the target RNA sequences.

29. A method for treating a viral infection, the method comprising administering to the subject: (a) tandem array comprising at least two CRISPR RNA (crRNA), wherein each crRNA comprises a guide sequence substantially complementary to a viral RNA sequence and a direct repeat (DR) sequence; and (b) a Cas protein or nucleic acid encoding the Cas protein.

30. The method of claim 29, wherein the Cas protein is Casl3.

31. The method of claim 29 or 30, wherein the Cas protein comprises a sequence at least 80% identical to a sequence selected from SEQ ID NOs:l-47.

32. The method of any of claims 29-31, wherein the Cas protein further comprises a localization signal or export signal.

33. The method of claim 32, wherein the Cas protein comprises an NES, wherein the NES comprises a sequence at least 80% identical to SEQ ID NO:58-59.

34. The method of claim 32, wherein the Cas protein comprises a nuclear localization signal (NLS), wherein the NLS comprises a sequence at least 80% identical to SEQ ID NO: 50- 57 and 323-935.

35. The method of claim 32, wherein the Cas protein comprises a localization signal, wherein the localization signal comprises a sequence at least 80% identical to SEQ ID NO: 60- 66

36. The method of any of clams 29-31 wherein the Cas protein comprises a sequence at least 80% identical to SEQ ID NOs: 68-100.

37. The method of any of claims 29-36, wherein the nucleic acid encoding the Cas protein comprises a sequence at least 80% identical to SEQ ID NOs: 132-133.

38. The method of any of claims 29-36, wherein the nucleic acid encoding the Cas protein comprises a sequence at least 80% identical to SEQ ID NOs: 147-166.

39. The method of any of claims 29-38, wherein the viral infection is a coronavirus infection and wherein each crRNA independently comprises a guide sequence substantially complementary to a Coronavirus genomic mRNA sequence or a Coronavirus subgenomic mRNA sequence.

40. The method of claim 39, wherein each crRNA independently comprises a guide sequence substantially complementary to a Coronavirus leader sequence, Coronavirus S sequence, Coronavirus E sequence, Coronavirus M sequence, N sequence, or Coronavirus S2M sequence.

41. The method of claim 39 or claim 40, wherein each crRNA independently comprises a guide sequence substantially complementary to a sequence at least at least 80% homologous to a sequence selected from SEQ ID NOs: 168-174, 176-181, 186, and 187.

42. The method of any of claims 39-41, wherein each crRNA independently comprises a guide sequence substantially at least 80% homologous to a sequence selected from SEQ ID NOs: 189-224.

43. The method of any of claims 39-42, wherein the tandem array comprises a sequence at least 80% homologous to SEQ ID NO: 275.

44. The method of any of claims 29-38, wherein the viral infection is an influenza infection and wherein each crRNA independently comprises a guide sequence substantially complementary to an influenza virus genomic RNA sequence or an influenza virus subgenomic RNA sequence.

45. The method of claim 44, wherein each crRNA independently comprises a guide sequence substantially complementary an influenza virus PB2 sequence, influenza virus PB1 sequence, influenza virus PA sequence, influenza virus NP sequence, or influenza virus M sequence.

46. The method of claim 44 or claim 45, wherein each crRNA independently comprises a guide sequence substantially complementary to a sequence at least at least 80% homologous to a sequence selected from SEQ ID NOs:225-244.

47. The method of any of claims 44-46, wherein each crRNA independently comprises a guide sequence substantially at least 80% homologous to a sequence selected from SEQ ID NOs: 245-264.

48. The method of any of claims 43-47, wherein the tandem array comprises a sequence at least 80% homologous to a sequence selected from SEQ ID NO: 276-279.

49. A delivery system comprising: a packaging plasmid a transfer plasmid, and an envelope plasmid, wherein the packaging plasmid comprises a nucleic acid sequence encoding a gag-pol polyprotein; the transfer plasmid comprises a nucleic acid sequence encoding a tandem array comprising at least two CRISPR RNA (crRNA), wherein each crRNA comprises a guide sequence and a direct repeat (DR) sequence and a nucleic acid sequence encoding a Cas protein; and the envelope plasmid comprises a nucleic acid sequence encoding an envelope protein.

50. The delivery system of claim 49, wherein the Cas protein comprises a sequence at least 80% identical to a sequence selected from SEQ ID NOs:l-47.

51. The delivery system of claim 49 or claim 50, wherein the Cas protein further comprises a localization signal or export signal.

52. The delivery system of claim 51, wherein the localization signal or export signal comprises a sequence 80% identical to a sequence selected from SEQ ID NOs:50-66 and 323- 935.

53. The delivery system of any of claims 49-52, wherein the envelope protein is a coronavirus spike glycoprotein.

54. The delivery system of any of claims claim 49-53, wherein the envelope protein comprises a sequence at least 80% identical to a sequence selected from SEQ ID NO:101-129.

55. The delivery system of any of claims 49-54, wherein each crRNA independently comprises a guide sequence substantially complementary to a Coronavirus genomic mRNA sequence or a Coronavirus subgenomic mRNA sequence.

56. The delivery system of any of claims 49-55, wherein each crRNA independently comprises a guide sequence substantially complementary to a Coronavirus leader sequence, Coronavirus S sequence, Coronavirus E sequence, Coronavirus M sequence, N sequence, or Coronavirus S2M sequence.

57. The delivery system of any of claims 49-56, wherein each crRNA independently comprises a guide sequence substantially complementary to a sequence at least at least 80% homologous to a sequence selected from SEQ ID NOs: 168-174, 176-181, 186, and 187.

58. The delivery system of any of claims 49-57, wherein each crRNA independently comprises a guide sequence substantially at least 80% homologous to a sequence selected from SEQ ID NOs: 189-224.

59. The delivery system of any of claims 49-58, wherein the tandem array comprises a sequence at least 80% homologous to SEQ ED NO: 275.

60. The delivery system of any of claims 49-52, wherein each crRNA independently comprises a guide sequence substantially complementary to an influenza virus genomic RNA sequence or an influenza virus subgenomic RNA sequence.

61. The delivery system of any of claims 49-52 and 60, wherein each crRNA independently comprises a guide sequence substantially complementary an influenza virus PB2 sequence, influenza virus PB 1 sequence, influenza virus PA sequence, influenza virus NP sequence, or influenza virus M sequence.

62. The delivery system of any of claims 49-52 and 60-61, wherein each crRNA independently comprises a guide sequence substantially complementary to a sequence at least at least 80% homologous to a sequence selected from SEQ ID NOs:225-244.

63. The delivery system of any of claims 49-52 and 60-62, wherein each crRNA independently comprises a guide sequence substantially at least 80% homologous to a sequence selected from SEQ ID NOs: 245-264.

64. The delivery system of any of claims 49-52 and 60-63, wherein the tandem array comprises a sequence at least 80% homologous to a sequence selected from SEQ ID NO: 276- 279.