US20160068917A1

US20160068917A1 - Adenoviruses and their use

Info

Publication number: US20160068917A1
Application number: US14/944,074
Authority: US
Inventors: Charles Chiu; Jean Patterson; Mary Michelle Leland; Kenneth Dee Carey; Dean Ehrdman
Original assignee: Government of United States, as Represented by Secretar; University of California; Texas Biomedical Research Institute
Current assignee: Government of United States, as Represented by Secretar; US Department of Health and Human Services; University of California; Texas Biomedical Research Institute
Priority date: 2013-01-15
Filing date: 2015-11-17
Publication date: 2016-03-10
Also published as: US20150037364A1; JP2016505267A; US9222142B2; EP2946016A1; WO2014113436A8; CN105189755A; EP2946016A4; WO2014113436A1

Abstract

Baboon Adenovirus (BaAdV)-2/4 and BaAdV-3 are disclosed herein. BaAdV-2/4 and BaAdV-3 polynucleotide, polypeptides and antibodies that specifically bind BaAdV-2/4 and/or BaAdV-3 are disclosed. Methods are disclosed for detecting BaAdV-2/4 and BaAdV-3. Methods are also disclosed for treating, preventing, and inducing an immune response to BaAdV-2/4 and/or BaAdV-3. Kits are also provided.

Description

PRIORITY CLAIM

This is a continuation of U.S. patent application Ser. No. 14/233,710, filed on Jan. 17, 2014 which is the U.S. national stage of PCT Application No. PCT/US2014/011624, filed on Jan. 15, 2014, which was published in English under PCT Article 21(2), and which claims the benefit of U.S. provisional application 61/752,876, filed on Jan. 15, 2013. The prior applications are incorporated herein by reference in their entirety.

STATEMENT OF GOVERNMENT SUPPORT

This invention was made with government support under Grant Nos. U54-AI057156, U54-AI57168, R56-AI089532, and R01-HL105704 awarded by the National Institutes of Health. The government has certain rights in the invention.

FIELD

This disclosure relates to the field of adenoviruses, including the viruses themselves, viral vectors, methods of detection, and methods of treatment.

BACKGROUND

Many emerging infectious diseases in humans, including those caused by Ebola virus and H5N1 avian influenza, are zoonotic (Morens et al., 2004, Nature 430: 242-249). Given the close phylogenetic relationship between humans and non-human primates (NHPs), humans are especially vulnerable to cross-species infections from pathogens harbored in apes and monkeys (Pedersen and Davies, Ecohealth 6: 496-508). The risk of disease transfer between NHPs and humans may be greatest in hotspots such as the forests of central and West Africa and the Amazon basin, where humans come into frequent contact with a diverse range of closely related species of NHPs (Pedersen and Davies, supra). Zoos and research facilities housing captive NHPs also represent settings in which cross-species transmission of emerging pathogens can occur (Chen et al., 2011, PLoS Pathog 7: e1002155; Miller and Fowler, 2012, Fowler's zoo and wild animal medicine: current therapy. St. Louis, Mo.: Elsevier/Saunders. xviii, 669 p.; Murphy et al., 2006, J Zoo Wildl Med 37: 219-233).
Adenoviruses (AdVs) are double-stranded DNA viruses that naturally infect a broad range of vertebrate hosts, including humans and NHPs (Wold and Horwitz, 2007, Adenoviruses. In: Fields B N, Knipe D M, Howley P M, editors. Fields Virology. 5th ed. Philadelphia: Wolters Kluwer Health/Lippincott Williams & Wilkins. pp. 2395-2436). In humans, infections caused by AdVs include conjunctivitis, gastroenteritis, hepatitis, myocarditis, and pneumonia (Wold and Horwitz, 2007, supra; Lewis et al., 2009 J Infect Dis 199: 1427-1434; Louie et al., 2008, Clin Infect Dis 46: 421-425. Members of the genus Mastadenovirus, which encompass the AdVs infecting primates, have been classified by the International Committee on Taxonomy of Viruses (ICTV) to include the 7 human AdV species A-G (HAdV-A to HAdV-G) and 1 simian AdV species A (SAdV-A) (Harrach et al., 2011, Family Adenoviridae. In: King A, Adams M, Carstens E, Lefkowitz E, editors. Virus Taxonomy: Classification and Nomenclature of Viruses Ninth Report of the International Committee on Taxonomy of Viruses. San Diego: Elsevier. pp. 95-111. Recently, members of a phylogenetically distinct AdV species group, SAdV-B, were also discovered in fecal samples from asymptomatic captive rhesus monkeys (Roy et al., 2012, Emerg Infect Dis 18: 1081-1088). Although AdVs are conventionally thought to exhibit a very narrow host range due to co-evolution with their respective hosts (Wold and Horwitz, 2007, supra; Roy et al., 2009, PLoS Pathog 5: e1000503), there is mounting evidence supporting the potential for cross-species transmission of AdVs between monkeys and humans. AdVs identified in fecal samples from NHPs were found to share a remarkable similarity to human strains, and could be classified phylogenetically into the conventional “human” species groups HAdV-A through HAdV-E (Roy et al., 2011, supra; Wevers et al., 2011, J Virol 85: 10774-10784). Large-scale serological surveys have detected antibodies to monkey AdVs in humans living in endemic regions (Ersching et al., 2010, Virology 407: 1-6; Xiang et al., 2006, Emerg Infect Dis 12: 1596-1599) Furthermore, a novel AdV, titi monkey adenovirus (TMAdV) was previously described as the cause of a fatal outbreak of pneumonia and hepatitis in a colony of New World titi monkeys, which was also associated with a cross-species respiratory infection in a scientist investigating the outbreak and household family member (Chen et al., 2011, supra). A need remains to identify NHP adenoviruses and determine which of these viruses can infect humans.

SUMMARY

Isolated baboon Adenovirus (BaAdV)-2/4 and BaAdV-3 are disclosed herein. In some embodiments, BaAdV-2/4 and BaAdV-3 polynucleotides, polypeptides and antibodies that specifically bind BaAdV-2/4 and/or BaAdV-3 are disclosed. In additional embodiments, methods are disclosed for detecting BaAdV-2/4 and BaAdV-3. In further embodiments, methods are disclosed for treating, preventing, and inducing an immune response to a BaAdV-2/4 and/or BaAdV-3 infection.
In some embodiments, an isolated nucleic acid is provided that includes a nucleotide sequence at least 100 nucleotides in length that has at least 90% sequence identity over its length to SEQ ID NO:1, SEQ ID NO: 2, SEQ ID NO: 3, or their complement. In other embodiments, an isolated nucleic acid comprising: (a) a nucleic acid sequence at least 90% identical to nucleotides 1-29686 and 29812-34402 of the nucleic acid sequence set forth as SEQ ID NO: 1; (b) a nucleic acid sequence at least 90% identical to nucleotides 1-11334 and 13060-34391 of the nucleic acid sequence set forth as SEQ ID NO: 2; or (c) a nucleotide sequence at least 90% identical to the nucleotide sequence set forth as nucleotides 1-11334 and 13060-34391 of SEQ ID NO: 3. In some specific non-limiting examples, these nucleic acids can be recombinant nucleic acids. In additional non-limiting examples, these nucleic acids are cDNAs. Viruses including these polynucleotides, including replication defective viruses are also provided. In additional embodiments, expression vectors encoding polypeptides encoded by these nucleic acids and host cells transformed with these nucleic acids are provided.
Additional embodiments include polypeptides encoded by these polynucleotides, and antibodies that bind these polypeptides.
These nucleic acids, polypeptides, viruses, expression vectors, host cells and antibodies are of use in methods for detecting, treating, preventing, and producing an immune response to a BaAdV-2/4 and/or BaAdV-3 infection.
The foregoing and other features and advantages will become more apparent from the following detailed description of several embodiments, which proceeds with reference to the accompanying figures.

BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A-1B. Epidemiological features of the baboon adenovirus outbreak. (A) Image of an adult female baboon and her infant. The outbreak was associated with cases of fatal pneumonia in previously healthy newborn baboons. (B) Map of the baboon nursery during the outbreak with cages situated in two separate rooms, showing the locations of baboons who died from pneumonia (skeleton), baboons who became clinically ill with respiratory symptoms but survived (black), and asymptomatic baboons (grey). The novel AdVs genetically characterized in this study (BaAdV_1,2,3,4) were isolated from nasal swabs from both sick (B5) and asymptomatic (B4, B8, and B9) baboons.

FIG. 2. Genomic coverage of novel baboon adenoviruses (BaAdV_1,2,3,4) by deep sequencing. Part of the viral genome was recovered directly from deep sequencing reads using a de novo assembly approach (black bars). After completion of the genome and confirmation by Sanger sequencing, deep sequencing reads are mapped to the corresponding AdV genome. The coverage (y-axis) achieved at each position along the genome (x-axis) is plotted on a logarithmic scale. Abbreviations: nt, nucleotide.

FIGS. 3A-3B. Genome organization of BaAdV₁and BaAdV_2,4and pairwise alignment with related adenoviruses. Maps of the genome organization corresponding to two baboon AdVs, BaAdV₁(A), a species SAdV-B AdV, and BaAdV_2,4(B), a species H AdV, are shown. Boxes above the central black line represent open reading frames (ORFs) encoded on the forward strand, while boxes below the black line represent reverse-strand encoded ORFs. Early region ORFs are shaded in gray. The scanning nucleotide pairwise identities of BaAdV₁(A) and BaAdV_2,4(B) relative to selected related human (light grey), simian (dark grey) or novel baboon (medium grey) AdVs are shown ranked in order of decreasing overall percent identity. The x-axis refers to the nucleotide position along the genome.

FIG. 4A-4D. Amino acid phylogenetic analysis of BaAdV₁, BaAdV_2,4, and BaAdV₃relative to other adenoviruses. (A) hexon, (B) penton base, (C) DNA polymerase, (D) fiber. Representative primate AdVs in species A-G, SAdV-A, and SAdV-B, as well as non-primate AdVs, were included in the phylogenetic analysis. Bayesian support levels are displayed at each branching point. The 4 novel BaAdVs identified in this study and the proposed “species H” designation are in bold. Abbreviations and GENBANK® accession numbers are described in the text.

FIG. 5A-5B. Amino acid pairwise identities of BaAdV₁and BaAdV_2,4relative to other adenoviruses. Comparisons are made against representative human, simian, and murine AdVs. The amino acid pairwise identity table is displayed as a heat map; grey scale corresponds to pairwise identities of 10-100% (bar).

FIG. 6A-6B. Evidence for recombination in species H adenovirus BaAdV₃. (A) Similarity (upper) and bootscanning (lower) plots of AdVs in species SAdV-B, F, G, and H relative to BaAdV3 are shown. Bootscanning analysis reveals a likely recombination breakpoint in the region corresponding to the divergent short fiber gene (asterisk). The x-axis refers to the nucleotide position. The genome organization map is annotated in the same fashion as in FIG. 3. (B) Shown is a hypothetical model in which BaAdV₃is generated by a recombination event involving BaAdV_2,4and the short fiber gene from an as-yet unidentified AdV. Abbreviations: nt, nucleotide.

SEQUENCE LISTING

A Sequence Listing is submitted herewith as an ASCII compliant text file named “Sequence_Listing.txt”, created on Nov. 17, 2015, and having a size of ˜564 kilobytes, as permitted under 37 CFR 1.821(c). The material in the aforementioned file is hereby incorporated by reference in its entirety. The nucleic and amino acid are shown using standard letter abbreviations for nucleotide bases, and three or one letter code for amino acids, as defined in 37 C.F.R. 1.822. Only one strand of each nucleic acid sequence is shown, but the complementary strand is understood as included by any reference to the displayed strand.
SEQ ID NO: 1 is the nucleic acid sequence of BaAdV-2.
SEQ ID NO: 2 is the nucleic acid sequence of BaAdV-4.
SEQ ID NO: 3 is the nucleic acid sequence of BaAdV-3.
SEQ ID NO: 4 is the nucleic acid sequence of BaAdV-1.
SEQ ID NOs: 5-39 are the amino acid sequences of polypeptides encoded by BaAdV-2.
SEQ ID NOs: 40-74 are the amino acid sequences of polypeptides encoded by BaAdV-4.
SEQ ID NOs: 75-109 are the amino acid sequences of polypeptides encoded by BaAdV-3.
SEQ ID NOs: 110-143 are the amino acid sequences of polypeptides encoded by BaAdV-1.
The location of the open reading frames for SEQ ID NO: 1-4 are provided in the Examples section.

DETAILED DESCRIPTION

Baboon adenoviruses are disclosed herein that cause flu-like symptoms in human and non-human primates. These adenoviruses are related to baboon adenovirus (BaAdV)-1, but are in a new adenovirus group that is intermediate between baboon adenovirus groups F and G. These adenoviruses include BaAdV-2 and BaAdv-2/4.
BaAdV-2/4 and BaAdV-3 polynucleotides, polypeptides and antibodies that specifically bind BaAdV-2/4 and/or BaAdV-3 are disclosed. In additional embodiments, methods are disclosed for detecting BaAdV-2/4 and BaAdV-3. Disclosed herein are diagnostic assays to detect BaAdV-3, BaAdV-2/4, BaAdV nucleic acids (genome and genes of both BaAdV-3 and BaAdV-2/4), BaAdV-2/4 and BaAdV-3 antibodies, and BaAdV-2/4 and BaAdV-3 polypeptides. The methods can be used to diagnose an earlier BaAdV-2/4 and/or BaAdV-3 infection in as subject.
In further embodiments, methods are disclosed for treating, preventing, and inducing an immune response to a BaAdV-2/4 and/or BaAdV-3 infection in a subject.

II. Terms

Unless otherwise noted, technical terms are used according to conventional usage. Definitions of common terms in molecular biology may be found in Benjamin Lewin, Genes V, published by Oxford University Press, 1994 (ISBN 0-19-854287-9); Kendrew et al. (eds.), The Encyclopedia of Molecular Biology, published by Blackwell Science Ltd., 1994 (ISBN 0-632-02182-9); and Robert A. Meyers (ed.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8). In order to facilitate review of the various embodiments of this disclosure, the following explanations of specific terms are provided:
Adenovirus: An family of icosahedral (20-sided) viruses that contain DNA. Two genuses, Mastadenovirus and Aviadenovirus are included in the adenovirus family. While there are over 40 serotype strains of adenovirus, most of which cause benign respiratory tract infections in humans, subgroup C serotypes 2 or 5 are predominantly used as vectors. The life cycle does not normally involve integration into the host genome, rather an adenovirus replicates as episomal elements in the nucleus of the host cell and does not insert into the genome. An “adenoviral vector” is a vector derived from publicly available adenoviral DNA. At a minimum, an adenoviral vector includes the inverted terminal repetitions of an adenovirus.
Administering or administration: Therapeutically or prophylactically administering an effective amount of a composition or medicament during the course of therapy. Prophylactic administration can occur prior to manifestation of symptoms characteristic of an adenovirus infection.
Animal: Living multicellular vertebrate organisms, a category which includes, for example, mammals and birds.
Antibody: A polypeptide substantially encoded by an immunoglobulin gene or immunoglobulin genes, or antigen binding fragments thereof, which specifically binds and recognizes an analyte (antigen) such as adenovirus polypeptide or an antigenic fragment of thereof. Immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon and mu constant region genes, as well as the myriad immunoglobulin variable region genes.
Antibodies exist, for example as intact immunoglobulins and as a number of well characterized fragments produced by digestion with various peptidases. For instance, Fabs, Fvs, and single-chain Fvs (scFvs) that specifically bind to an adenovirus would be adenovirus-specific binding agents. A scFv protein is a fusion protein in which a light chain variable region of an immunoglobulin and a heavy chain variable region of an immunoglobulin are bound by a linker, while in dsFvs, the chains have been mutated to introduce a disulfide bond to stabilize the association of the chains. The term also includes genetically engineered forms such as chimeric antibodies (such as humanized murine antibodies), heteroconjugate antibodies such as bispecific antibodies). See also, Pierce Catalog and Handbook, 1994-1995 (Pierce Chemical Co., Rockford, Ill.); Kuby, J., Immunology, 3^rdEd., W.H. Freeman & Co., New York, 1997.
Antibody fragments are defined as follows: (1) Fab, the fragment which contains a monovalent antigen-binding fragment of an antibody molecule produced by digestion of whole antibody with the enzyme papain to yield an intact light chain and a portion of one heavy chain; (2) Fab′, the fragment of an antibody molecule obtained by treating whole antibody with pepsin, followed by reduction, to yield an intact light chain and a portion of the heavy chain; two Fab′ fragments are obtained per antibody molecule; (3) (Fab′)₂, the fragment of the antibody obtained by treating whole antibody with the enzyme pepsin without subsequent reduction; (4) F(ab′)₂, a dimer of two Fab′ fragments held together by two disulfide bonds; (5) Fv, a genetically engineered fragment containing the variable region of the light chain and the variable region of the heavy chain expressed as two chains; and (6) single chain antibody (“SCA”), a genetically engineered molecule containing the variable region of the light chain, the variable region of the heavy chain, linked by a suitable polypeptide linker as a genetically fused single chain molecule. The term “antibody,” as used herein, also includes antibody fragments either produced by the modification of whole antibodies or those synthesized de novo using recombinant DNA methodologies.
Typically, a naturally occurring immunoglobulin has heavy (H) chains and light (L) chains interconnected by disulfide bonds. There are two types of light chain, lambda (2) and kappa (κ). There are five main heavy chain classes (or isotypes) which determine the functional activity of an antibody molecule: IgM, IgD, IgG, IgA and IgE.
Each heavy and light chain contains a constant region and a variable region, (the regions are also known as “domains”). In combination, the heavy and the light chain variable regions specifically bind the antigen. Light and heavy chain variable regions contain a “framework” region interrupted by three hypervariable regions, also called “complementarity-determining regions” or “CDRs.” The extent of the framework region and CDRs have been defined (see, Kabat et al., Sequences of Proteins of Immunological Interest, U.S. Department of Health and Human Services, 1991, which is hereby incorporated by reference in its entirety). The Kabat database is now maintained online. Other databases include the IMGT database. The sequences of the framework regions of different light or heavy chains are relatively conserved within a species. The framework region of an antibody, that is the combined framework regions of the constituent light and heavy chains, serves to position and align the CDRs in three-dimensional space.
The CDRs are primarily responsible for binding to an epitope of an antigen. The CDRs of each chain are typically referred to as CDR1, CDR2, and CDR3, numbered sequentially starting from the N-terminus, and are also typically identified by the chain in which the particular CDR is located. Thus, a V_HCDR3 is located in the variable domain of the heavy chain of the antibody in which it is found, whereas a V_LCDR1 is the CDR1 from the variable domain of the light chain of the antibody in which it is found. Light chain CDRs are sometimes referred to as CDR L1, CDR L2, and CDR L3. Heavy chain CDRs are sometimes referred to as CDR H1, CDR H2, and CDR H3.
References to “V_H” or “VH” refer to the variable region of an immunoglobulin heavy chain, including that of an antibody fragment, such as Fv, scFv, dsFv or Fab. References to “V_L” or “VL” refer to the variable region of an immunoglobulin light chain, including that of an Fv, scFv, dsFv or Fab.
A “monoclonal antibody” is an antibody produced by a single clone of B-lymphocytes or by a cell into which the light and heavy chain genes of a single antibody have been transfected. Monoclonal antibodies are produced by methods known to those of skill in the art, for instance by making hybrid antibody-forming cells from a fusion of myeloma cells with immune spleen cells. These fused cells and their progeny are termed “hybridomas.” Monoclonal antibodies include humanized monoclonal antibodies. In some examples monoclonal antibodies are isolated from a subject. The amino acid sequences of such isolated monoclonal antibodies can be determined.
“Polyclonal” antibodies are antibodies that are obtained from different B-lymphocytes that specifically bind the same antigen; the antibodies can bind several epitopes of the same antigen. In some embodiments, these antibodies are produced by inoculation of a suitable mammal, such as, but not limited to, a mouse, rabbit or goat, with the antigen. Many methodologies are known in the art for the production of polyclonal antibodies that are designed to produce high titer, high affinity antisera.
A “humanized” immunoglobulin is an immunoglobulin including a human framework region and one or more CDRs from a non-human (such as a mouse, rat, or synthetic) immunoglobulin. The non-human immunoglobulin providing the CDRs is termed a “donor,” and the human immunoglobulin providing the framework is termed an “acceptor.” In one embodiment, all the CDRs are from the donor immunoglobulin in a humanized immunoglobulin. Constant regions need not be present, but if they are, they must be substantially identical to human immunoglobulin constant regions, such as at least about 85-90%, such as about 95% or more identical. Hence, all parts of a humanized immunoglobulin, except possibly the CDRs, are substantially identical to corresponding parts of natural human immunoglobulin sequences. A “humanized antibody” is an antibody comprising a humanized light chain and a humanized heavy chain immunoglobulin. A humanized antibody binds to the same antigen as the donor antibody that provides the CDRs. The acceptor framework of a humanized immunoglobulin or antibody may have a limited number of substitutions by amino acids taken from the donor framework. Humanized or other monoclonal antibodies can have additional conservative amino acid substitutions which have substantially no effect on antigen binding or other immunoglobulin functions. Humanized immunoglobulins can be constructed by means of genetic engineering (for example, see U.S. Pat. No. 5,585,089).
Antibody affinity is a measurement of specific binding of an antibody to its antigen. In one embodiment, affinity is calculated by a modification of the Scatchard method described by Frankel et al., Mol. Immunol., 16:101-106, 1979. In another embodiment, binding affinity is measured by an antigen/antibody dissociation rate. In yet another embodiment, a high binding affinity is measured by a competition radioimmunoassay. In several examples, a high binding affinity is at least about 1×10⁻⁸M. In other embodiments, a high binding affinity is at least about 1.5×10⁻⁸, at least about 2.0×10⁻⁸, at least about 2.5×10⁻⁸, at least about 3.0×10⁻⁸, at least about 3.5×10⁻⁸, at least about 4.0×10⁻⁸, at least about 4.5×10⁻⁸, or at least about 5.0×10⁻⁸M.
The phrase “specifically (or selectively) binds” or “specifically (or selectively) immunoreactive with,” when referring to a protein or peptide, refers to a binding reaction that is determinative of the presence of the protein, often in a heterogeneous population of proteins and other biologics. Thus, under designated immunoassay conditions, the specified antibodies bind to a particular protein at least two times the background and more typically more than 10 to 100 times background. Specific binding to an antibody under such conditions requires an antibody that is selected for its specificity for a particular protein. For example, antibodies that specifically bind BaAdV-3, polymorphic variants, alleles, orthologs, and conservatively modified variants, or splice variants, or portions thereof, can be selected to obtain only those antibodies that are specifically immunoreactive with BaAdV-3 and not with other proteins, such as those of BaAdV-1 and/or BaAdV-2/4. Similarly, antibodies that specifically bind BaAdV-2/4, polymorphic variants, alleles, orthologs, and conservatively modified variants, or splice variants, or portions thereof, can be selected to obtain only those antibodies that are specifically immunoreactive with BaAdV-2/4 and not with other proteins, such as those of BaAdV-1 and/or BaAdV-3. This selection can be achieved by subtracting out antibodies that cross-react with other molecules. A variety of immunoassay formats can be used to select antibodies specifically immunoreactive with a particular protein, as described herein.
Antisense, Sense, and Antigene: Double-stranded DNA (dsDNA) has two strands, a 5′->3′ strand, referred to as the plus strand, and a 3′->5′ strand, referred to as the minus strand. Because RNA polymerase adds nucleic acids in a 5′->3′ direction, the minus strand of the DNA serves as the template for the RNA during transcription. Thus, the RNA formed will have a sequence complementary to the minus strand, and identical to the plus strand (except that the base uracil is substituted for thymine).
Antisense molecules are molecules that are specifically hybridizable or specifically complementary to either RNA or the plus strand of DNA. Sense molecules are molecules that are specifically hybridizable or specifically complementary to the minus strand of DNA. Antigene molecules are either antisense or sense molecules directed to a DNA target.
Aptamer: A non-naturally occurring nucleic acid having a desirable action on a target. A desirable action includes, but is not limited to, binding of the target, catalytically changing the target, reacting with the target in a way which modifies/alters the target or the functional activity of the target, covalently attaching to the target as in a suicide inhibitor, facilitating the reaction between the target and another molecule. Aptamer action can be specific binding affinity for a target molecule, such target molecule being a three dimensional chemical structure other than a polynucleotide that binds to the nucleic acid ligand through a mechanism which predominantly depends on Watson/Crick base pairing or triple helix binding, wherein the nucleic acid ligand is not a nucleic acid having the known physiological function of being bound by the target molecule.
An “siRNA” molecule or an “RNAi” molecule refers to a nucleic acid that forms a double stranded RNA, which double stranded RNA has the ability to reduce or inhibit expression of a gene or target gene when the siRNA expressed in the same cell as the gene or target gene. “siRNA” thus refers to the double stranded RNA formed by the complementary strands. The complementary portions of the siRNA that hybridize to form the double stranded molecule typically have substantial or complete identity. In one embodiment, an siRNA refers to a nucleic acid that has substantial or complete identity to a target gene and forms a double stranded siRNA. The sequence of the siRNA can correspond to the full length target gene, or a subsequence thereof. Typically, the siRNA is at least about 15-50 nucleotides in length (e.g., each complementary sequence of the double stranded siRNA is 15-50 nucleotides in length, and the double stranded siRNA is about 15-50 base pairs in length, preferable about preferably about 20-30 base nucleotides, preferably about 20-25 or about 24-29 nucleotides in length, e.g., 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. See also PCT/US03/07237, herein incorporated by reference in its entirety.
The term “antisense” refers to an oligomeric compound or molecule that is at least partially complementary to a target nucleic acid molecule to which it hybridizes. Antisense compounds or molecules can include, but are not limited to, oligonucleotides, oligonucleosides, oligonucleotide analogs, oligonucleotide mimetics, and chimeric combination.
An siRNA or antisense molecule or RNAi molecule is “specific” for a target nucleic acid if it reduces expression of the nucleic acid by at least about 10% when the siRNA or RNAi is expressed in a cell that expresses the target nucleic acid.
Baboon Adenovirus (BaAdV): A term used to refer to the genetic components of the virus, e.g., the genome and RNA transcripts thereof, proteins encoded by the genome (including structural and nonstructural proteins), and viral particles of a baboon adenovirus, such as B. A nucleic acid sequence as it refers to a BaAdV, such as BaAdV-3 and BaAdV-2/4 can refers to nucleic acids and polypeptide polymorphic variants, alleles, mutants, and interspecies homologs that: (1) have a nucleotide sequence that has greater than about 90%, preferably 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or greater nucleotide sequence identity, preferably over a region of over a region of at least about 25, 50, 100, 200, 500, 1000, or more nucleic acids, up to the full length sequence, to the nucleotide sequence of SEQ ID NO:1, SEQ ID NO: 2 and SEQ ID NO: 3; (2) bind to antibodies, e.g., polyclonal or monoclonal antibodies, raised against an immunogen comprising an amino acid sequence of a protein encoded by an open reading frame (ORF) of SEQ ID NO: 1-3; and conservatively modified variants thereof; (3) specifically hybridize under stringent hybridization conditions to an anti-sense strand corresponding to a nucleic acid sequence of SEQ ID NO:1, SEQ ID NO: 2 and SEQ ID NO: 3 and variants thereof; (4) encoding a protein having an amino acid sequence that has greater than about 60% nucleotide sequence identity, 65%, 70%, 75%, 80%, 85%, 90%, preferably 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or greater nucleotide sequence identity, preferably over a region of over a region of at least about 25, 50, 100, 200, 500, 1000, or more amino acids, to a polypeptide (such as a short fiber, E1, E3, E4, etc. protein) encoded by an open reading frame of SEQ ID NO: 1, 2 and 3. The locations of the open reading frames are shown in the attached appendices, and amino acid sequences of the encoded polypeptides are provided.
A “polypeptide encoded by BaAdV” or “polypeptide encoded by the nucleotide sequence” comprising identity to a BaAdV open reading frame (ORF) refers to structural and non-structural adenovirus proteins: (1) encoded by nucleic acids that have a nucleotide sequence that has greater than about 60% nucleotide sequence identity, 65%, 70%, 75%, 80%, 85%, 90%, preferably 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or greater nucleotide sequence identity, preferably over a region of over a region of at least about 25, 50, 100, 200, 500, 1000, or more nucleic acids, up to the full length sequence, to the nucleotide sequence of SEQ ID NO:1, SEQ ID NO: 2 and SEQ ID NO: 3; (2) specifically bind to antibodies, e.g., polyclonal or monoclonal antibodies, raised against an immunogen comprising an amino acid sequence of a protein encoded by an open reading frame of SEQ ID NO: 1, SEQ ID NO: 2 and SEQ ID NO: 3; and conservatively modified variants thereof; (3) encode a protein having an amino acid sequence that has greater than about 60% nucleotide sequence identity, 65%, 70%, 75%, 80%, 85%, 90%, preferably 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or greater, preferably over a region of at least about 25, 50, 100, 200, 500, 1000 or more amino acids, to a protein encoded by an open reading frame of SEQ ID NO: 1, SEQ ID NO: 2 and SEQ ID NO: 3, such as to one of SEQ ID NOs: 5-109. The amino acid sequence of the structural and non-structural viral proteins can be easily identified by one of skill in the art, using the algorithms disclosed herein, by aligning the presently disclosed sequence with other adenovirus sequences.
A “BaAdV infection” refers to the invasion by, multiplication and/or presence of BaAdV in a cell or a subject.
Binding or stable binding: An oligonucleotide binds or stably binds to a target nucleic acid if a sufficient amount of the oligonucleotide forms base pairs or is hybridized to its target nucleic acid, to permit detection of that binding. Binding can be detected by either physical or functional properties of the target:oligonucleotide complex. Binding between a target and an oligonucleotide can be detected by any procedure known to one skilled in the art, including both functional or physical binding assays. Binding may be detected functionally by determining whether binding has an observable effect upon a biosynthetic process such as expression of a gene, DNA replication, transcription, translation and the like.
Physical methods of detecting the binding of complementary strands of DNA or RNA are well known in the art, and include such methods as DNase I or chemical footprinting, gel shift and affinity cleavage assays, Northern blotting, dot blotting and light absorption detection procedures. For example, a method which is widely used, because it is so simple and reliable, involves observing a change in light absorption of a solution containing an oligonucleotide (or an analog) and a target nucleic acid at 220 to 300 nm as the temperature is slowly increased. If the oligonucleotide or analog has bound to its target, there is a sudden increase in absorption at a characteristic temperature as the oligonucleotide (or analog) and target dissociate or melt.
The binding between an oligomer and its target nucleic acid is frequently characterized by the temperature (T_m) at which 50% of the oligomer is melted from its target. A higher (T_m) means a stronger or more stable complex relative to a complex with a lower (T_m).
Biological sample: A sample from a living organism, including sections of tissues such as biopsy and autopsy samples, and frozen sections taken for histologic purposes. Such samples include blood and blood fractions or products (e.g., serum, plasma, platelets, red blood cells, and the like), sputum, cloacal swabs, mucosa, tissue, cultured cells, e.g., primary cultures, explants, and transformed cells, biological fluids, stool, urine, etc. A biological sample is typically obtained from a eukaryotic organism. The tissue sampled can be, for instance, skin, brain (e.g., cerebrum, cerebellum, optic lobe), spinal cord, adrenals, pectoral muscle, lung, heart, liver, crop, proventriculus, ventriculus, duodenum, small intestine, large intestine, cloaca, kidney, bursa of fabricus, spleen, pancreas, adrenal gland, bone marrow, lumbosacral spinal cord, or blood. Contacting a sample refers to exposing the sample under conditions suitable for a reaction to occur.
Capsid: The protein covering, or outer coat, of a virus particle. The capsid is a protein coat that covers the nucleoprotein core or nucleic acid of a virion. The capsid generally shows icosahedral symmetry and in some viruses (not adenoviruses) is enclosed in an envelope. The capsid is built up of subunits (some integer multiple of 60, the number required to give strict icosahedral symmetry) that self assemble in a pattern typical of a particular virus. The subunits are often packed, in smaller capsids, into 5 or 6 membered rings (pentamers or hexamers) that constitute the morphological unit (capsomere). A capsid is required for viral infection of a cell.
Detecting: Determining the presence, using any method, of the virus or viral particles including viral peptides, inside cells, on cells, and/or in medium with which cells or the virus have come into contact. The methods are exemplified by, but not limited to, the observation of cytopathic effect, detection of viral protein, such as by immunofluorescence, ELISA, or Western blot hybridization, detection of viral nucleic acid sequence, such as by PCR, RT-PCR, Southern blots, and Northern blots, nucleic acid hybridization, nucleic acid arrays, and the like.
Expression Vector: A plasmid, a virus or another medium, known in the art, into which a nucleic acid sequence for encoding a desired protein can be inserted or introduced.
Essential Gene: A gene required for viral replication, packaging or infection. Deletion of an essential gene renders a virus replication defective. For example, in an adenovirus, E1 and E2 are essential genes.
Functional Deletion: A mutation in a sequence that has an effect equivalent to deletion of the sequence, for example eliminating the function of a packaging signal or an essential gene product by a deletion, insertion, or substitution.
Functional effect: In the context of assays for testing agents that modulate activity of BaAdV, or for treating or preventing BaAdV infection, includes the determination of a parameter that is indirectly or directly under the influence of BaAdV, e.g., a phenotypic or chemical effect, such as the ability to increase or decrease viral genome replication, viral RNA and protein production, virus packaging, viral particle production (particularly replication competent viral particle production), cell receptor binding, viral transduction, cellular infection, antibody binding, inducing a cellular or humoral immune response, viral protein enzymatic activity, etc. “Functional effects” include in vitro, in vivo, and ex vivo activities. Such functional effects can be measured by any means known to those skilled in the art, e.g., changes in spectroscopic characteristics (e.g., fluorescence, absorbance, refractive index); hydrodynamic (e.g., shape); chromatographic; or solubility properties for a protein; measuring inducible markers or transcriptional activation of a protein; measuring binding activity or binding assays, e.g. binding to antibodies; measuring changes in ligand or substrate binding activity; measuring viral replication; measuring cell surface marker expression; measurement of changes in protein levels; measurement of RNA stability; identification of downstream or reporter gene expression (CAT, luciferase, 0-gal, GFP and the like), e.g., via chemiluminescence, fluorescence, colorimetric reactions, antibody binding, and inducible markers.
Functionally Equivalent: Sequence alterations, in either the transfer or packaging vector sequences, that yield the same results as described herein. Such sequence alterations can include, but are not limited to, conservative substitutions, deletions, mutations, frameshifts, and insertions. In an adenoviral vector deleted for E1 of the invention, deletions in an another gene, such as E4, are functionally equivalent to a similar vector including an E3 deletion. In addition, alterations of the adenoviral vector sequence which yield enhanced encapsidation of the transfer vector genome, are functionally equivalent to the transfer vector of the invention.
Heterologous: A heterologous sequence is a sequence that is not normally (i.e. in the wild-type sequence) found adjacent to a second sequence. In one embodiment, the sequence is from a different genetic source, such as a virus or organism, than the second sequence.
Host cell: A cell that is susceptible to transformation, transfection, transduction, conjugation, and the like with an exogenous nucleic acid construct or expression vector. Host cells can be from mammals, plants, bacteria, yeast, fungi, insects, animals, etc. A host cell can be from a human or a non-human primate.
Infective: A virus or vector is “infective” when it transduces a cell, replicates, and (without the benefit of any complementary virus or vector) spreads progeny vectors or viruses of the same type as the original transducing virus or vector to other cells in an organism or cell culture, where the progeny vectors or viruses have the same ability to reproduce and spread throughout the organism or cell culture. Thus, for example, a nucleic acid encoding an adenoviral particle is not infective if the nucleic acid cannot be packaged (e.g. if the adenoviral particle lacks a packaging site), even though the nucleic acid can be used to transfect a cell. Similarly, an adenoviral nucleic acid packaged by an adenovrial particle is not infective if it does not encode the adenoviral capsid proteins that it is packaged in.
Immune response: A reaction of the immune system to an antigen in the body of a host, which includes generation of an antigen-specific antibody and/or cellular cytotoxic response. The term further refers to an immune system response that leads to a condition of induce sensitivity to an immunogenic product.
Inverted Terminal Repetition (ITR): A sequence found in adenovirus located the end of each strand, these sequences are inverted repeats. When the virus is denatured the repeats enable the formation of “panhandle” structures of 100-140 bp from the single nucleic acid strands.
Isolated: An “isolated” nucleic acid has been substantially separated or purified away from other nucleic acid sequences and in the cell of the organism in which the nucleic acid naturally occurs, i.e., other chromosomal and extrachromosomal DNA and RNA. The term “isolated” thus encompasses nucleic acids purified by standard nucleic acid purification methods. The term also embraces nucleic acids prepared by recombinant expression in a host cell as well as chemically synthesized nucleic acids. The term “isolated” as used herein with respect to nucleic acids, such as DNA or RNA, refers to molecules separated from other DNAs, or RNAs, respectively that are present in the natural source of the macromolecule. Isolated is meant to include nucleic acid fragments which are not naturally occurring as fragments and would not be found in the natural state. The term isolated as used herein also refers to a nucleic acid or peptide that is substantially free of cellular material, viral material, or culture medium when produced by recombinant DNA techniques, or chemical precursors, or other chemicals when chemically synthesized.
Label: A detectable moiety or any atom, molecule or a portion thereof, the presence, absence or level of which is directly or indirectly monitorable. A variety of detectable moieties are well known to those skilled in the art, and can be any material detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means. Such detectable labels can include, but are not limited to, magnetic beads, fluorescent dyes, radiolabels, enzymes, and colorimetric labels such as colloidal gold or colored glass or plastic beads.
Mammal: This term includes both human and non-human mammals. Similarly, the term “subject” includes both human and veterinary subjects.
Nucleic acid: Deoxyribonucleotides or ribonucleotides and polymers thereof in either single- or double-stranded form, and complements thereof. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions) and complementary sequences, as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions can be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., Nucleic Acid Res. 19:5081 (1991); Ohtsuka et al., J. Biol. Chem. 260:2605-2608 (1985); Rossolini et al., Mol. Cell. Probes 8:91-98 (1994)). The term nucleic acid is used interchangeably with gene, cDNA, mRNA, oligonucleotide, and polynucleotide. A particular nucleotide sequence also implicitly encompasses “splice variants,” which as the name suggests, are products of alternative splicing of a gene. After transcription, an initial nucleic acid transcript can be spliced such that different (alternate) nucleic acid splice products encode different polypeptides. Mechanisms for the production of splice variants vary, but include alternate splicing of exons. Alternate polypeptides derived from the same nucleic acid by read-through transcription are also encompassed by this definition. Any products of a splicing reaction, including recombinant forms of the splice products, are included in this definition. A polynucleotide is generally a linear nucleotide sequence, including sequences of greater than 100 nucleotide bases in length.
Operably linked: A first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Generally, operably linked DNA sequences are contiguous and, where necessary to join two protein coding regions, in the same reading frame.
ORF (open reading frame): A series of nucleotide triplets (codons) coding for amino acids without any termination codons. These sequences are usually translatable into a peptide. Generally, these are a length of DNA or RNA sequence capable of being translated into a peptide normally located between a start or initiation signal and a termination signal. Exemplary non-limiting open reading frames encode a polypeptide set forth as one of SEQ ID NOs: 5-109.
Packaging cell: A cell that provides packaging functions in trans for a gene introduced into a cell with a transfer vector, but which does not encapsidate its own genome.
Packaging Vector: Packaging vector nucleic acids lack the nucleic acids necessary for packaging of a DNA corresponding to the packaging vector nucleic acid into an adenoviral capsid. That is, packaging vector nucleic acids are not themselves encapsidated in the viral particles which they encode, i.e. they are not infective. The packaging vector optionally includes all of the components necessary for production of viral particles, or optionally includes a subset of the components necessary for viral packaging. For instance, a packaging cell may be transformed with more than one packaging vector, each of which has a complementary role in the production of an adenoviral particle.
Two (or more) adenoviral-based packaging vectors are “complementary” when they together encode all of the functions necessary for adenovirus packaging, and when each individually does not encode all of the functions necessary for packaging. For example, when two vectors transduce a single cell and together they encode the information for production of adenovirus packaging particles, the two vectors are “complementary.” The use of complementary vectors increases the safety of any packaging cell made by transformation with a packaging vector by reducing the possibility that a recombination event will produce an infective virus.
Adenoviral packaging cell lines are cells including nucleic acid molecules that encode adenoviral capsid proteins which can be used to form adenoviral particles. The adenoviral particles are competent to package target adenovirus which has a packaging site.
Polypeptide or peptide or protein: A polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non-naturally occurring amino acid polymer. Macromolecular structures such as polypeptide structures can be described in terms of various levels of organization. For a general discussion of this organization (see, e.g., Alberts et al., Molecular Biology of the Cell (3^rded., 1994) and Cantor and Schimmel, Biophysical Chemistry Part I: The Conformation of Biological Macromolecules (1980)). “Primary structure” refers to the amino acid sequence of a particular peptide. “Secondary structure” refers to locally ordered, three dimensional structures within a polypeptide. These structures are commonly known as domains, e.g., enzymatic domains, extracellular domains, transmembrane domains, pore domains, and cytoplasmic tail domains. Domains are portions of a polypeptide that form a compact unit of the polypeptide and are typically 15 to 350 amino acids long. Exemplary domains include domains with enzymatic activity. Typical domains are made up of sections of lesser organization such as stretches of 3-sheet and a-helices. “Tertiary structure” refers to the complete three dimensional structure of a polypeptide monomer. “Quaternary structure” refers to the three dimensional structure formed by the noncovalent association of independent tertiary units. Anisotropic terms are also known as energy terms.
The term “amino acid” refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids. Naturally occurring amino acids are those encoded by the genetic code. Amino acids can be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, can be referred to by their commonly accepted single-letter codes Amino acid substitutions, deletions or additions to individual or a small percentage of amino acids in the encoded sequence is a conservatively modified variant, where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles of the invention. The following eight groups each contain amino acids that are conservative substitutions for one another: 1) Alanine (A), Glycine (G); 2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W); 7) Serine (S), Threonine (T); and 8) Cysteine (C), Methionine (M) (see, e.g., Creighton, Proteins (1984)).
Recombinant: A non-naturally occurring molecule, such as a nucleic acid molecule or protein. In some embodiments, non-naturally occurring nucleic acid molecule is a DNA encoding a protein that is operably linked to a heterologous regulatory element, such as a promoter or an enhancer, a cDNA molecule, or a viral genome that has been engineered to be deficient for a specific nucleic acid sequence, such as a viral particles that include this nucleic acid will be replication deficient, attenuated, and/or deficient from the production of a protein normally encoded by the virus.
Sequence identity: In the context of two or more nucleic acids or polypeptide sequences that correspond to each other refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (i.e., about 60% identity, preferably 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher identity over a specified region, when compared and aligned for maximum correspondence over a comparison window or designated region) as measured using, for example, a BLAST or BLAST 2.0 sequence comparison algorithms with default parameters described below, or by manual alignment and visual inspection (see, e.g., NCBI web site ncbi.nlm nih.gov/BLAST or the like). Such sequences are then said to be “substantially identical” and are embraced by the term “substantially identical.’ This definition also refers to, or can be applied to, the compliment of a test sequence. The definition also includes sequences that have deletions and/or additions, as well as those that have substitutions. As described below, the preferred algorithms can account for gaps and the like. Preferably, identity exists for a specified entire sequence or a specified portion thereof or over a region of the sequence that is at least about 25 amino acids or nucleotides in length, or more preferably over a region that is 50-100 amino acids or nucleotides in length. A corresponding region is any region within the reference sequence.
For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Preferably, default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters. A comparison window includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from 20 to 600, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence can be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted (e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by manual alignment and visual inspection, e.g., Current Protocols in Molecular Biology (Ausubel et al., eds. 1995 supplement)).
One example of algorithm that is suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., Nuc. Acids Res. 25:3389-3402 (1977) and Altschul et al., J MoL Biol. 215:403-410 (1990), respectively. BLAST and BLAST 2.0 are used, with the parameters described herein, to determine percent sequence identity for the nucleic acids and proteins of the invention. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (ncbi.nlm.nih.gov). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N=−4 and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a word length of 3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)) alignments (B) of 50, expectation (E) of 10, M=5, N=−4, and a comparison of both strands.
Pharmaceutically acceptable carriers: The pharmaceutically acceptable carriers useful in this invention are conventional. Remington's Pharmaceutical Sciences, by E. W. Martin, Mack Publishing Co., Easton, Pa., 15th Edition (1975), describes compositions and formulations suitable for pharmaceutical delivery of the fusion proteins herein disclosed.
In general, the nature of the carrier will depend on the particular mode of administration being employed. For instance, parenteral formulations usually comprise injectable fluids that include pharmaceutically and physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol or the like as a vehicle. For solid compositions (e.g., powder, pill, tablet, or capsule forms), conventional non-toxic solid carriers can include, for example, pharmaceutical grades of mannitol, lactose, starch, or magnesium stearate. In addition to biologically-neutral carriers, pharmaceutical compositions to be administered can contain minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate.
Stringent conditions: Conditions under which a probe will hybridize to its target subsequence, typically in a complex mixture of nucleic acids, but to no other sequences. The term “hybridize” refers to the process by which single strands of nucleic acid sequences form double-helical segments through hydrogen bonding between complementary nucleotides. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Probes, “Overview of principles of hybridization and the strategy of nucleic acid assays” (1993). Generally, stringent conditions are selected to be about 5-10° C. lower than the thermal melting point (T_m) for the specific sequence at a defined ionic strength pH. The T. is the temperature (under defined ionic strength, pH, and nucleic concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at T_m, 50% of the probes are occupied at equilibrium). Stringent conditions can also be achieved with the addition of destabilizing agents such as formamide. For selective or specific hybridization, a positive signal is at least two times background, preferably 10 times background hybridization. Exemplary stringent hybridization conditions can be as following: 50% fonnamide, 5×SSC, and 1% SDS, incubating at 42° C., or, 5×SSC, 1% SDS, incubating at 65° C., with wash in 0.2×SSC, and 0.1% SDS at 65° C. Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides which they encode are substantially identical. This occurs, for example, when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code. In such cases, the nucleic acids typically hybridize under moderately stringent hybridization conditions. Exemplary “moderately stringent hybridization conditions” include a hybridization in a buffer of 40% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 1×SSC at 45° C. A positive hybridization is at least twice background. Those of ordinary skill will readily recognize that alternative hybridization and wash conditions can be utilized to provide conditions of similar stringency. Additional guidelines for determining hybridization parameters are provided in numerous reference (e.g., and Current Protocols in Molecular Biology, ed. Ausubel, et al.).
Subject: Any animal, including, but not limited to, humans, baboons, and other non-human primates, that presents one or more symptoms indicative of BaAdV infection.
Test agent or agent: Any molecule or compound, either naturally occurring or synthetic, e.g., protein, oligopeptide (e.g., from about 5 to about 25 amino acids in length, preferably from about 10 to 20 or 12 to 18 amino acids in length, preferably 12, 15, or 18 amino acids in length), small organic molecule, polysaccharide, lipid, fatty acid, polynucleotide, oligonucleotide, etc., to be tested for the capacity to directly or indirectly modulation tumor cell proliferation. The test agent can be in the form of a library of test compounds, such as a combinatorial or randomized library that provides a sufficient range of diversity. Test agents are optionally linked to a fusion partner, e.g., targeting compounds, rescue compounds, dimerization compounds, stabilizing compounds, addressable compounds, and other functional moieties. Conventionally, new chemical entities with useful properties are generated by identifying a test agent (called a “lead agent”) with some desirable property or activity, e g, inhibiting activity, creating variants of the lead compound, and evaluating the property and activity of those variant compounds. Often, high throughput screening (HTS) methods are employed for such an analysis. Agents can be inhibitors, activators, or modulators of BaAdV nucleic acid and polypeptide sequences, and are used to refer to activating, inhibitory, or modulating molecules identified using in vitro and in vivo assays of the BaAdV nucleic acid and polypeptide sequences. Inhibitors are agents that, e.g., bind to, partially or totally block activity, decrease, prevent, delay activation, inactivate, desensitize, or down regulate the activity or expression of BaAdV, e.g., antagonists. Activators are agents that increase, open, activate, facilitate, enhance activation, sensitize, agonize, or up regulate BaAdV activity, e.g., agonists Inhibitors, activators, or modulators also include genetically modified versions of BaAdV, e.g., versions with altered activity, as well as naturally occurring and synthetic ligands, substrates, antagonists, agonists, antibodies, peptides, cyclic peptides, nucleic acids, antisense molecules, ribozymes, or small chemical molecules for example.
The phrase “small organic molecule” refers to an organic molecule, either naturally occurring or synthetic, that has a molecular weight of more than about 50 daltons and less than about 2500 daltons, preferably less than about 2000 daltons, preferably between about 100 to about 1000 daltons, more preferably between about 200 to about 500 daltons.
Therapeutically effective amount: A dose that produces effects for which it is administered. The exact dose will depend on the purpose of the treatment, and will be ascertainable by one skilled in the art using known techniques (see, e.g., Lieberman, Pharmaceutical Dosage Forms (vols. 1-3, 1992); Lloyd, The Art, Science and Technology of Pharmaceutical Compounding (1999); and Pickar, Dosage Calculations (1999)).
Treating or treatment: Includes the application or administration of a composition to a subject, or application or administration of a composition to a cell or tissue from a subject who has been infected with BaAdV, or has symptoms of BaAdV infection, with the purpose of curing, healing, alleviating, relieving, altering, remedying, ameliorating, improving, or affecting the disease or condition, the symptom of the disease or condition, or the risk of the disease or condition. The term “preventing” or “prevention” includes stopping or hindering a disease, disorder, or symptoms associated with BaAdV infection before it develops in full.
Vaccine: A pharmaceutical composition comprising at least one immunologically active component that induces an immunological response in an animal and possibly but not necessarily one or more additional components that enhance the immunological activity of the active component. A vaccine can additionally comprise further components typical to pharmaceutical compositions. The immunologically active component of a vaccine can comprise complete virus particles in either their original form or as attenuated particles in a so called modified live vaccine (MLV) or particles inactivated by appropriate methods in a so called killed vaccine (KV). A vaccine comprising antigenic substances can be administered for the purpose of inducing a specific and active immunity against a disease provoked by a BaAdV infection. A vaccine can also provide passive immunity in the form of antibodies previously generated against BaAdV antigens.
Vector: A nucleic acid molecule as introduced into a host cell, thereby producing a transformed host cell. A vector may include nucleic acid sequences that permit it to replicate in the host cell, such as an origin of replication. A vector may also include sequences encoding one or more therapeutic genes and/or selectable marker genes and other genetic elements known in the art. A vector can transduce, transform or infect a cell, thereby causing the cell to express nucleic acids and/or proteins other than those native to the cell. A vector optionally includes materials to aid in achieving entry of the nucleic acid into the cell, such as a viral particle, liposome, protein coating or the like. A vector may be a viral vector, derived from a virus, such as an adenoviral vector.
Unless otherwise explained, 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 disclosure belongs. The singular terms “a,” “an,” and “the” include plural referents unless context clearly indicates otherwise. Similarly, the word “or” is intended to include “and” unless the context clearly indicates otherwise. It is further to be understood that all base sizes or amino acid sizes, and all molecular weight or molecular mass values, given for nucleic acids or polypeptides are approximate, and are provided for description. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of this disclosure, suitable methods and materials are described below. The term “comprises” means “includes.” All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including explanations of terms, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

Baboon Adenovirus (BaAdV) Nucleic Acids

The baboon adenovirus (BaAdV) nucleic acid sequence disclosed herein include nucleic acid sequences at least about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99% identical, or about 100% identical to nucleotides 1-34402 of BaAdV-3 (SEQ ID NO: 3) and/or nucleotides 1-34391 of BaAdV-2/4 (SEQ ID NO: 1 and SEQ ID NO: 2), or nucleotides of at least 100, at least 200, at least 300, at least 400 or at least 500 nucleotides in length. Nucleic acids sequences and adenoviruses including a nucleic acid sequence at least about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% identical to an open reading frame from SEQ ID NOs: 1, 2 and 3 are also provided. The nucleic acid sequences are also provided that are the strand which is complementary to the sequences of SEQ ID NO: 1, 2 and 3, as well as the RNA and cDNA sequences corresponding to the open reading frames and their complementary strands. Further included are nucleic acid sequences which are greater than 95 to 98%, such as about 99 to 99.9% homologous or identical to SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3. Nucleic acids that include, or consist of the nucleic acid sequence sent forth as one of SEQ ID NOs: 1, 2, and 3, and degenerate variants thereof, are also provided herein. I
Nucleic acids are also provided that include or consist of (a) a nucleic acid sequence at least about 90%, 91%, 92%, 93%, 95%, 95%, 96%, 97%, 98%, 99% or 100% identical to nucleotides 1-29685 and 29867-34391 of the nucleic acid sequence set forth as SEQ ID NO: 1; (b) a nucleic acid sequence at least about 990%, 91%, 92%, 93%, 95%, 95%, 96%, 97%, 98%, 99% or 100% identical to nucleotides 1-29865 and 29867-34391 of the nucleic acid sequence set forth as SEQ ID NO: 2; (c) a nucleotide sequence at least about 90%, 91%, 92%, 93%, 95%, 95%, 96%, 97%, 98%, 99% or 100% identical to the nucleotide sequence set forth as nucleotides 1-28677 and 29812-34402 of SEQ ID NO: 3. Nucleic acids are also provided that include or consist of a nucleic acid sequence at least about 90%, 91%, 92%, 93%, 95%, 95%, 96%, 97%, 98%, 99% or 100% identical to an open reading frame of SEQ ID NO 1, SEQ ID NO: 2 or SEQ ID NO: 3. Nucleic acids are also provided that include or consist of an open reading frame of SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3.
Nucleic acids are also provided that encode a polypeptide at least about 90%, 01%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence set forth as one of SEQ ID NOs: 5-109. In some embodiments, nucleic acids are provided that encode a polypeptide comprising or consisting of the amino acid sequence set forth as one of SEQ ID NOs: 5-10. In some embodiments, cDNAs are provided that encode a polypeptide at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence set forth as one of SEQ ID NOs: 5-109. In some embodiments, nucleic acids, or degenerate variants thereof, are provided that encode a polypeptide with an amino acid sequence set forth as one of SEQ ID NOs: 5-109. These nucleic acids can be cDNAs.
In some embodiments, a nucleic acid molecule is provided containing Ad ITR sequences of BaAdV-1 and/or BaAdV-2/4. In other embodiments, a nucleic acid is provided including a BaAdV-1 and BaAdV-2/4 nucleic acid sequence encoding a desired gene product, including but not limited to an early or a late gene product, a long fiber or a short fiber, or polymerase. These nucleic acids can be cDNAs. Still other nucleic acid molecules constructed using the sequences disclosed herein will be readily apparent to one of skill in the art, in view of the information provided herein. For example, nucleic acids are provided that include a nucleotide sequence at least 50, at least 100 nucleotides, at least 250, at least 500, at least 1000, at least 1500, at least 2000, or at least 3,000 nucleotides in length that has at least about 91%, 92%, 93%, 94%, 95%, 96%, 97% 98%, 99% or 100% sequence identity over its length to SEQ ID NO:1 and/or SEQ ID NO: 2 and/or SEQ ID NO: 3, and/or their complements. In specific non-limiting examples, these nucleic acids are non-naturally occurring.
The BaAdV-1 and BaAdV-2/4 adenoviral nucleic acid sequences can be used as therapeutic agents (such as by including a nucleic acid encoding a therapeutic moiety) and in construction of a variety of vector systems and host cells. As used herein, a vector includes any suitable nucleic acid molecule including, naked DNA, a plasmid, a virus, a cosmid, or an episome. These sequences and products may be used alone or in combination with other adenoviral sequences or fragments, or in combination with elements from other adenoviral or non-adenoviral sequences. The adenoviral sequences can be used as antisense delivery vectors, gene therapy vectors, or vaccine vectors.
In one embodiment, the baboon Ad gene regions identified herein may be used in a variety of vectors for delivery of a heterologous molecule to a cell. For example, vectors are generated for expression of an adenoviral capsid protein (or fragment thereof) for purposes of generating a viral vector in a packaging host cell. Such vectors may be designed for expression in trans. Alternatively, such vectors are designed to provide cells which stably contain sequences which express desired adenoviral functions, e.g., one or more of E1a, E1b, the terminal repeat sequences, E2a, E2b, E4, E4ORF6 region.
In addition, the adenoviral gene sequences and fragments thereof can be used to provide helper functions necessary for production of helper-dependent viruses (e.g., adenoviral vectors deleted of essential functions or adeno-associated viruses (AAV)). Methods of producing rAAV using adenoviral helper functions have been described at length in the literature with human adenoviral serotypes (see U.S. Pat. No. 6,258,595; U.S. Pat. No. 5,871,982; PCT Publication No. WO 99/14354; PCT Publication No. WO 99/15685; and PCT Publication No. WO 99/47691. The baboon adenoviral gene sequences that provide the necessary helper functions (such as E1a, E1b, E2a and/or E4 ORF6) can be useful in providing the necessary adenoviral function while minimizing or eliminating the possibility of recombination with any other adenoviruses present in the rAAV-packaging cell which are typically of human origin.
Alternatively, recombinant adenoviral baboon vectors can be utilized in these methods. Such recombinant adenoviral baboon vectors may include, e.g., a hybrid baboon Ad/AAV in which baboon Ad sequences flank a rAAV expression cassette composed of, e.g., AAV 3′ and/or 5′ ITRs and a transgene under the control of regulatory sequences which control its expression. One of skill in the art will recognize that still other baboon adenoviral vectors and/or gene sequences are useful for production of rAAV and other viruses dependent upon adenoviral helper functions.
In still another embodiment, nucleic acid molecules are designed for delivery and expression of one or more selected adenoviral gene product in a host cell to achieve a desired physiologic effect. For example, a nucleic acid molecule containing sequences encoding an adenovirus E1a protein can be delivered to a subject for use as a cancer therapeutic. Optionally, such a molecule is formulated in a lipid-based carrier and preferentially targets cancer cells. Such a formulation may be combined with other cancer therapeutics (e.g., cisplatin, taxol, or the like). Still other uses for the adenoviral sequences provided herein will be readily apparent to one of skill in the art.
In addition, one of skill in the art will readily understand that the adenoviral sequences disclosed herein can be readily adapted for use for a variety of viral and non-viral vector systems for in vitro, ex vivo or in vivo delivery of therapeutic and immunogenic molecules. For example, the genomes disclosed herein can be utilized in a variety of recombinant adenoviral (rAd) and non-rAd vector systems. Such vectors systems may include, but are not limited to, plasmids, lentiviruses, retroviruses, poxviruses, vaccinia viruses, and adeno-associated viral systems, among others. Molecules which include polynucleotides including the baboon Ad DNA sequences disclosed herein can be in the form of naked DNA, a plasmid, a virus or any other genetic element.
In one embodiment, the baboon adenoviral gene regions identified herein can be used as or in a variety of vectors for delivery of a heterologous molecule to a cell. For example, vectors are generated for expression of an adenoviral capsid protein (or fragment thereof) for purposes of generating a viral vector in a packaging host cell. Such vectors may be designed for expression in trans. Alternatively, such vectors are designed to provide cells which stably contain sequences which express desired adenoviral functions, e.g., one or more of E1a, E1b, the terminal repeat sequences, E2a, E2b, E4, E4 ORF region.
Methods of producing recombinant (r)AAV using adenoviral helper functions have been described with human adenoviral serotypes (see, for example, U.S. Pat. No. 6,258,595; U.S. Pat. No. 5,871,982; PCT Publication No. WO 99/14354; PCT Publication No. WO 99/15685; and PCT Publication No. WO 99/47691. These methods may also be used in production of non-human serotype AAV, including non-human primate AAV serotypes. The baboon adenoviral genes that provide the necessary helper functions (e.g., E1a, E1b, E2a and/or E4 ORF6) can be particularly useful in providing the necessary adenoviral function. Without being bound by theory, they can minimize or eliminate the possibility of recombination with any other adenoviruses present in the rAAV-packaging cell which are typically of human origin. Thus, selected genes or open reading frames of the adenoviral sequences of the invention may be utilized in these rAAV production methods. Recombinant adenoviral simian vectors include, e.g., a hybrid baboon adenovirus (Ad)/AAV in which baboon adenovirus Ad sequences flank a rAAV expression cassette composed of, e.g., AAV 3′ and/or 5′ ITRs and a transgene under the control of regulatory sequences which control its expression. One of skill in the art will recognize that still other simian adenoviral vectors and/or gene sequences of the invention will be useful for production of rAAV and other viruses dependent upon adenoviral helper.
Molecules useful for production of the polypeptides are also disclosed herein. Such molecules which include polynucleotides including the baboon adenoviral nucleic acid sequences of the invention can be in the form of naked DNA, a plasmid, a virus or any other genetic element. Any protein can be encoded by these vectors, including markers and therapeutic proteins. Thus, the vectors can be used for the delivery of a heterologous polypeptide in a target cell. In some embodiment, the nucleic acid encoding a heterologous polypeptide is operably linked to one or more expression control sequences, such as a promoter and/or an enhancer. One of skill in the art can readily engineer the adenoviruses nucleic acids disclosed herein to include a heterologous nucleic acid sequence encoding a polypeptide of interest, and express the polypeptide in a host cell. Similarly, heterologous promoters and enhancers can be operably linked to a nucleic acid encoding an adenovirus polypeptide.

Expression

To obtain high level expression of a cloned gene or genome, such as a polypeptide encoded by an open reading frame disclosed herein, such as, but not limited to, a polypeptide at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to one of SEQ ID NOs: 5-109, one typically subclones the nucleic acid into an expression vector that contains a strong promoter to direct transcription, a transcription/translation terminator, and if for a nucleic acid encoding a protein, a ribosome binding site for translational initiation. The open reading frames include any of those listed in the accompanying sequence information. Suitable bacterial promoters are well known in the art and described (e.g., in Sambrook et al., and Ausubel et al, supra. Bacterial expression systems for expressing the protein are available in, e.g., E. coli, Bacillus sp., and Salmonella (Palva et al., Gene 22:229-235 (1983); Mosbach et al., Nature 302:543-545 (1983)). Kits for such expression systems are commercially available. Eukaryotic expression systems for mammalian cells, yeast, and insect cells are well known in the art and are also commercially available. Retroviral expression systems can be used.
Selection of the promoter used to direct expression of a heterologous nucleic acid depends on the particular application. The promoter is preferably positioned about the same distance from the heterologous transcription start site as it is from the transcription start site in its natural setting. As is known in the art, however, some variation in this distance can be accommodated without loss of promoter function. Heterologous refers to portions of a nucleic acid indicates that the nucleic acid comprises two or more subsequences that are not found in the same relationship to each other in nature. For instance, the nucleic acid is typically recombinantly produced, having two or more sequences from unrelated genes arranged to make a new functional nucleic acid, e.g., a promoter from one source and a coding region from another source. Similarly, a heterologous protein indicates that the protein comprises two or more subsequences that are not found in the same relationship to each other in nature (e.g., a fusion protein).
In addition to the promoter, the expression vector typically contains a transcription unit or expression cassette that contains all the additional elements required for the expression of the nucleic acid in host cells. A typical expression cassette thus contains a promoter operably linked to the nucleic acid sequence encoding the nucleic acid of choice and signals required for efficient polyadenylation of the transcript, ribosome binding sites, and translation termination. Additional elements of the cassette can include enhancers and, if genomic DNA is used as the structural gene, introns with functional splice donor and acceptor sites.
In addition to a promoter sequence, the expression cassette should also contain a transcription termination region downstream of the structural gene to provide for efficient termination. The termination region can be obtained from the same gene as the promoter sequence or can be obtained from different genes.
The particular expression vector used to transport the genetic information into the cell is not particularly critical. Any of the conventional vectors used for expression in eukaryotic or prokaryotic cells can be used. Standard bacterial expression vectors include plasmids such as pBR322 based plasmids, pSKF, pET23D, and fusion expression systems such as MBP, GST, and LacZ. Epitope tags can also be added to recombinant proteins to provide convenient methods of isolation, e.g., c-myc. A heterologous adenoviral vector can be used. Sequence tags can be included in an expression cassette for nucleic acid rescue. Markers such as fluorescent proteins, green or red fluorescent protein, 13-gal, CAT, and the like can be included in the vectors as markers for vector transduction.
Expression vectors containing regulatory elements from eukaryotic viruses are typically used in eukaryotic expression vectors, e.g., SV40 vectors, papilloma virus vectors, retroviral vectors, and vectors derived from Epstein-Barr virus. Other exemplary eukaryotic vectors include pMSG, pAV009/A⁺, pMT010/A⁺, pMAMneo-5, baculovirus pDSVE, and any other vector allowing expression of proteins under the direction of the CMV promoter, SV40 early promoter, SV40 later promoter, metallothionein promoter, murine mammary tumor virus promoter, Rous sarcoma virus promoter, polyhedrin promoter, or other promoters shown effective for expression in eukaryotic cells.
Expression of proteins from eukaryotic vectors can also be regulated using inducible promoters. With inducible promoters, expression levels are tied to the concentration of inducing agents, such as tetracycline, by the incorporation of response elements for these agents into the promoter. Generally, high level expression is obtained from inducible promoters only in the presence of the inducing agent; basal expression levels are minimal.
Vectors can have a regulatable promoter, e.g., tet-regulated systems and the RU-486 system (see, e.g., Gossen & Bujard, PNAS 89:5547 (1992); Oligino et al., Gene Ther. 5:491-496 (1998); Wang et al., Gene Ther. 4:432-441 (1997); Neering et al., Blood 88:1147-1155 (1996); and Rendahl et al., Nat. Biotechnol. 16:757-761 (1998)). These impart small molecule control on the expression of the candidate target nucleic acids. This beneficial feature can be used to determine that a desired phenotype is caused by a transfected cDNA rather than a somatic mutation.
Some expression systems have markers that provide gene amplification such as thymidine kinase and dihydrofolate reductase. Alternatively, high yield expression systems not involving gene amplification are also suitable, such as using a baculovirus vector in insect cells, with a sequence of choice under the direction of the polyhedrin promoter or other strong baculovirus promoters.
The elements that are typically included in expression vectors also include a replicon that functions in E. coli, a gene encoding antibiotic resistance to permit selection of bacteria that harbor recombinant plasmids, and unique restriction sites in nonessential regions of the plasmid to allow insertion of eukaryotic sequences. The particular antibiotic resistance gene chosen is not critical, as any of the many resistance genes known in the art are suitable. The prokaryotic sequences are preferably chosen such that they do not interfere with the replication of the DNA in eukaryotic cells, if necessary.
Standard transfection methods are used to produce bacterial, mammalian, yeast or insect cell lines that express large quantities of protein, which are then purified using standard techniques (see, e.g., Colley et al., J. Biol. Chem. 264:17619-17622 (1989); Guide to Protein Purification, in Methods in Enzymology, vol. 182 (Deutscher, ed., 1990)). Transformation of eukaryotic and prokaryotic cells are performed according to standard techniques (see, e.g., Morrison, J Bact. 132:349-351 (1977); Clark-Curtiss & Curtiss, Methods in Enzymology 101:347-362 (Wu et al., eds, 1983)).
Any of the well-known procedures for introducing foreign nucleotide sequences into host cells can be used. These include the use of calcium phosphate transfection, polybrene, protoplast fusion, electroporation, biolistics, liposomes, microinjection, plasma vectors, viral vectors and any of the other well-known methods for introducing cloned genomic DNA, cDNA, synthetic DNA or other foreign genetic material into a host cell (see, e.g., Sambrook et al., supra). It is only necessary that the particular genetic engineering procedure used be capable of successfully introducing at least one gene into the host cell capable of expressing BaAdV proteins and nucleic acids. The host cells can be human cells, or non-human primate cells.
After the expression vector is introduced into the cells, the transfected cells are cultured under conditions favoring expression of the protein of choice, which is recovered from the culture using standard techniques identified below.
Either naturally occurring or recombinant BaAdV proteins can be purified for use in diagnostic assays, for making antibodies (for diagnosis and therapy) and vaccines, and for assaying for anti-viral compounds. Naturally occurring protein can be purified, e.g., from primate tissue samples. Recombinant protein can be purified from any suitable expression system.

BaAdV Polypeptides

BaAdV polypeptides, such as those encoded by the open reading frames specified herein, and functional fragments thereof, can be purified to substantial purity by standard techniques, including selective precipitation with such substances as ammonium sulfate; column chromatography, immunopurification methods, and others (see, e.g., Scopes, Protein Purification: Principles and Practice (1982); U.S. Pat. No. 4,673,641; Ausubel et aL, supra; and Sambrook et al., supra). Exemplary BaAdV polypeptides are provided herein, such as polypeptides at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to one of SEQ ID NOs: 5-109. In specific non-limiting examples, the polypeptide comprises, or consists of, the amino acid sequence set forth as one of SEQ ID NOs: 5-109.
A number of procedures can be employed when recombinant protein is being purified. For example, proteins having established molecular adhesion properties can be reversible fused to the protein. With the appropriate ligand or substrate, a specific protein can be selectively adsorbed to a purification column and then freed from the column in a relatively pure form. The fused protein is then removed by enzymatic activity. Finally, protein could be purified using immunoaffinity columns Recombinant protein can be purified from any suitable source, include yeast, insect, bacterial, and mammalian cells.
Recombinant proteins can be expressed and purified by transformed bacteria in large amounts, typically after promoter induction; but expression can be constitutive. Promoter induction with IPTG is one example of an inducible promoter system. Bacteria are grown according to standard procedures in the art. Fresh or frozen bacteria cells are used for isolation of protein.
Proteins expressed in bacteria can form insoluble aggregates (“inclusion bodies”). Several protocols are suitable for purification of protein inclusion bodies. For example, purification of inclusion bodies typically involves the extraction, separation and/or purification of inclusion bodies by disruption of bacterial cells, e.g., by incubation in a buffer of 50 mM TRIS/HCL pH 7.5, 50 mM NaCl, 5 mM MgCl2, 1 mM DTT, 0.1 mM ATP, and 1 mM PMSF. The cell suspension can be lysed using 2-3 passages through a French Press, homogenized using a Polytron (Brinkman Instruments) or sonicated on ice. Alternate methods of lysing bacteria are apparent to those of skill in the art (see, e.g., Sambrook et al., supra; Ausubel et al., supra).
If necessary, the inclusion bodies are solubilized, and the lysed cell suspension is typically centrifuged to remove unwanted insoluble matter. Proteins that formed the inclusion bodies can be renatured by dilution or dialysis with a compatible buffer. Suitable solvents include, but are not limited to urea (from about 4 M to about 8 M), formamide (at least about 80%, volume/volume basis), and guanidine hydrochloride (from about 4 M to about 8 M). Some solvents which are capable of solubilizing aggregate-forming proteins, for example SDS (sodium dodecyl sulfate), 70% formic acid, are inappropriate for use in this procedure due to the possibility of irreversible denaturation of the proteins, accompanied by a lack of immunogenicity and/or activity. Although guanidine hydrochloride and similar agents are denaturants, this denaturation is not irreversible and renaturation can occur upon removal (by dialysis, for example) or dilution of the denaturant, allowing re-formation of immunologically and/or biologically active protein. Other suitable buffers are known to those skilled in the art. Human proteins are separated from other bacterial proteins by standard separation techniques, e.g., with Ni-NTA agarose resin.
Alternatively, it is possible to purify recombinant protein from bacteria periplasm. After lysis of the bacteria, the periplasmic fraction of the bacteria can be isolated by cold osmotic shock in addition to other methods known to skill in the art. To isolate recombinant proteins from the periplasm, the bacterial cells are centrifuged to form a pellet. The pellet is resuspended in a buffer containing 20% sucrose. To lyse the cells, the bacteria are centrifuged and the pellet is resuspended in ice-cold 5 mM MgSO4 and kept in an ice bath for approximately 10 minutes. The cell suspension is centrifuged and the supernatant decanted and saved. The recombinant proteins present in the supernatant can be separated from the host proteins by standard separation techniques well known to those of skill in the art.
Solubility fractionation can be used as a standard protein separation technique for purifying proteins. As an initial step, particularly if the protein mixture is complex, an initial salt fractionation can separate many of the unwanted host cell proteins (or proteins derived from the cell culture media) from the recombinant protein of interest. The preferred salt is ammonium sulfate. Ammonium sulfate precipitates proteins by effectively reducing the amount of water in the protein mixture. Proteins then precipitate on the basis of their solubility. The more hydrophobic a protein is, the more likely it is to precipitate at lower ammonium sulfate concentrations. A typical protocol includes adding saturated ammonium sulfate to a protein solution so that the resultant ammonium sulfate concentration is between 20-30%. This concentration will precipitate the most hydrophobic of proteins. The precipitate is then discarded (unless the protein of interest is hydrophobic) and ammonium sulfate is added to the supernatant to a concentration known to precipitate the protein of interest. The precipitate is then solubilized in buffer and the excess salt removed if necessary, either through dialysis or diafiltration. Other methods that rely on solubility of proteins, such as cold ethanol precipitation, are well known to those of skill in the art and can be used to fractionate complex protein mixtures.
The molecular weight of the protein can be used to isolate it from proteins of greater and lesser size using ultrafiltration through membranes of different pore size (for example, Amicon or Millipore membranes). As a first step, the protein mixture is ultrafiltered through a membrane with a pore size that has a lower molecular weight cut-off than the molecular weight of the protein of interest. The retentate of the ultrafiltration is then ultrafiltered against a membrane with a molecular cut off greater than the molecular weight of the protein of interest. The recombinant protein will pass through the membrane into the filtrate. The filtrate can then be chromatographed as described below.
The protein can also be separated from other proteins on the basis of its size, net surface charge, hydrophobicity, and affinity for ligands or substrates using column chromatography. In addition, antibodies raised against proteins can be conjugated to column matrices and the proteins immunopurified. All of these methods are well known in the art. It will be apparent to one of skill that chromatographic techniques can be performed at any scale and using equipment from many different manufacturers (e.g., Pharmacia Biotech).
The polypeptides disclosed herein can be used to detect the presence of antibodies that specifically bind BaAdV-2/4 or BaAdV-3 antibodies in a biological sample from a subject. The biological sample can be any sample, including, but not limited to, a blood or serum sample. The method includes contacting the biological sample with one or more of the polypeptides disclosed herein for a sufficient time to for any antibodies to form an immune complex with the one or more polypeptides, and detecting the presence of the immune complex. Methods for detecting the presence of an immune complex are known in the art, and are disclosed below. In several embodiments, the methods include the use of secondary antibodies that specifically bind human antibodies. In some example, the secondary antibodies are labeled.

Probes, Primers, and Detecting BaAdV Nucleic Acids

A BaAdV infection, such as a BaAdV-2/4 and a BaAdV-3 infection, can be detected based on the level of the particular BaAdV RNA or DNA in a biological sample. Primers and probes that are specific to a BaAdV can be used for detection of BaAdV, diagnosis of a BaAdV infection, confirm an earlier infection, and determine BaAdV viral load. In some embodiments, probes and/or primers that specifically bind BaAdV-2/4 can be used for detection of BaAdV-2/4, diagnosis, and determination of BaAdV-2/4 viral load. In other embodiments, probes and/or primers that specifically bind BaAdV-3 can be used for detection of BaAdV-3, diagnosis, and determination of BaAdV-3 viral load. In further embodiments, these methods distinguish a BaAdV-3 infection, such as from a BaAdV-2/4 infection and/or a BaAdV-1 infection. In further embodiments, primers from BaAdV-2/4 can be used for detection of BaAdV-2/4, diagnosis, and determination of BaAdV-2/4 viral load. In further embodiments, these methods distinguish a BaAdV-2/4 infection, such as from a BaAdV-3 infection and/or a BaAdV-1 infection. In some embodiments, the method distinguishes BaAdV-2/4 and/or BaAdV-3 from BaAdV-1. In additional embodiments, the assay is a multiplex assay.
Any suitable primer can be used to detect the genome, nucleic acid sub sequence, ORF, or protein of choice, for example using methods described in US Published Patent Application No. 2003/0104009. In some examples, the subject nucleic acid compositions can be used as single- or double-stranded probes or primers for the detection of BaAdV-2/4 mRNA or cDNA generated from such mRNA, as obtained can be present in a biological sample (e.g., extracts of human cells). In other examples, the subject nucleic acid compositions can be used as single- or double-stranded probes or primers for the detection of BaAdV-3 mRNA or cDNA generated from such mRNA, as obtained can be present in a biological sample (e.g., extracts of human cells). In some embodiments, the probe or primer is specific to the short fiber gene of BaAdV-2/4 or BaAdV-3.
The BaAdV-2/4 and BaAdV-3 polynucleotides can also be used to generate additional copies of the polynucleotides, to generate antisense oligonucleotides, and as triple-strand forming oligonucleotides. For example, two oligonucleotide primers can be employed in a polymerase chain reaction (PCR) based assay to amplify a portion of BaAdV cDNA derived from a biological sample, wherein at least one of the oligonucleotide primers is specific for (i.e., hybridizes to) the BaAdV polynucleotide. In some examples, the primers specifically bind BaAdV-3 nucleic acid, and thus can be used to delineate BaAdV-3 from BaAdV-2/4 and/or BaAdV-1. In other examples, the primers specifically bind BaAdV-2/4 nucleic acid, and thus can be used to delineate BaAdV-2/4 from BaAdV-3 and/or BaAdV-1. In specific, non-limiting examples, the probes and/or primers specifically bind a nucleic acid encoding the short fiber polypeptide.
The primers can be at least or about 12, 15, 16, 18, 20, 22, 24, 25, 30, 35, 40, 45, or 50 nucleotides (nt) or are, for instance, from about 12 to 50 nt in length, 15 to 30 nt in length, 15 to 25 nt in length, or 20 to 30 nt in length) fragments of a contiguous sequence of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, or other polynucleotide sequence encoding a BaAdV-2/4 or BaAdV-3 polypeptide. The amplified cDNA is then separated and detected using techniques well known in the art, such as gel electrophoresis. Similarly, oligonucleotide probes that specifically hybridize to a BaAdV-2/4 or BaAdV-3 polynucleotide can be used in a hybridization assay to detect the presence of the BaAdV-2/4 or BaAdV-3 polynucleotide in a biological sample, respectively.
For PCR, a temperature of about 36° C. is typical for low stringency amplification, although annealing temperatures may vary between about 32° C. and 48° C. depending on primer length. For high stringency PCR amplification, a temperature of about 62° C. is typical, although high stringency annealing temperatures can range from about 50° C. to about 65° C., depending on the primer length and specificity. Typical cycle conditions for both high and low stringency amplifications include a denaturation phase of 90° C.-95° C. for 30 sec-2 min., an annealing phase lasting 30 sec.-2 min, and an extension phase of about 72° C. for 1-2 min Protocols and guidelines for low and high stringency amplification reactions are provided (e.g., in Innis et al. (1990) PCR Protocols, A Guide to Methods and Applications, Academic Press, Inc. N.Y.).
In some embodiments, methods are provided for detecting a Baboon adenovirus (BaAdV)-3 or BaAdV-2/4 nucleic acid. The method includes the steps of: (a) contacting a sample suspected of comprising an adenoviral nucleic acid with at least one primer that hybridizes under stringent conditions to the nucleotide sequence set forth as SEQ ID NO:1, SEQ ID NO: 2, and/or SEQ ID NO: 3; (b) performing a PCR reaction; and (c) detecting presence or absence of a reaction product from the PCR reaction, wherein the presence of the reaction product detects the BaAdV-3 or a BaAdV-2/4 adenovirus.
The probes for BaAdV-2/4 and BaAdV-3 polynucleotides (natural or derived) are of a length or have a sequence which allows the detection of unique viral sequences by hybridization. While about 6-8 nucleotides may be useful, longer sequences may be more effective, e.g., sequences of about 10-12 nucleotides, or about 15, 16, 17, 18, 19, 20 nucleotides or more. In some embodiments, these sequences will derive from regions which lack heterogeneity among viral isolates.
Nucleic acid probes or primers specific to BaAdV-2/4 and/or BaAdV-3 can be generated using the polynucleotide sequences disclosed herein. In some embodiments, the probes are at least about 12, 15, 16, 18, 20, 22, 24, or 25 nucleotide (nt) fragments of a contiguous sequence of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, or other polynucleotide sequence encoding a BaAdV polypeptide, such as degenerate variants of BaAdV-2/4 and/or BaAdV-3. Nucleic acid probes can be less than about 200 bp, 150 bp, 100 bp, 75 bp, 50 bp, 60 bp, 40 bp, 30 bp, 25 by 2 kb, 1.5 kb, 1 kb, 0.5 kb, 0.25 kb, 0.1 kb, or 0.05 kb in length. The probes can be produced by, for example, chemical synthesis, PCR amplification, generation from longer polynucleotides using restriction enzymes, or other methods well known in the art. Generally, primers and probes are identical to a BaAdV nucleic acid sequence and different from a non-BaAdV sequence. As noted above, primers and probes can be used to distinguish BaAdV-2/4 and BaAdV-3 from each other, and from BaAdV-1.
The polynucleotides described herein, particularly where used as a probe in a diagnostic assay, can be detectably labeled. Exemplary detectable labels include, but are not limited to, radiolabels, fluorochromes, (e.g. fluorescein isothiocyanate (FITC), rhodamine, Texas Red, phycoerythrin, allophycocyanin, 6-carboxyfluorescein (6-FAM), 2′,7′-dimethoxy-4′,5′-dichloro-6-carboxyfluorescein, 6-carboxy-X-rhodamine (ROX), 6-carboxy-2′,4′,T,4,7-hexachlorofluorescein (HEX), 5-carboxyfluorescein (5-FAM) or N,N,N′,N′-tetramethyl-6-carboxyrho-damine (TAMRA)), radioactive labels, (e.g. .sup.32p, .sup.35S, and sup.3H), and the like. The detectable label can involve two stage systems (e.g., biotin-avidin, hapten-anti-hapten antibody, and the like).
Non-PCR-based, sequence specific DNA amplification techniques can also be used with the invention to detect BaAdV sequences. An example of such techniques includes, but is not limited to, the Invader assay (see, e.g., Kwiatkowski et al. Mol Diagn. December 1999, 4:353-64 and U.S. Pat. No. 5,846,717).
In other embodiments, solid substrates, such as arrays, are provided that include any of the polynucleotides described herein. The polynucleotides are immobilized on the arrays using methods known in the art. An array can have one or more different polynucleotides.
Any suitable qualitative or quantitative methods known in the art for detecting specific BaAdV nucleic acid (e.g., RNA or DNA) can be used. BaAdV nucleic acid can be detected by, for example, in situ hybridization in tissue sections, using methods that detect single base pair differences between hybridizing nucleic acid (e.g., using the INVADER® technology described in, for example, U.S. Pat. No. 5,846,717), by reverse transcriptase-PCR, or in Northern blots containing poly A mRNA, and other methods well known in the art. For detection of BaAdV-2/4 and BaAdV-3 polynucleotides in blood or blood-derived samples, the use of methods that allow for detection of single base pair mismatches is preferred.
Using the BaAdV-2/4 and BaAdV-3 nucleic acid as a basis, nucleic acid probes (e.g., including oligomers of at least about 8 nucleotides or more, see above) can be prepared, either by excision from recombinant polynucleotides or synthetically, which probes hybridize with the desired BaAdV nucleic acid, and thus are useful in detection of a specific BaAdV virus in a sample, and identification of infected individuals, as well as further characterization of the viral genome(s). In some examples, the probes and primers can be designed to detect both BaAdV-2/4 and BaAdV-3. In some examples, the probes and primers distinguish BaAdV-2/4 and BaAdV-3 from BaAdV-1. In other embodiments, the probes and primers can be designed to detect BaAdV-2/4 only. In some examples, the probes and primers distinguish BaAdV-2/4 from BaAdV-3 and BaAdV-1. In further embodiments, the probes and primers can be designed to detect BaAdV-3 only. In some examples, the probes and primers distinguish BaAdV-3 from BaAdV-2/4 and BaAdV-1.
Nucleic acid probes can be prepared using routine methods, including automated oligonucleotide synthetic methods. A complement to any unique portion of the BaAdV-2/4 and/or BaAdV-3 genome will be satisfactory, for example a portion of the genome that allows for distinguishing the BaAdV of interest from other viruses that may be present in the sample, e.g., other BaAdV such as BaAdV-1 or other adenoviruses. For use as probes, complete complementarity is desirable, though it can be unnecessary as the length of the fragment is increased.
For use of such probes as diagnostics, the biological sample to be analyzed, such as blood or serum, can be treated, if desired, to extract the nucleic acids contained therein. The resulting nucleic acid from the sample can be subjected to gel electrophoresis or other size separation techniques; alternatively, the nucleic acid sample can be dot blotted without size separation. The probes are usually labeled with a detectable label. Suitable labels, and methods for labeling probes are known in the art, can include, for example, radioactive labels incorporated by nick translation or kinasing, biotin, fluorescent probes, and chemiluminescent probes. The nucleic acids extracted from the sample are then treated with the labeled probe under hybridization conditions of suitable stringencies.
The probes can be made completely complementary to the BaAdV-2/4 and/or BaAdV-3 genome or portion thereof (e.g., to all or a portion of a sequence encoding a BaAdV polypeptide). Therefore, usually high stringency conditions are desirable in order to prevent or at least minimize false positives. However, conditions of high stringency should only be used if the probes are complementary to regions of the viral genome which lack heterogeneity among BaAdV viral isolates. The stringency of hybridization is determined by a number of factors during hybridization and during the washing procedure, including temperature, ionic strength, length of time, and concentration of formamide (Sambrook et al. (1989), “Molecular Cloning; A Laboratory Manual,” Second Edition (Cold Spring Harbor Press, Cold Spring Harbor, N.Y.)).
Generally, it is expected that the BaAdV-2/4 or BaAdV-3 sequences will be present in a biological sample (e.g., blood, cells, and the liked) obtained from an infected individual at relatively low levels, such as at approximately 10²-10⁴BaAdV-2/4 or BaAdV-3 sequences per 10⁶cells. This level can require that amplification techniques be used in hybridization assays. Such techniques are known in the art.
For example, the Enzo Biochemical Corporation “Bio-Bridge” system uses terminal deoxynucleotide transferase to add unmodified 3′-poly-dT-tails to a DNA probe. The poly dT-tailed probe is hybridized to the target nucleotide sequence, and then to a biotin-modified poly-A. PCT Publication No. WO84/03520 and European Application No. EPA124221 describe a DNA hybridization assay in which: (1) analyte is annealed to a single-stranded DNA probe that is complementary to an enzyme-labeled oligonucleotide; and (2) the resulting tailed duplex is hybridized to an enzyme-labeled oligonucleotide. European Published Patent Application No. 204510 describes a DNA hybridization assay in which analyte DNA is contacted with a probe that has a tail, such as a poly-dT tail, an amplifier strand that has a sequence that hybridizes to the tail of the probe, such as a poly-A sequence, and which is capable of binding a plurality of labeled strands.
One technique can first involve amplification of the target BaAdV-2/4 and/or BaAdV-3 sequences in sera approximately 10,000 fold, e.g., to approximately 10 sequences/mL. This can be accomplished, for example, by the polymerase chain reactions (PCR) technique (Saiki et al. (1986), by Mullis, U.S. Pat. No. 4,683,195, and by Mullis et al. U.S. Pat. No. 4,683,202). Other amplification methods are well known in the art.
The probes, or alternatively nucleic acid from the samples, can be provided in solution for such assays, or can be affixed to a support (e.g., solid or semi-solid support). Examples of supports that can be used are nitrocellulose (e.g., in membrane or microtiter well form), polyvinyl chloride (e.g., in sheets or microtiter wells), polystyrene latex (e.g., in beads or microtiter plates, polyvinylidine fluoride, diazotized paper, nylon membranes, activated beads, and Protein A beads.
Probes (or sample nucleic acid) can be provided on an array for detection. Arrays can be created by, for example, spotting polynucleotide probes onto a substrate (e.g., glass, nitrocellulose, and the like) in a two-dimensional matrix or array. The probes can be bound to the substrate by either covalent bonds or by non-specific interactions, such as hydrophobic interactions. Samples of polynucleotides can be detectably labeled (e.g., using radioactive or fluorescent labels) and then hybridized to the probes. Double stranded polynucleotides, comprising the labeled sample polynucleotides bound to probe polynucleotides, can be detected once the unbound portion of the sample is washed away. Techniques for constructing arrays and methods of using these arrays are described in EP 799 897; WO 97/29212; WO 97/27317; EP 785 280; WO 97/02357; U.S. Pat. No. 5,593,839; U.S. Pat. No. 5,578,832; EP 728 520; U.S. Pat. No. 5,599,695; EP 721 016; U.S. Pat. No. 5,556,752; WO 95/22058; and U.S. Pat. No. 5,631,734. Arrays are particularly useful where, for example a single sample is to be analyzed for the presence of two or more nucleic acid target regions, as the probes for each of the target regions, as well as controls (both positive and negative) can be provided on a single array. Arrays thus facilitate rapid and convenience analysis.

BaAdV Antibodies

Antibodies raised against BaAdV-2/4 and/or BaAdV-3 can serve a wide variety of purposes, as described herein, which include, but are not limited to, diagnostic assays for the detection of BaAdV-2/4 and/or BaAdV-3. These antibodies can also be used for treatment. The antibody specifically binds a BaAdV-2/4 polypeptide, or as a BaAdV-3 polypeptide. Specific, non-limiting examples include an antibody that specifically binds a polypeptide at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%,or 100% identical to one of SEQ ID NOs: 5-109. The antibodies include polyclonal or monoclonal antibodies. In some embodiments, the antibody specifically binds to a polypeptide encoded by one of SEQ ID NOs: 1-3, wherein the antibody does not specifically bind to a polypeptide encoded by SEQ ID NO: 4.
A number of immunogens comprising portions of a BaAdV-2/4 and/or BaAdV-3 protein, virus or nucleic acid can be used to produce antibodies specifically reactive with the BaAdV-2/4 and/or BaAdV-3. In some embodiments, the antibody specifically binds BaAdV-2/4 and not BaAd-3 or BaAdV-1. In other embodiments, the antibody specifically binds BaAdV-3 and not BaAd-2/4 or BaAdV-1. In further embodiments, the antibody specifically binds BaAdV-3 and BaAd-2/4 but not BaAdV-1. In several non-limiting examples, the antibody specifically binds one of SEQ ID NO: 5-109. The antibody can be a monoclonal antibody, or a fragment thereof that specifically binds one of SEQ ID NOs: 5-109.
In some embodiments, a recombinant BaAdV-2/4 or BaAdV-3 protein or an antigenic fragment thereof, can be isolated as described herein. Recombinant protein can be expressed in eukaryotic or prokaryotic cells as described above, and purified as generally described above. Recombinant protein can then be used as an immunogen for the production of monoclonal or polyclonal antibodies. Alternatively, a synthetic peptide derived from the sequences disclosed herein and conjugated to a carrier protein can be used an immunogen. Naturally occurring protein can also be used either in pure or impure form. The product is then injected into an animal capable of producing antibodies. Either monoclonal or polyclonal antibodies can be generated, for subsequent use in immunoassays to measure the polypeptide.
Methods of producing an antibody that specifically binds a BaAdV-2/4 or BaAdV-3 are disclosed herein. For preparation of antibodies, e.g., recombinant, monoclonal, or polyclonal antibodies, many technique can be used (see, e.g., Kohler & Milstein, Nature 256:495-497 (1975); Kozbor et al., Immunology Today 4: 72 (1983); Cole et al., pp. 77-96 in Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc. (1985); Coligan, Current Protocols in Immunology (1991); Harlow & Lane, Antibodies, A Laboratory Manual (1988); and Goding, Monoclonal Antibodies: Principles and Practice (2d ed. 1986)).
Methods of production of polyclonal antibodies are known to those of skill in the art. An inbred strain of mice (e.g., BALB/C mice) or rabbits is immunized with the protein using a standard adjuvant, such as Freund's adjuvant, and a standard immunization protocol. The animal's immune response to the immunogen preparation is monitored by taking test bleeds and determining the titer of reactivity to the beta subunits. When appropriately high titers of antibody to the immunogen are obtained, blood is collected from the animal and antisera are prepared. Further fractionation of the antisera to enrich for antibodies reactive to the protein can be done if desired (see, Harlow & Lane, supra).
Monoclonal antibodies can be obtained by various techniques familiar to those skilled in the art. Briefly, spleen cells from an animal immunized with a desired antigen, such as a BaAdV-2/4 or BaAdV-3 polypeptide, are immortalized, commonly by fusion with a myeloma cell (see, Kohler & Milstein, Eur. J. Immunol. 6:511-519 (1976)). Alternative methods of immortalization include transformation with Epstein Barr Virus, oncogenes, or retroviruses, or other methods well known in the art. Colonies arising from single immortalized cells are screened for production of antibodies of the desired specificity and affinity for the antigen, and yield of the monoclonal antibodies produced by such cells can be enhanced by various techniques, including injection into the peritoneal cavity of a vertebrate host. Alternatively, one can isolate DNA sequences which encode a monoclonal antibody or a binding fragment thereof by screening a DNA library from human B cells according to the general protocol outlined by Huse, et al., Science 246:1275-1281 (1989).
Monoclonal antibodies and polyclonal sera are collected and titered against the immunogen protein in an immunoassay, for example, a solid phase immunoassay with the immunogen immobilized on a solid support. Typically, polyclonal antisera with a titer of 10⁴or greater are selected and tested for their cross reactivity against non-BaAdV proteins and nucleic acids, using a competitive binding immunoassay. Specific polyclonal antisera and monoclonal antibodies will usually bind with a Kd of at least about 0.1 mM, more usually at least about 1 uM, preferably at least about 0.1 uM or better, and most preferably, 0.01 uM or better. Antibodies specific only for a particular BaAdV protein can also be made by subtracting out other cross-reacting proteins. In this manner, antibodies that bind only to the protein of choice can be obtained.
Phage display technology can be used to identify antibodies and heteromeric Fab fragments that specifically bind to selected antigens, such as a BaAdV-2/4 or BaAdV-3 polypeptide (see, e.g., McCafferty et al., Nature 348:552-554 (1990); Marks et al., Biotechnology 10:779-783 (1992)). Antibodies can also be made bispecific, i.e., able to recognize two different antigens (see, e.g., WO 93/08829, Traunecker et al., EMBO J. 10:3655-3659 (1991); and Suresh et al., Methods in Enzymology 121:210 (1986)). Antibodies can also be heteroconjugates, e.g., two covalently joined antibodies, or immunotoxins (see, e.g., U.S. Pat. No. 4,676,980, WO 91/00360; WO 92/200373; and EP 03089).
Chimeric antibodies can be used, which is an antibody molecule in which (a) the constant region, or a portion thereof, is altered, replaced or exchanged so that the antigen binding site (variable region) is linked to a constant region of a different or altered class, effector function and/or species, or an entirely different molecule which confers new properties to the chimeric antibody, e.g., an enzyme, toxin, hormone, growth factor, drug, etc.; or (b) the variable region, or a portion thereof, is altered, replaced or exchanged with a variable region having a different or altered antigen specificity.
Humanized or primatized antibodies can be used. Generally, a humanized antibody has one or more amino acid residues introduced into it from a source which is non-human. These non-human amino acid residues are often referred to as import residues, which are typically taken from an import variable domain. Methods for humanizing or primatizing non-human antibodies are well known in the art. Humanization can be essentially performed following the method of Winter and co-workers (see, e.g., Jones et al., Nature 321:522-525 (1986); Riechmann et al., Nature 332:323-327 (1988); Verhoeyen et al., Science 239:1534-1536 (1988) and Presta, Curr. Op. Struct. Biol. 2:593-596 (1992)), by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody. Accordingly, such humanized antibodies are chimeric antibodies (U.S. Pat. No. 4,816,567), wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non-human species. In practice, humanized antibodies are typically human antibodies in which some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies.
Antibody fragments are encompassed by the present disclosure, such as Fab, F(ab)₂, and Fv which include a heavy chain and light chain variable region. These antibody fragments retain the ability to selectively bind with the antigen. These fragments include:
(1) Fab, the fragment which contains a monovalent antigen-binding fragment of an antibody molecule, can be produced by digestion of whole antibody with the enzyme papain to yield an intact light chain and a portion of one heavy chain;
(2) Fab′, the fragment of an antibody molecule can be obtained by treating whole antibody with pepsin, followed by reduction, to yield an intact light chain and a portion of the heavy chain; two Fab′ fragments are obtained per antibody molecule;
(3) (Fab′)₂, the fragment of the antibody that can be obtained by treating whole antibody with the enzyme pepsin without subsequent reduction; F(ab′)₂is a dimer of two Fab′ fragments held together by two disulfide bonds;
(4) Fv, a genetically engineered fragment containing the variable region of the light chain and the variable region of the heavy chain expressed as two chains; and
(5) Single chain antibody (such as scFv), defined as a genetically engineered molecule containing the variable region of the light chain, the variable region of the heavy chain, linked by a suitable polypeptide linker as a genetically fused single chain molecule.
(6) A dimer of a single chain antibody (scFV₂), defined as a dimer of a scFV. This has also been termed a “miniantibody.”
Methods of making these fragments are known in the art (see for example, Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, New York, 1988).
In some embodiments, the antibodies and antigen binding fragments thereof can be conjugated to an effector molecule, such as a label or a toxin. Useful detection agents include fluorescent compounds, including fluorescein, fluorescein isothiocyanate, rhodamine, 5-dimethylamine-1-napthalenesulfonyl chloride, phycoerythrin, lanthanide phosphors and the like. Bioluminescent markers are also of use, such as luciferase, Green fluorescent protein, Yellow fluorescent protein. An antibody or antigen binding fragment thereof can also be labeled with enzymes that are useful for detection, such as horseradish peroxidase, β-galactosidase, luciferase, alkaline phosphatase, glucose oxidase and the like. When an antibody or antigen binding fragment thereof is labeled with a detectable enzyme, it can be detected by adding additional reagents that the enzyme uses to produce a reaction product that can be discerned. For example, when the agent horseradish peroxidase is present the addition of hydrogen peroxide and diaminobenzidine leads to a colored reaction product, which is visually detectable. An antibody or antigen binding fragment thereof may also be labeled with biotin, and detected through indirect measurement of avidin or streptavidin binding. It should be noted that the avidin itself can be labeled with an enzyme or a fluorescent label.
An antibody or antigen binding fragment thereof may be labeled with a magnetic agent, such as gadolinium. Antibodies and antigen binding fragments can also be labeled with lanthanides (such as europium and dysprosium), and manganese. Paramagnetic particles such as superparamagnetic iron oxide are also of use as labels. An antibody or antigen binding fragment may also be labeled with a predetermined polypeptide epitopes recognized by a secondary reporter (such as leucine zipper pair sequences, binding sites for secondary antibodies, metal binding domains, epitope tags). In some embodiments, labels are attached by spacer arms of various lengths to reduce potential steric hindrance.
An antibody can also be labeled with a radiolabeled amino acid. The radiolabel may be used for both diagnostic and therapeutic purposes. Examples of labels for polypeptides include, but are not limited to, the following radioisotopes or radionucleotides: ³H, ¹⁴C, ¹⁵N, ³⁵S, ⁹⁰Y, ⁹⁹Tc, ¹¹¹In, ¹²⁵I, ¹³¹I¹.
An antibody or antigen binding fragment can also be derivatized with a chemical group such as polyethylene glycol (PEG), a methyl or ethyl group, or a carbohydrate group. These groups may be useful to improve the biological characteristics of the antibody, such as to increase serum half-life or to increase tissue binding.
Means of detecting such labels are well known to those of skill in the art. Thus, for example, radiolabels may be detected using photographic film or scintillation counters, fluorescent markers may be detected using a photodetector to detect emitted illumination. Enzymatic labels are typically detected by providing the enzyme with a substrate and detecting the reaction product produced by the action of the enzyme on the substrate, and colorimetric labels are detected by simply visualizing the colored label.

Detecting BaAdV Polypeptides

A BaAdV infection, such as a BaAdV-2/4 and a BaAdV-3 infection, can be detected based on the level of the particular BaAdV polypeptide sample. Antibodies that are specific to a BaAdV can be used for detection of BaAdV, diagnosis of a BaAdV infection, confirm an earlier infection, and determine BaAdV viral load. In some embodiments, antibodies that specifically bind BaAdV-2/4 can be used for detection of BaAdV-2/4, diagnosis, and determination of BaAdV-2/4 viral load. In other embodiments, antibodies that specifically bind BaAdV-3 can be used for detection of BaAdV-3, diagnosis, and determination of BaAdV-3 viral load. In further embodiments, these methods distinguish a BaAdV-3 infection, such as from a BaAdV-2/4 infection and/or a BaAdV-1 infection. In further embodiments, antibodies that specifically bind BaAdV-2/4 can be used for detection of BaAdV-2/4, diagnosis, and determination of BaAdV-2/4 viral load. In further embodiments, these methods distinguish a BaAdV-2/4 infection, such as from a BaAdV-3 infection and/or a BaAdV-1 infection. In some embodiments, the method distinguishes BaAdV-2/4 and/or BaAdV-3 from BaAdV-1.
Thus, in certain embodiments, methods are provided that utilize an antibody specifically binds BaAdV-2/4 and not BaAd-3 or BaAdV-1 polypeptide(s), and thus can be used for the specific detection of BaAdV-2/4. Thus, the antibody can be used to distinguish (delineate) a BaAdV-2/4 infection from a BaAd3- and BaAdV-1 infection. In other embodiments, methods are provided that utilize an antibody specifically binds BaAdV-3 and not BaAd-2/4 or BaAdV-1 polypeptide(s), and thus can be utilized for specific detection of BaAdV-3. Thus, the antibody can be used to distinguish (delineate) a BaAdV-infection from a BaAdV-1 and BaAd-2/4 infection. In further embodiments, methods are provided that utilize an antibody that specifically binds both BaAdv-3 and BaAdv-2/4 polypeptides, and thus can be utilized to specifically detect both BaAdV-3 and BaAd-2/4, but not BaAdV-1. Thus, the antibody can be used to distinguish (delineate) a BaAdV-3/BaAdV-2/4 infection from a BaAdV-1 infection. In some embodiments, the antibody is a monoclonal antibody. In other embodiments, the antibody is directly labeled. In some non-limiting examples, the antibody specifically binds a BaAdV-2/4 polypeptide, and/or a BaAdV-3 polypeptide, such as polypeptide at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100% identical to one of SEQ ID NOs: 5-109.
Once the specific antibodies against a BaAdV protein, virus or nucleic acid in are available, the antigen can be detected and/or quantified using any of a number of well recognized immunological binding assays (see, e.g., U.S. Pat. Nos. 4,366,241; 4,376,110; 4,517,288; and 4,837,168). BaAdV viral particles can be detected based on an epitope defined by the viral proteins as presented in a viral particle and/or an epitope defined by a viral protein that is separate from a viral particle. As used in this context, then, “antigen” is meant to refer to a BaAdV polypeptide as well as BaAdV viral particles. For a review of the general immunoassays, see also Methods in Cell Biology: Antibodies in Cell Biology, volume 37 (Asai, ed. 1993); Basic and Clinical Immunology (Stites & Terr, eds., 7th ed. 1991) Immunological binding assays (or immunoassays) typically use an antibody that specifically binds to a protein or antigen of choice. The antibody can be produced by any of a number of means well known to those of skill in the art and as described above Immunoassays for detecting BaAdV protein, virus and nucleic acid in samples can be either competitive or noncompetitive, and can be either quantitative or non-quantitative.
Noncompetitive immunoassays are assays in which antigen is directly detected and, in some instances the amount of antigen directly measured. Enzyme mediated immunoassays such as immunofluorescence assays (IFA), enzyme linked immunosorbent assays (ELISA), immunoblotting (western), and capture assays can be readily adapted to accomplish the noncompetitive detection of the BaAdV proteins.
An ELISA method effective for the detection of the BaAdV can, for example, be as follows: (1) bind an antibody or antigen to a substrate; (2) contact the bound receptor with a fluid or tissue sample containing the virus, a viral antigen, or antibodies to the virus; (3) contact the above with an antibody bound to a detectable moiety (e.g., horseradish peroxidase enzyme or alkaline phosphatase enzyme); (4) contact the above with the substrate for the enzyme; (5) contact the above with a color reagent; (6) observe color change. The above method can be readily modified to detect presence of an anti-BaAdV antibody in the sample or a specific BaAdV polypeptide as well as the virus.
Western blot (immunoblot) analysis can be used to detect and quantify the presence of BaAdV antigen in the sample. The technique generally comprises separating sample proteins by gel electrophoresis on the basis of molecular weight, transferring the separated proteins to a suitable solid support, (such as a nitrocellulose filter, a nylon filter, or derivatized nylon filter), and incubating the sample with the antibodies that specifically bind the BaAdV antigen. The anti-BaAdV antigen antibodies specifically bind to the BaAdV antigen on the solid support. These antibodies can be directly labeled or alternatively can be subsequently detected using labeled antibodies (e.g., labeled sheep anti-mouse antibodies) that specifically bind to the anti-BaAdV antigen antibodies.
Other assay formats include liposome immunoassays (LIA), which use liposomes designed to bind specific molecules (e.g., antibodies) and release encapsulated reagents or markers. The released chemicals are then detected according to standard techniques (see Monroe et al., Amer. ClM. Prod. Rev. 5:34-41 (1986)).
A BaAdV antigen and/or a patient's antibodies to the virus can be detected utilizing a capture assay. Briefly, to detect antibodies to BaAdV in a patient sample, antibodies to the patient's immunoglobulin, e.g., anti-IgG (or IgM) are bound to a solid phase substrate and used to capture the patient's immunoglobulin from serum. BaAdV, or reactive fragments of BaAdV, are then contacted with the solid phase followed by addition of a labeled antibody. The amount of patient BaAdV specific antibody can then be quantitated by the amount of labeled antibody binding. In some embodiments, a method is provided for detecting a baboon adenovirus (BaAdV)-3 or a BaAdV-2/4 infection in a subject. The method includes the steps of: (a) contacting a sample from the subject suspected of having an infection caused by the BaAdV-3 or the BaAdV-2/4 with a BaAdv-3 or BaAdv-2/4 polypeptide, wherein the sample comprises antibodies from the subject, and(b) detecting the binding of the antibodies to the polypeptide, thereby detecting the BaAdV-3 or a BaAdV-2/4 infection.
In competitive assays, BaAdV antigen present in a sample can be detected indirectly by detecting a decrease in a detectable signal associated with a known, added (exogenous) BaAdV antigen displaced (competed away) from an anti-BaAdV antigen antibody by the unknown BaAdV antigen present in a sample.
Competitive assays can also be adapted to provide for an indirect measurement of the amount of BaAdV antigen present in the sample. Briefly, serum or other body fluids from the subject is reacted with an antibody bound to a substrate (e.g. an ELISA 96-well plate). Excess serum is thoroughly washed away. A labeled (enzyme-linked, fluorescent, radioactive, etc.) monoclonal antibody is then reacted with the previously reacted BaAdV virus-antibody complex. The amount of inhibition of monoclonal antibody binding is measured relative to a control. MABs can also be used for detection directly in samples by IFA for MABs specifically reactive for the antibody-virus complex.
A hapten inhibition assay is another competitive assay. In this assay the known BaAdV antigen can be immobilized on a solid substrate. A known amount of anti-BaAdV antibody is added to the sample, and the sample is then contacted with the immobilized BaAdV antigen. The amount of anti-BaAdV antibody bound to the known immobilized BaAdV antigen is inversely proportional to the amount of BaAdV antigen present in the sample. The amount of immobilized antibody can be detected by detecting either the immobilized fraction of antibody or the fraction of the antibody that remains in solution. Detection can be direct where the antibody is labeled or indirect by the subsequent addition of a labeled moiety that specifically binds to the antibody as described above.
Immunoassays in the competitive binding format can also be used for crossreactivity determinations. For example, a BaAdV antigen can be immobilized to a solid support. Proteins can be added to the assay that compete for binding of the antisera to the immobilized antigen. The ability of the added proteins to compete for binding of the antisera to the immobilized protein is compared to the ability of the BaAdV antigen to compete with itself. The percent crossreactivity for the above proteins is calculated, using standard calculations. Those antisera with less than 10% crossreactivity with each of the added proteins listed above are selected and pooled. The cross-reacting antibodies are optionally removed from the pooled antisera by immunoabsorption with the added considered proteins, e.g., distantly related homologs.
The immunoabsorbed and pooled antisera can then be used in a competitive binding immunoassay as described above to compare a second protein, thought to be perhaps an allele or polymorphic variant of a BaAdV antigen, to the immunogen protein. In order to make this comparison, the two proteins are each assayed at a wide range of concentrations and the amount of each protein required to inhibit 50% of the binding of the antisera to the immobilized protein is determined. If the amount of the second protein required to inhibit 50% of binding is less than 10 times the amount of the BaAdV antigen that is required to inhibit 50% of binding, then the second protein is said to specifically bind to the polyclonal antibodies generated to BaAdV antigen.
Immunoassays (both competitive and non-competitive) also often use a labeling agent to specifically bind to and label the complex formed by the antibody and antigen. The labeling agent can itself be one of the moieties comprising the antibody/antigen complex. Thus, the labeling agent can be a labeled BaAdV protein nucleic acid or a labeled anti-BaAdV antibody. Alternatively, the labeling agent can be a third moiety, such a secondary antibody that specifically binds to the antibody/antigen complex (a secondary antibody is typically specific to antibodies of the species from which the first antibody is derived). Other proteins capable of specifically binding immunoglobulin constant regions, such as protein A or protein G can also be used as a label agent. These proteins exhibit a strong non-immunogenic reactivity with immunoglobulin constant regions from a variety of species (see, e.g., Kronval et al., J. Immunol. 111:1401-1406 (1973); Akerstrom et al., J. Immunol. 135:2589-2542 (1985)). The labeling agent can be modified with a detectable moiety, such as biotin, to which another molecule can specifically bind, such as streptavidin. A variety of detectable moieties are well known to those skilled in the art, and can be any material detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means. Such detectable labels have been well-developed in the field of immunoassays and can include, but are not limited to, magnetic beads (e.g., DYNABEADS™), fluorescent dyes (e.g., fluorescein isothiocyanate, Texas red, rhodamine, and the like), radiolabels (e.g., 3H, 125j 35s, 14,e, or --¹²P), enzymes (e.g., horse radish peroxidase, alkaline phosphatase and others commonly used in an ELISA), and colorimetric labels such as colloidal gold or colored glass or plastic beads (e.g., polystyrene, polypropylene, latex, etc.).
The label can be coupled directly or indirectly to the desired component of the assay according to methods well known in the art. As indicated above, a wide variety of labels can be used, with the choice of label depending on sensitivity required, ease of conjugation with the compound, stability requirements, available instrumentation, and disposal provisions.
Non-radioactive labels are often attached by indirect means. Generally, a ligand molecule (e.g., biotin) is covalently bound to the molecule. The ligand then binds to another molecules (e.g., streptavidin) molecule, which is either inherently detectable or covalently bound to a signal system, such as a detectable enzyme, a fluorescent compound, or a chemiluminescent compound. The ligands and their targets can be used in any suitable combination with antibodies that recognize BaAdV antigen, or secondary antibodies that recognize anti-BaAdV antigen.
The molecules can also be conjugated directly to signal generating compounds, e.g., by conjugation with an enzyme or fluorophore, see above. Enzymes of interest as labels will primarily be hydrolases, particularly phosphatases, esterases and glycosidases, or oxidotases, particularly peroxidases. Fluorescent compounds include fluorescein and its derivatives, rhodamine and its derivatives, dansyl, umbelliferone, etc. Chemiluminescent compounds include luciferin, and 2,3-dihydrophthalazinediones, e.g., luminol For a review of various labeling or signal producing systems that can be used, see U.S. Pat. No. 4,391,904.
Means of detecting labels are well known to those of skill in the art. Thus, for example, where the label is a radioactive label, means for detection include a scintillation counter or photographic film as in autoradiography. Where the label is a fluorescent label, it can be detected by exciting the fluorochrome with the appropriate wavelength of light and detecting the resulting fluorescence. The fluorescence can be detected visually, by the use of electronic detectors such as charge coupled devices (CCDs) or photomultipliers and the like. Similarly, enzymatic labels can be detected by providing the appropriate substrates for the enzyme and detecting the resulting reaction product. Colorimetric or chemiluminescent labels can be detected simply by observing the color associated with the label. Thus, in various dipstick assays, conjugated gold often appears pink, while various conjugated beads appear the color of the bead.
Some assay formats do not require the use of labeled components. For instance, a micro-agglutination test can also be used to detect the presence of BaAdV in test samples. Briefly, latex beads are coated with an antibody and mixed with a test sample, such that BaAdV in the tissue or body fluids that is specifically reactive with the antibody crosslink with the receptor, causing agglutination. The agglutinated antibody-virus complexes within a precipitate, visible with the naked eye or by spectrophotometer. Other assays include serologic assays, in which the relative concentrations of IgG and IgM are measured.
One of skill in the art will appreciate that it is often desirable to minimize non-specific binding in immunoassays. Particularly, where the assay involves an antigen or antibody immobilized on a solid substrate it is desirable to minimize the amount of non-specific binding to the substrate. Means of reducing such non-specific binding are well known to those of skill in the art. Typically, this technique involves coating the substrate with a proteinaceous composition. In particular, protein compositions such as bovine serum albumin (BSA), nonfat powdered milk, and gelatin are widely used with powdered milk being most preferred.
In the diagnostic methods described above, the sample can be taken directly from a subject or in a partially purified form. The sample can be any sample of interest, including blood, serum or plasma. The antibody specific for a particular BaAdV (the primary reaction) reacts by binding to the virus. Thereafter, a secondary reaction with an antibody bound to, or labeled with, a detectable moiety can be added to enhance the detection of the primary reaction. Generally, in the secondary reaction, an antibody or other ligand which is reactive, either specifically or nonspecifically with a different binding site (epitope) of the virus will be selected for its ability to react with multiple sites on the complex of antibody and virus. Thus, for example, several molecules of the antibody in the secondary reaction can react with each complex formed by the primary reaction, making the primary reaction more detectable.

Assays for Modulators of BaAdV

Modulation of a BaAdV, such as BaAdV-2/4 or BaAdV-3, can be assessed using a variety of in vitro and in vivo assays, including cell-based models. Such assays can be used to test for inhibitors and activators of BaAdV-2/4 and/or BaAdV-3. Modulators of BaAdV-2/4 and/or BaAdV-3 are tested using either recombinant or naturally occurring protein of choice. Modulation can include, but is not limited to, modulation of infection, replication, receptor binding, cell entry, particle formation, and the like.
Measurement of modulation of a BaAdV-2/4 and/or BaAdV-3 polypeptide, or a cell expressing BaAdV-2/4 and/or BaAdV-3, either recombinant or naturally occurring, can be performed using a variety of assays, in vitro, in vivo, and ex vivo, as described herein. A suitable physical, chemical or phenotypic change that affects activity, e.g., enzymatic activity, cell surface marker expression, viral replication and proliferation can be used to assess the influence of a test compound on the polypeptide of this invention. When the functional effects are determined using intact cells or animals, one can also measure a variety of effects.
Assays to identify compounds with BaAdV-2/4 and/or BaAdV-3 modulating activity can be performed in vitro. Such assays can use full length BaAdV-2/4 or BaAdV-3 polypeptide or a variant thereof, or a mutant thereof, or a fragment thereof. Purified recombinant or naturally occurring protein can be used in the in vitro methods of the invention. The recombinant or naturally occurring protein can be part of a cellular lysate or a cell membrane. As disclosed below, the binding assay can be either solid state or soluble. Preferably, the protein or membrane is bound to a solid support, either covalently or non-covalently. Often, the in vitro assays of the invention are substrate or ligand binding or affinity assays, either non-competitive or competitive. Other in vitro assays include measuring changes in spectroscopic (e.g., fluorescence, absorbance, refractive index), hydrodynamic (e.g., shape), chromatographic, or solubility properties for the protein.
A high throughput binding assay can be performed in which the protein or a fragment thereof is contacted with a potential modulator and incubated for a suitable amount of time. In one embodiment, the potential modulator is bound to a solid support, and the protein is added. In another embodiment, the protein is bound to a solid support. A wide variety of modulators can be used, as described below, including small organic molecules, peptides, antibodies, etc. A wide variety of assays can be used to identify BaAdV-2/4 and/or BaAdV-3-modulator binding, including labeled protein-protein binding assays, electrophoretic mobility shifts, immunoassays, enzymatic assays, and the like. In some cases, the binding of the candidate modulator is determined through the use of competitive binding assays, where interference with binding of a known ligand or substrate is measured in the presence of a potential modulator. Either the modulator, the known ligand, or substrate is bound first; then the competitor is added. After the protein is washed, interference with binding, either of the potential modulator or of the known ligand or substrate, is determined. Often, either the potential modulator or the known ligand or substrate is labeled.
A cell-based assay can be used in which the BaAdV-2/4 or BaAdV-3 is expressed in a cell, and functional, physical, chemical and phenotypic changes are assayed to identify viral modulators. Any suitable functional effect can be measured as described herein, in addition to viral inhibition assays as are well known in the art. The BaAdV-2/4 or BaAdV-3 can be naturally occurring or recombinant. Also, fragments of the BaAdV-2/4 or BaAdV-3 or chimeric proteins can be used in cell based assays. In addition, point mutants in essential residues required by the catalytic site can be used in these assays.
In one embodiment, high throughput screening methods involve providing a combinatorial small organic molecule or peptide library containing a large number of potential therapeutic compounds (potential modulator or ligand compounds). Such “combinatorial chemical libraries” or “ligand libraries” are then screened in one or more assays, as described herein, to identify those library members (particular chemical species or subclasses) that display a desired characteristic activity. The compounds thus identified can serve as conventional “lead compounds” or can themselves be used as potential or actual therapeutics.
A combinatorial chemical library is a collection of diverse chemical compounds generated by either chemical synthesis or biological synthesis, by combining a number of chemical “building blocks” such as reagents. For example, a linear combinatorial chemical library such as a polypeptide library is formed by combining a set of chemical building blocks (amino acids) in every possible way for a given compound length (i.e., the number of amino acids in a polypeptide compound). Millions of chemical compounds can be synthesized through such combinatorial mixing of chemical building blocks. The assay can also be used to screen libraries of molecular agents, such as antibodies or inhibitory RNAs, or to screen libraries of small molecules.
Preparation and screening of combinatorial chemical libraries is well known to those of skill in the art. Such combinatorial chemical libraries include, but are not limited to, peptide libraries (see, e.g., U.S. Pat. No. 5,010,175, Furka, Int. J. Pept. Prot. Res. 37:487-493 (1991) and Houghton et al., Nature 354:84-88 (1991)). Other chemistries for generating chemical diversity libraries can also be used. Such chemistries include, but are not limited to: peptoids (e.g., PCT Publication No. WO 91/19735), encoded peptides (e.g., PCT Publication No. WO 93/20242), random bio-oligomers (e.g., PCT Publication No. WO 92/00091), benzodiazepines (e.g., U.S. Pat. No. 5,288,514), diversomers such as hydantoins, benzodiazepines and dipeptides (Hobbs et al., Proc. Nat. Acad. Sci. USA 90:6909-6913 (1993)), vinylogous polypeptides (Hagihara et al., J. Amer. Chem. Soc. 114:6568 (1992)), nonpeptidal peptidomimetics with glucose scaffolding (Hirschmann et al., J. Amer. Chem. Soc. 114:9217-9218 (1992)), analogous organic syntheses of small compound libraries (Chen et al., I Amer. Chem. Soc. 116:2661 (1994)), oligocarbamates (Cho et al., Science 261:1303 (1993)), and/or peptidyl phosphonates (Campbell et al., I Org. Chem. 59:658 (1994)), nucleic acid libraries (see Ausubel, Berger and Sambrook, all supra), peptide nucleic acid libraries (see, e.g., U.S. Pat. No. 5,539,083), antibody libraries (see, e.g., Vaughn et al., Nature Biotechnology, 14(3):309-314 (1996)), carbohydrate libraries (see, e.g., Liang et al., Science, 274:1520-1522 (1996) and U.S. Pat. No. 5,593,853), small organic molecule libraries (see, e.g., benzodiazepines, Baum C&EN, January 18, page 33 (1993); isoprenoids, U.S. Pat. No. 5,569,588; thiazolidinones and metathiazanones, U.S. Pat. No. 5,549,974; pyrrolidines, U.S. Pat. Nos. 5,525,735 and 5,519,134; morpholino compounds, U.S. Pat. No. 5,506,337; benzodiazepines, U.S. Pat. No. 5,288,514, and the like).
Devices for the preparation of combinatorial libraries are commercially available (see, e.g., 357 MPS, 390 MPS, Advanced Chem Tech, Louisville Ky., Symphony, Rainin, Woburn, Mass., 433A Applied Biosystems, Foster City, Calif., 9050 Plus, Millipore, Bedford, Mass.). In addition, numerous combinatorial libraries are themselves commercially available (see, e.g., ComGenex, Princeton, N.J., Asinex, Moscow, Ru, Tripos, Inc., St. Louis, Mo., ChemStar, Ltd, Moscow, RU, 3D Pharmaceuticals, Exton, Pa., Martek Biosciences, Columbia, Md., etc.).
A solid state or soluble high throughput assaying using a BaAdV-2/4 or BaAdV-3, or a cell or tissue expressing a BaAdV-2/4 or BaAdV-3 protein can be used. A solid phase based in vitro assay can be used in a high throughput format can be used where BaAdV-2/4 and/or BaAdV-3 is attached to a solid phase. Any one of the assays described herein can be adapted for high throughput screening.
In high throughput assays, either soluble or solid state, it is possible to screen up to several thousand different modulators or ligands in a single day. This methodology can be used for BaAdV-2/4 or BaAdV-3 in vitro, or for cell-based or membrane-based assays comprising a BaAdV. In particular, each well of a microtiter plate can be used to run a separate assay against a selected potential modulator, or, if concentration or incubation time effects are to be observed, every 5-10 wells can test a single modulator. Thus, a single standard microtiter plate can assay about 100 (e.g., 96) modulators. If 1536 well plates are used, then a single plate can easily assay from about 100- about 1500 different compounds. It is possible to assay many plates per day; assay screens for up to about 6,000, 20,000, 50,000, or more than 100,000 different compounds are possible using the integrated systems of the invention.
For a solid state reaction, the protein of interest or a fragment thereof, e.g., an extracellular domain, or a cell or membrane comprising the protein of interest or a fragment thereof as part of a fusion protein can be bound to the solid state component, directly or indirectly, via covalent or non-covalent linkage. A tag for covalent or non-covalent binding can be any of a variety of components. In general, a molecule which binds the tag (a tag binder) is fixed to a solid support, and the tagged molecule of interest is attached to the solid support by interaction of the tag and the tag binder.
A number of tags and tag binders can be used, based upon known molecular interactions well described in the literature. For example, where a tag has a natural binder, for example, biotin, protein A, or protein G, it can be used in conjunction with appropriate tag binders (avidin, streptavidin, neutravidin, the Fc region of an immunoglobulin, etc.). Antibodies to molecules with natural binders such as biotin are also widely available and appropriate tag binders (see, SIGMA Immunochemicals 1998 catalogue SIGMA, St. Louis Mo.).
Similarly, any haptenic or antigenic compound can be used in combination with an appropriate antibody to form a tag/tag binder pair. Thousands of specific antibodies are commercially available and many additional antibodies are described in the literature. For example, in one common configuration, the tag is a first antibody and the tag binder is a second antibody which recognizes the first antibody. In addition to antibody-antigen interactions, receptor-ligand interactions are also appropriate as tag and tag-binder pairs. For example, agonists and antagonists of cell membrane receptors (e.g., cell receptor-ligand interactions such as transferrin, c-kit, viral receptor ligands, cytokine receptors, chemokine receptors, interleukin receptors, immunoglobulin receptors and antibodies, the cadherein family, the integrin family, the selectin family, and the like (see, e.g., Pigott & Power, The Adhesion Molecule Facts Book I (1993)). Similarly, toxins and venoms, viral epitopes, hormones (e.g., opiates, steroids, etc.), intracellular receptors (e.g. which mediate the effects of various small ligands, including steroids, thyroid hormone, retinoids and vitamin D; peptides), drugs, lectins, sugars, nucleic acids (both linear and cyclic polymer configurations), oligosaccharides, proteins, phospholipids and antibodies can all interact with various cell receptors.
Synthetic polymers, such as polyurethanes, polyesters, polycarbonates, polyureas, polyamides, polyethyleneimines, polyarylene sulfides, polysiloxanes, polyimides, and polyacetates can also form an appropriate tag or tag binder. Many other tag/tag binder pairs are also useful in assay systems described herein, as would be apparent to one of skill upon review of this disclosure.
Common linkers such as peptides, polyethers, and the like can also serve as tags, and include polypeptide sequences, such as poly gly sequences of between about 5 and 200 amino acids. Such flexible linkers are known to persons of skill in the art. For example, polyethylene glycol linkers are available from Shearwater Polymers, Inc. Huntsville, Ala. These linkers optionally have amide linkages, sulfhydryl linkages, or heterofunctional linkages.
Tag binders are fixed to solid substrates using any of a variety of methods currently available. Solid substrates are commonly derivatized or functionalized by exposing all or a portion of the substrate to a chemical reagent which fixes a chemical group to the surface which is reactive with a portion of the tag binder. For example, groups which are suitable for attachment to a longer chain portion would include amines, hydroxyl, thiol, and carboxyl groups Aminoalkylsilanes and hydroxyalkylsilanes can be used to functionalize a variety of surfaces, such as glass surfaces. The construction of such solid phase biopolymer arrays is well described in the literature (e.g., Merrifield, J. Am. Chem. Soc. 85:2149-2154 (1963) (describing solid phase synthesis of, e.g., peptides); Geysen et al., J. Immun. Meth. 102:259-274 (1987) (describing synthesis of solid phase components on pins); Frank & Doring, Tetrahedron 44:60316040 (1988) (describing synthesis of various peptide sequences on cellulose disks); Fodor et al., Science, 251:767-777 (1991); Sheldon et al., Clinical Chemistry 39(4):718-719 (1993); and Kozal et al., Nature Medicine 2(7):753759 (1996) (all describing arrays of biopolymers fixed to solid substrates)). Non-chemical approaches for fixing tag binders to substrates include other common methods, such as heat, cross-linking by UV radiation, and the like.
The compounds tested as modulators of BaAdV-2/4 or BaAdV-3 can be any small organic molecule, or a biological entity, such as a protein, e.g., an antibody or peptide, a sugar, a nucleic acid, e.g., an antisense oligonucleotide or a ribozyme or siRNA, or a lipid.
Alternatively, modulators can be genetically altered versions of a BaAdV. Typically, test compounds will be small organic molecules, peptides, circular peptides, siRNA, antisense molecules, ribozymes, and lipids.
Essentially any chemical compound can be used as a potential modulator or ligand in the assays of the invention, although most often compounds can be dissolved in aqueous or organic (especially DMSO-based) solutions are used. The assays are designed to screen large chemical libraries by automating the assay steps and providing compounds from any convenient source to assays, which are typically run in parallel (e.g., in microtiter formats on microtiter plates in robotic assays). It will be appreciated that there are many suppliers of chemical compounds, including Sigma (St. Louis, Mo.), Aldrich (St. Louis, Mo.), Sigma-Aldrich (St. Louis, Mo.), Fluka Chemika-Biochemica Analytika (Buchs Switzerland) and the like.

Treating/Preventing BaAdV and Pharmaceutical Compositions

Embodiments described herein further relate to the therapeutic, prophylactic and research uses of various techniques to block or modulate the expression of BaAdV-2/4 and/or BaAdV-3 viral proteins or propagation of the virus. Methods are also provided for inducing an immune response to BaAdV-2/4 and/or BaAdV-3. Modulators of BaAdV-2/4 and/or BaAdV-3 useful for treating or preventing BaAdV-2/4 and/or BaAdV-3 can include, but is not limited to, genetically modified versions of BaAdV-2/4 and/or BaAdV-3, e.g., versions with altered activity, heat killed and attenuated viruses, as well as naturally occurring and synthetic ligands, substrates, antagonists, agonists, antibodies, peptides, cyclic peptides, aptamers, nucleic acids, antisense molecules, ribozymes, siRNA molecules, miRNA molecules, and small chemical molecules, as is well known in the art.
Methods of treating or preventing a Baboon adenovirus (BaAdV)-2/4 or BaAdV-3 infection in a subject are provided herein. These methods include administering to the subject a therapeutically effective dose of one or more of an agents identified using the assays disclosed herein, the nucleic acid molecules discloses herein, the polypeptides disclosed herein or an immunogenic fragment thereof, a replication defective adenovirus disclosed herein, or an antibody disclosed herein.
Methods of inducing an immune response to a Baboon adenovirus (BaAdV)-2/4 or BaAdV-3 are disclosed herein. These methods include administering to the subject a therapeutically effective dose of one or more of an agents identified using the assays disclosed herein, the nucleic acid molecules discloses herein, the polypeptides disclosed herein or an immunogenic fragment thereof, a replication defective adenovirus disclosed herein, or an antibody disclosed herein. The subject can be any subject of interest, including a human or a non-human primate.
In some embodiments, an aptamer is administered to the subject. The aptamer is an siRNA or antisense molecule comprising a double-stranded region of about 15 to about 60 nucleotides in length and has at least 90% identity over its length to a corresponding segment of SEQ ID NO:1, SEQ ID NO: 2 or SEQ ID NO: 3.
Further disclosed herein are BaAdV-2/4 and BaAdV-3 vaccines for therapeutic or prophylactic purposes. Within certain aspects, BaAdV-2/4 and/or BaAdV-3 virus, proteins or peptides and immunogenic fragments thereof, and/or polynucleotides, as well as anti-BaAdV-2/4 and anti-BaAdV-3 antibodies and/or T cells, can be incorporated into pharmaceutical compositions or immunogenic compositions. Whole virus vaccines (live and attenuated, or replication incompetent, or killed) or subunit vaccines, such as structural or non-structural BaAdV-2/4 and/or BaAdV-3 proteins or immunogenic fragments thereof, can be used to treat or prevent BaAdV-2/4 and/or BaAdV-3 infections, respectively by eliciting an immune response in a subject. Alternatively, a pharmaceutical composition can comprise an antigen-presenting cell (e.g., a dendritic cell) transfected with a BaAdV-2/4 or BaAdV-3 polynucleotide such that the antigen-presenting cell expresses a BaAdV-2/4 or BaAdV-3 peptide, respectively.
Nucleic acid vaccines encoding a genome, structural protein or non-structural protein or a fragment thereof of BaAdV-2/4 and/or BaAdV-3 can also be used to elicit an immune response to treat or prevent BaAdV-2/4 and/or BaAdV-3 infection, respectively. Numerous gene delivery techniques are well known in the art, such as those described by Rolland (1998) Crit. Rev. Therap. Drug Carrier Systems 15:143-198, and references cited therein. Appropriate nucleic acid expression systems contain the necessary DNA sequences for expression in the patient (such as a suitable promoter and terminating signal). In a preferred embodiment, the DNA can be introduced using a viral expression system (e.g., vaccinia, pox virus, retrovirus, or adenovirus), which can involve the use of a non-pathogenic (defective), replication competent virus. Suitable systems are disclosed, for example, in Fisher-Hoch et al. (1989) Proc. Natl. Acad. Sci. USA 86:317-321; Flexner et al. (1989) Ann. N.Y. Acad. Sci. 569:86-103; Flexner et al. (1990) Vaccine 8:17-21; U.S. Pat. Nos. 4,603,112, 4,769,330, 4,777,127 and 5,017,487; PCT Publication No. WO 89/01973; Great Britain Publication No. 2,200,651; European Publication No. 0,345,242; PCT Publication No. WO 91/02805; Berkner (1988) Biotechniques 6:616-627; Rosenfeld et al. (1991) Science 252:431-434; Kolls et al. (1994) Proc. Natl. Acad. Sci. USA 91:215-219; Kass-Eisler et al. (1993) Proc. Natl. Acad. Sci. USA 90:11498-11502; Guzman et al. (1993) Circulation 88:2838-2848; and Guzman et al. (1993) Cir. Res. 73:1202-1207. Techniques for incorporating DNA into such expression systems are well known to those of ordinary skill in the art. The DNA can also be “naked,” as described, for example, in Ulmer et al. (1993) Science 259:1745-1749 and reviewed by Cohen (1993) Science 259:1691-1692. The uptake of naked DNA can be increased by coating the DNA onto biodegradable beads, which are efficiently transported into the cells. It will be apparent that a vaccine can comprise both a polynucleotide and a polypeptide component. Such vaccines can provide for an enhanced immune response.
Vaccine preparation is generally described in, for example, Powell and Newman, eds., Vaccine Design (the subunit and adjuvant approach), Plenum Press (NY, 1995). Vaccines can be designed to generate antibody immunity and/or cellular immunity such as that arising from CTL or CD4+ T cells.
A non-specific immune response enhancer can be any substance that enhances an immune response to an exogenous antigen. Examples of non-specific immune response enhancers include adjuvants, biodegradable microspheres (e.g., polylactic galactide) and liposomes (into which the compound is incorporated; see, e.g., U.S. Pat. No. 4,235,877). Most adjuvants contain a substance designed to protect the antigen from rapid catabolism, such as aluminum hydroxide or mineral oil, and a stimulator of immune responses, such as lipid A, Bortadella pertussis or Mycobacterium tuberculosis derived proteins. Suitable adjuvants are commercially available as, for example, Freund's Incomplete Adjuvant and Complete Adjuvant (Difco Laboratories, Detroit, Mich.); Merck Adjuvant 65 (Merck and Company, Inc., Rahway, N.J.); AS-2 (SmithKline Beecham); aluminum salts such as aluminum hydroxide gel (alum) or aluminum phosphate; salts of calcium, iron or zinc; an insoluble suspension of acylated tyrosine; acylated sugars; cationically or anionically derivatized polysaccharides; polyphosphazenes; biodegradable microspheres; monophosphoryl lipid A and quil A. Cytokines, such as GM-CSF or interleukin-2, -7, or -12, can also be used as adjuvants. These are of use in inducing an immune response.
Pharmaceutical compositions and vaccines can also contain other compounds, which can be biologically active or inactive. For example, one or more immunogenic portions of other antigens can be present, either incorporated into a fusion polypeptide or as a separate compound, within the composition or vaccine. Polypeptides can, but need not be, conjugated to other macromolecules as described, for example, within U.S. Pat. Nos. 4,372,945 and 4,474,757. Pharmaceutical compositions and vaccines can generally be used for prophylactic and therapeutic purposes.
Formulations suitable for oral administration can consist of (a) liquid solutions, such as an effective amount of the packaged nucleic acid suspended in diluents, such as water, saline or PEG 400; (b) capsules, sachets or tablets, each containing a predetermined amount of the active ingredient, as liquids, solids, granules or gelatin; (c) suspensions in an appropriate liquid; and (d) suitable emulsions. Tablet forms can include one or more of lactose, sucrose, mannitol, sorbitol, calcium phosphates, corn starch, potato starch, microcrystalline cellulose, gelatin, colloidal silicon dioxide, talc, magnesium stearate, stearic acid, and other excipients, colorants, fillers, binders, diluents, buffering agents, moistening agents, preservatives, flavoring agents, dyes, disintegrating agents, and pharmaceutically compatible carriers. Lozenge forms can comprise the active ingredient in a flavor, e.g., sucrose, as well as pastilles comprising the active ingredient in an inert base, such as gelatin and glycerin or sucrose and acacia emulsions, gels, and the like containing, in addition to the active ingredient, carriers known in the art.
Aerosol formulations (i.e., they can be “nebulized”) are administered via inhalation. Aerosol formulations can be placed into pressurized acceptable propellants, such as dichlorodifluoromethane, propane, nitrogen, and the like.
Formulations suitable for parenteral administration, for example, by intraarticular (in the joints), intravenous, intramuscular, intradermal, intraperitoneal, and subcutaneous routes, include aqueous and non-aqueous, isotonic sterile injection solutions, which can contain antioxidants, buffers, bacteriostats, and solutes that render the formulation isotonic with the blood of the intended recipient, and aqueous and non-aqueous sterile suspensions that can include suspending agents, solubilizers, thickening agents, stabilizers, and preservatives. Compositions can be administered, for example, by intravenous infusion, inhalation, parenterally, orally, topically, intradermally, intraperitoneally, intravenously, intravesically, rectally or intrathecally. The formulations can be presented in unit-dose or multi-dose sealed containers, such as ampules and vials. Pharmaceutically acceptable carriers are determined in part by the particular composition being administered (e.g., nucleic acid, protein, modulatory compounds or transduced cell), as well as by the particular method used to administer the composition. Accordingly, there are a wide variety of suitable formulations of pharmaceutical compositions of the present invention (see, e.g., Remington's Pharmaceutical Sciences, 17^thed., 1989).
Such compositions can also comprise buffers (e.g., neutral buffered saline or phosphate buffered saline), carbohydrates (e.g., glucose, mannose, sucrose or dextrans), mannitol, proteins, polypeptides or amino acids such as glycine, antioxidants, bacteriostats, chelating agents such as EDTA or glutathione, adjuvants (e.g., aluminum hydroxide), solutes that render the formulation isotonic, hypotonic or weakly hypertonic with the blood of a recipient, suspending agents, thickening agents and/or preservatives. Alternatively, compositions of the present invention can be formulated as a lyophilizate. Compounds can also be encapsulated within liposomes using well known technology.
Injection solutions and suspensions can be prepared from sterile powders, granules, and tablets of the kind previously described. Cells transduced by nucleic acids for ex vivo therapy can also be administered intravenously or parenterally.
The dose administered to a subject should be sufficient to affect a beneficial therapeutic response in the subject over time, and/or to induce an immune response. The dose will be determined by the efficacy of the particular agent employed and the condition of the subject, as well as the body weight or surface area of the subject to be treated. The size of the dose also will be determined by the existence, nature, and extent of any adverse side-effects that accompany the administration of a particular vector, or transduced cell type in a particular subject. In some embodiments, the agent is the agent is administered orally, topically, intraarticularly, intravenously, intramuscularly, intradermally, intraperitoneally or subcutaneously.
For administration, compounds and transduced cells of the present invention can be administered at a rate determined by the LD-50 of the inhibitor, vector, or transduced cell type, and the side-effects of the inhibitor, vector or cell type at various concentrations, as applied to the mass and overall health of the patient. Administration can be accomplished via single or divided doses.
Pharmaceutical and vaccine compositions can be presented in unit-dose or multi-dose containers, such as sealed ampoules or vials. Such containers are preferably hermetically sealed to preserve sterility of the formulation until use. In general, formulations can be stored as suspensions, solutions or emulsions in oily or aqueous vehicles. Alternatively, a vaccine or pharmaceutical composition can be stored in a freeze-dried condition requiring only the addition of a sterile liquid carrier immediately prior to use.

Additional Diagnostic and Therapeutic Methods

Methods are also provided for identifying subjects and managing the therapeutic treatment of subjects, such as those subjects who are at an increased risk of a BaAdV-2/4 or a BaAdV-3 infection. In some embodiments the methods include using the BaAdV-2/4 or a BaAdV-3 nucleic acids, polypeptides or antibodies disclosed herein to detect a BaAdV-2/4 or a BaAdV-3 infection in a subject. The subject can be at increased risk for infection, such as a worker in a primate colony, such as one that houses baboons. The subject can also be an individual who has contact with a worker in a primate colony, such as, but not limited to, a household member. In some embodiments, the subject can be asymptomatic.
The provided methods of identifying BaAdV-2/4 or a BaAdV-3 can be used to assist a clinician in selection of a therapy for an infected subject. These therapies include, but are not limited to, therapeutically effective amounts of anti-viral agents and/or BaAdV-2/4 or a BaAdV-3 polypeptides, polynucleotides and/or antibodies sufficient to induce an immune response to BaAdV-2/4 or a BaAdV-3.
In some embodiments, the disclosed methods of identifying BaAdV-2/4 or a BaAdV-3 can be used to identify subjects that are at risk of developing a symptomatic infection. If the subject is identified as having a BaAdV-2/4 or a BaAdV-3 infection (e.g., by detection of a BaAdV-2/4 or a BaAdV-3 nucleic acid, polypeptide, or antibodies), but is not symptomatic, then the subject is treated.
In several embodiments, the disclosed methods of identifying BaAdV-2/4 or BaAdV-3 can be used to assist a clinician in selection and/or monitoring of a therapy for a subject. In additional embodiments, a subject receiving therapy (e.g., subject with BaAdV-2/4 or a BaAdV-3 infection) can be monitored for the presence of BaAdV-2/4 and/or a BaAdV-3 polynucleotide, polypeptide and/or antibodies in a biological sample from the subject. In some embodiments, the subject is initially identified as having a BaAdV-2/4 or a BaAdV-3 infection (e.g., by detection of a BaAdV-2/4 or a BaAdV-3 polypeptide, polynucleotide or antibody in a biological sample from the subject as described herein). The subject is administered a therapeutic agent of interest. In some examples, if a level of a BaAdV-2/4 or a BaAdV-3 polypeptide, polynucleotide or antibody decreases following administration of the therapeutic agent, as compared to a control, then the therapy is effective. In other examples, if the level of a BaAdV-2/4 or a BaAdV-3 polypeptide, polynucleotide or antibody increases or does not change after administration of the therapeutic agent, as compared to a control, then the therapy is ineffective. In some examples, if more severe symptoms of BaAdV-2/4 or a BaAdV-3 infection appear in the subject, the treatment can be stopped, or the dosage of the therapeutic agent can be increased.
The control can be a standard value. The control can be the level of the BaAdV-2/4 or a BaAdV-3 polypeptide, polynucleotide or antibody in a control sample, such as, but not limited to, a sample from the subject at a prior time-point, such as prior to initiation of therapy, or can be the level of the BaAdV-2/4 or a BaAdV-3 polypeptide, polynucleotide or antibody in a sample from a subject with a known infection.
Methods for determining the prognosis of a BaAdV-2/4 or a BaAdV-3 infection are also provided. In some examples, if a level of a BaAdV-2/4 or a BaAdV-3 polypeptide, polynucleotide or antibody is decreased as compared to a control, then the subject will not develop an active infection with BaAdV-2/4 or a BaAdV-3. In other examples, if the level of a BaAdV-2/4 or a BaAdV-3 polypeptide, polynucleotide or antibody is increased (or does not change), as compared to a control, then the subject will develop an active infection with BaAdV-2/4 or a BaAdV-3. The control can be a standard value. The control can be the level of the BaAdV-2/4 or a BaAdV-3 polypeptide, polynucleotide or antibody in a control sample, such as, but not limited to, a sample from the subject prior to infection, or can be the level of the BaAdV-2/4 or a BaAdV-3 polypeptide, polynucleotide or antibody in a sample from a subject known not to be infected.
In some embodiments, the subject can be monitored daily, weekly, biweekly, monthly, bi-monthly, quarterly, or annually.

Kits

The invention further provides diagnostic reagents and kits comprising one or more such reagents for use in a variety of diagnostic assays, including for example, immunoassays such as ELISA and “sandwich” type immunoassays, as well as nucleic acid assay, e.g., PCR assays. In a related embodiment, the assay is performed in a flow-through or strip test format, wherein the binding agent is immobilized on a membrane, such as nitrocellulose.
In some embodiments, the kit includes a container comprising a nucleic acid molecule as disclosed herein, a polypeptide encoded by the nucleic acid or an immunogenic fragment thereof, a vector comprising the nucleic acid, a host cell comprising the vector, an adenovirus comprising the nucleic acid, or an antibody that specifically binds the polypeptide, or a primer that hybridizes to the nucleotide sequence set forth SEQ ID NO:1, SEQ ID NO: 2 or SEQ ID NO: 3 under highly stringent conditions, and instructions for using the kit.
In additional embodiments, the kit can include the polypeptide as disclosed herein, and instructions for the detection of the presence of antibodies that specifically bind Baboon adenovirus (BaAdV)-3 or BaAdV-4 in a sample from a subject. In further embodiments, the kit includes an antibody as disclosed herein and instructions for the detection of the presence of a Baboon adenovirus (BaAdV)-3 or BaAdV-4 polypeptide in a sample from a subject.
The kit can include one or more probes or primers specific for a BaAd-3 or a BaAdv-2/4 nucleic acid sequence. The kit can include one or more antibodies, such as a monoclonal or polyclonal antibody that specifically binds a BaAdV-3 or BaAdv-2/4 polypeptide. The kit can also include one or more BaAdV-2/4 or BaAdv-3 polypeptides.
In several embodiments, such kits can include at least a first peptide, or a first antibody or antigen binding fragment of the invention, a functional fragment thereof, or a cocktail thereof, or a first nucleic acid molecule, and means for signal generation. The kit's components can be pre-attached to a solid support, or can be applied to the surface of a solid support when the kit is used. The signal generating means can come pre-associated with an antibody or nucleic acid of the invention or can require combination with one or more components, e.g., buffers, nucleic acids, antibody-enzyme conjugates, enzyme substrates, or the like, prior to use.
Kits can also include additional reagents, e.g., blocking reagents for reducing nonspecific binding to the solid phase surface, washing reagents, enzyme substrates, enzymes, and the like. The solid phase surface can be in the form of microtiter plates, microspheres, or other materials suitable for immobilizing nucleic acids, proteins, peptides, or polypeptides. An enzyme that catalyzes the formation of a chemiluminescent or chromogenic product or the reduction of a chemiluminescent or chromogenic substrate is one such component of the signal generating means. Such enzymes are well known in the art. Where a radiolabel, chromogenic, fluorigenic, or other type of detectable label or detecting means is included within the kit, the labeling agent can be provided either in the same container as the diagnostic or therapeutic composition itself, or can alternatively be placed in a second distinct container means into which this second composition can be placed and suitably aliquoted. Alternatively, the detection reagent and the label can be prepared in a single container means, and in most cases, the kit will also typically include a means for containing the vial(s) in close confinement for commercial sale and/or convenient packaging and delivery.
The kit can include one or more containers for storing a disclosed antibody, nucleic acid or polypeptide, as well as and a label or package insert on or associated with the container. Suitable containers include, for example, bottles, vials, syringes, etc. The containers may be formed from a variety of materials such as glass or plastic. The container holds a composition which is effective for diagnosis and/or treatment. In some embodiments, the container can have a sterile access port (for example the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle). The label or package insert indicates that the contents are used for treating the particular condition, or for detection/diagnosis.
In some embodiments, the kit includes instructional materials, such as the package insert, which discloses means of use of a BaAdv-3 or BaAd-2/4 polypeptide, nucleic acid, or antibody. The instructional materials may be written, in an electronic form (such as a computer diskette or compact disk) or may be visual (such as video files). The kits may also include additional components to facilitate the particular application for which the kit is designed. Thus, for example, the kit may additionally contain means of detecting a label (such as enzyme substrates for enzymatic labels, filter sets to detect fluorescent labels, appropriate secondary labels such as a secondary antibody, or the like). The kits may additionally include buffers and other reagents routinely used for the practice of a particular method.
The disclosure is illustrated by the following non-limiting Examples.

EXAMPLES

Adenoviruses (AdVs) are DNA viruses that infect and cause a broad range of clinical illnesses in vertebrate hosts, including humans and nonhuman primates. As disclosed below, a novel AdV species was identified, provisionally named “species H”, linked to an outbreak of acute respiratory illness in captive baboons (4 of 9) at a primate research facility, with a case fatality rate of 50%. AdVs isolated from baboons (BaAdVs) during the outbreak, including the two baboons that died from pneumonia, were untypeable by neutralization assays using sera reactive to HAdV species A-F and SAdV-A. Among the 4 BAdVs characterized by whole-genome sequencing, one (BaAdV₁) was a member of the recently described monkey SAdV-B species, while the remaining 3 AdVs BaAdV₂, BaAdV₃, and BaAdV₄(genetically identical to BaAdV₂) were members of species H. BaAdV₃, a closely related species H AdV to BaAdV_2,4, was the only AdV among the 4 isolated from a clinically ill baboon, and thus thought to be the cause of the pneumonia outbreak. Although BaAdV₃shared >90% genomic sequence identity overall with BaAdV_2,4, the significant divergence in the short fiber protein (˜58% amino acid identity) and bootscan analysis suggested that BaAdV₃is a rare species H recombinant of unknown origin. In support of this possibility, specific neutralizing antibodies to BaAdV₁and BaAdV_2,4, but not BaAdV₃, were detected in both present-day healthy baboons and staff personnel at the primate research facility. These results implicate a novel species H AdV in a fatal pneumonia outbreak in a baboon colony, and further establish the potential for cross-species transmission of AdVs between humans and nonhuman primates.

Example 1

Materials and Methods

Animals:
All studies were performed in accordance with established guidelines. No animal research protocol was used, as only excess clinical samples were analyzed.
Biosafety:
Analysis of post-necropsy tissues and cultivation of the novel baboon adenoviruses described in this study were performed under Biosafety Level 2 (BSL-2) or BSL-3 conditions.
Outbreak Management and Investigation:
The original outbreak lasted approximately 3 weeks. Affected baboons were quarantined immediately after development of respiratory symptoms. The two fatal cases died or were humanely euthanized 5 and 13 days after onset of clinical signs. Daily reports on clinical and epidemiological parameters were tracked and recorded by veterinary and management staff.
In response to the outbreak, all incubator rooms were decontaminated with paraformaldehyde gas. Cages, walls, floors, and all exposed work area surfaces were cleaned with 2.6% buffered glutaraldehyde (METRICIDE™) or bleach. Disposable protective suits and gloves were worn at all times when feeding or otherwise in contact with infant baboons for a period of at least 2 weeks. Hematological testing and cultures for bacterial, mycoplasma, and fungi were performed. Samples were also tested for RSV, influenza, parainfluenza, human adenovirus, and herpesviruses including CMV. In addition, respiratory samples were also sent out to an outside laboratory and tested for Bordetella pertussis, Chlamydia spp., Mycoplasma spp. Ureaplasma spp. Legionella spp., and hantavirus. AdV typing by virus neutralization testing using sera reactive against HAdV species A-F and SAdV-A viruses was also performed.
Pathology:
Gross and histopathological analyses of necropsy tissues were performed by a board-certified veterinary pathologist. Necropsy tissues were fixed in 10% formalin and embedded in paraffin. Five μm sections were then cut using a microtome, stained with hematoxylin and eosin (H&E) and visualized under light microscopy.
Nucleic Acid Extraction:
Total nucleic acid was extracted from cultured AdV supernatant using commercially available kits (Qiagen, Valencia, Calif.). 200 μL of sample were passed through a 0.4 μm filter to remove bacteria and cellular debris and then treated with RNase (Invitrogen, Carlsbad, Calif.).
Virus Cultivation:
All inoculations of monkey cells (PMK, or primary monkey kidney; CyMK, or cynomolgus monkey kidney; and Vero, African green monkey kidney) were made using primary nasal swab specimens. Inoculations of human cells and cell lines were made with P1 virus after a single passage in monkey cells. Cell or cell lines were grown in media consisting of Hank's medium (for A549 cells) or Dulbecco's modified Eagle's medium (DMEM) (for other cells) supplemented with 1× nonessential amino acids (Invitrogen, Carlsbad, Calif.), 10% fetal bovine serum, 100U of penicillin/mL and 100 μg of streptomycin/mL. After achieving 80-90% confluency, cell culture media were changed to maintenance media with 2% FBS and inoculated with 200 μL of clinical sample or 100 μL of passaged viral supernatant. Prior to inoculation, nasal samples were clarified by centrifugation for 10 min×4000 g; lung tissue was homogenized using a tissue homogenizer in 5 volumes of buffer. Prior to passaging, cell culture supernatant was subjected to 3 freeze-thaw cycles and clarified as above. Viral replication was monitored over 2 weeks by visual inspection under light microscopy for cytopathic effect (CPE). Viral supernatants were quantified by an end-point dilution assay.
Deep Sequencing Library Preparation:
Deep sequencing libraries were prepared for whole-genome AdV sequencing using a variation of the TruSeq protocol (Illumina, San Diego, Calif.) (Chen et al., 2011, PLoS Pathog 7: e1002155). Briefly, nucleic acid extracts were randomly amplified to cDNA using a Round A/B procedure as previously described (Chen et al., 2011, J. Vis. Exp.; Greninger et al., 2010, PLoS One 5: e13381) and then digested using the restriction enzyme BpmI (New Engladn Biolabs, Ipswich, Mass.) for 2 hr at 37° C., followed by end-repair and A-tailing with Klenow and Taq polymerase, respectively (Invitrogen, Carlsbad, Calif.). Size selection targeting 200-300 bp fragments was then performed using AMPURE® beads, followed by attachment of adapters containing 6-nucleotide barcode tags using DNA ligase. Final libraries were quantified using the Bioanalyzer DNA 12000 chip (Agilent) and SYBR FAST® qPCR system (KAPA Biosystems), pooled into a single lane, and sequenced on an Illumina HiSeq2000 instrument (100-bp paired-end sequencing).
De Novo Viral Genome Assembly:
Raw deep sequencing reads were initially trimmed by removal of adapters, primers, and low-complexity/low-quality sequences. De novo assembly of partial AdV genomes was performed using the PRICE assembler (Grard et al., 2012, PloS Pathogens 8: e1002924). Gaps were filled by BLASTn or BLASTx alignments of the deep sequencing reads to reference simian and human AdVs in GENBANK® (Altschul et al., 1990, J Mol Biol 215: 403-410), followed by manual assembly using GENEIOUS® software (Drummond et al., 2010, Geneious v5.6.3. Available on the internet from geneious.com, as downloaded November, 2012). Regions with little or no sequence coverage were confirmed by PCR and Sanger sequencing. After assembly of the full viral genomes corresponding to the 4 AdV isolates BaAdV_1,2,3,4, trimmed deep sequencing reads were then mapped to the AdV genome using GENEIOUS® software with the following parameters (no gaps allowed, maximum mismatches allowed per read of 5%, and maximum ambiguity of 1).
Structural Features and Phylogenetic Analysis:
Predicted coding regions in the BaAdV_1,2,3,4genomes were identified using the fully annotated genome sequences of species F and G AdVs in GENBANK® as a reference. First, each BaAdV genome was aligned to the most similar reference genome in GENBANK®, followed by identification of all open reading frames (ORFs) using GENEIOUS®. The candidate ORF that best matched the corresponding ORF in the annotated reference genome was selected. The GT-AG intron start-stop signal was used to pinpoint the correct ORF for spliced genes. To confirm the accuracy of the predicted coding regions, each identified ORF was then aligned using BLASTx to a reference database consisting of all adenoviral proteins in GenBank. Whole-genome nucleotide pairwise identity plots (window size of 100) and amino acid pairwise identity calculations were performed in Geneious. Similarity and bootscanning plots were generated using SIMPLOT® (Lole et al., 1999, J Virol 73: 152-160), with a window size of 1000 bp and step size of 50 bp.
To construct the amino acid phylogeny trees corresponding to the hexon, penton base, DNA polymerase, and short/long fiber proteins, the translated protein sequences corresponding to representative human and simian AdVs in species groups A-G, SAdV-A, and SAdV-B, as well as non-primate AdVs, were first downloaded from GENBANK®. Multiple sequence alignments were then performed using the FFT-NS-Ix1000 algorithm of MAFFT at default parameters (Katoh et al., 2002, Nucleic Acids Res 30: 3059-3066). A phylogenetic tree was constructed in Geneious using the Jukes-Cantor neighbor-joining method and 100,000 bootstrap replicates, using mouse adenovirus A (MADV-A) as an outgroup.
Baboon Adenovirus Neutralization Assay (Human and Baboon Sera):
Viral stocks of BaAdV₁, BaAdV₂, and BaAdV₃were generated by passaging in Vero E6 cells, aliquotted, and quantitated by end-point dilution. To perform the virus neutralization assay, 100 μL of viral supernatant or control serum was mixed to the correct dilution and incubated for 1 hour at 37° C. After incubation, the mixture was inoculated into wells containing 4,000 Vero E6 cells per well and incubated at 37° C., 5% CO₂. Cells in the plate wells were observed every other day for evidence of CPE. For wells that showed inhibition of viral CPE at the screening dilution of 1:10, the corresponding serum samples were diluted in six 2-fold steps and then retested. The reciprocal of the highest dilution where replicate well monolayers showed <3+ CPE was taken as the neutralizing antibody titer.
Human Adenovirus Types A-F Cross-Neutralization Assay (Rabbit Typing Sera):
Seven pools of rabbit hyperimmune reference sera at the California DPH, collectively containing antibodies to human AdV serotypes 1 through 41 (species A-F), were available for testing. For each pool, 100 μL of rabbit sera and 100 μL of viral supernatant at a TCID₅₀of 10³/mL were mixed to the screening dilution of 1:10 and used to inoculate Vero E6 cells. Cells in plate wells were observed every other day for 2 weeks for evidence of CPE. For wells that showed inhibition of viral CPE at the screening dilution of 1:10, the corresponding serum samples were diluted in six 2-fold steps and then retested. An individual rabbit serum reactive to HAdV-40 and HAdV-41 (the species F AdVs) was used for confirmatory testing.
Human Adenovirus Type G Indirect Cross-Neutralization Assay (Baboon Sera):
Since neutralizing reference sera to human HAdV-52 (species G) was not available, the serum sample from baboon B107, shown previously to be positive for neutralizing antibody to species SAdV-B and H AdVs (Table 2), was tested for cross-neutralization of HAdV-52 in an indirect neutralization assay. To perform the assay, 100 μL HAdV-52 supernatant at a TCID₅₀of 10³/mL was mixed with serum from baboon B107 to the screening dilution of 1:10 and used to inoculate Vero E6 cells. Cells in plate wells were observed every other day for 2 weeks for evidence of CPE.
Nucleotide Sequence Accession Numbers:
GENBANK® accession numbers for the adenoviral sequences used in FIGS. 3, 4, and 5 are as follows: CAdV-1 (canine adenovirus 1), AC_—000003; NC_—002501; HAdV-1, AC_—000017; HAdV-3, DQ086466; HAdV-4, AY458656; HAdV-7, AC_—000018; HAdV-8, AF532578; HAdV-12, NC_—001460; HAdV-14, FJ822614; HAdV-18, GU191019; HAdV-21, AY601633; HADV-36, GQ384080; HAdV-40, NC_—001454; HAdV-41, DQ315364; HAdV-48, EF153473; HAdV-49, DQ393829; HAdV-50, AY737798; HAdV-52, DQ923122; MAdV-2 (murine adenovirus 2), NC_—014899; PAdV-A (porcine adenovirus A), AC_—000009; SAdV-1, AY771780; SAdV-3, NC_—006144; SAdV-6, JQ776547; SAdV-7, DQ792570; SAdV-18, FJ025931; SAdV-20, HQ605912; SAdV-21, AC_—000010; SAdV-22, AY530876; SAdV-48, HQ241818; SAdV-49, NC_—015225; SAdV-50, HQ241820; SAdV-A1139, JN880448; SAdV-A1163, JN880449; SAdV-A1173, JN880450; SAdV-A1258, JN880451; SAdV-A1312, JN880454; SAdV-A1335, JN880456; TMAdV (titi monkey adenovirus), HQ913600; TSAdV (tree shrew adenovirus), NC_—004453. These sequences are incorporated by reference herein in their entirety as available on Jan. 2, 2013.

Example 2

Outbreak of Fatal Pneumonia in a Baboon Colony

In one outbreak, 4 of 9 infant baboons at the TBRI developed an acute respiratory infection shortly after being isolated from birth in preparation for a research study on respiratory syncytial virus (FIGS. 1A and B). The index case (FIG. 1B, B1) was a female infant baboon. After birth, she was admitted to the nursery, maintained in an incubator for 1 week, and then moved to an individual cage in a dedicated nursery bay. At 12 days of age, she was noted to be sneezing with clear mucous discharge. No fever was present. Laboratories revealed a normal complete blood count (CBC) with a white blood cell (WBC) count of 5.6×10⁶/mL (57% neutrophils). Her condition deteriorated rapidly over the next 4 days with the development of progressive malaise, anorexia, >20% loss of body weight, and shortness of breath (dyspnea). Body temperature dropped below 95° F. Chest radiographs revealed a bilateral interstitial pneumonia. Despite aggressive treatment with antibiotics (ampicillin and gentamicin), oxygen, and intravenous fluids, she died 13 days after onset of symptoms and at 25 days of age.
On necropsy, the lung tissue was hemorrhagic with patchy regions of consolidation. Neutrophils were evident in the airways with extension into the minor airways, interstitium, and alveolar spaces. Notably, intranuclear inclusions were evident throughout the respiratory epithelium, and were most evident in the major airways. The tonsils contained multifocal areas of necrosis with increased numbers of neutrophils, and mediastinal lymph nodes contained excess inflammatory cells. Mild cellular necrosis was noted in the liver. Histologic lesions were not observed in the heart, kidney, adrenal glands, or spleen. The final pathologic diagnosis was bronchointerstitial pneumonia, probably viral in etiology, with accompanying tonsillitis, lymphadenitis, and mild liver necrosis. Although a Gram stain of the lung tissue was negative for organisms, bacterial cultures grew methicillin-sensitive Staphylococcus aureus (MSSA) and rare Kluyvera ascorbata (Sarria et al., 2001, Clin Infect Dis 33: E69-74). Tests from lung tissue were negative for Bordetella pertussis, Chlamydophila spp., Mycoplasma spp., Ureaplasma spp. Legionella spp., and hantavirus. A respiratory viral culture of lung tissue was positive for AdV. The isolate was untypeable by virus neutralization testing at an outside laboratory using sera reactive to HAdV species A-F and SAdV-A.
The second case (FIG. 1B, B2) was a male infant baboon. He was also admitted to the nursery upon birth, maintained in an incubator during the first week of life, and then moved to an individual cage in the nursery bay. At 16 days of age, he began sneezing and coughing up milk through his nose. The WBC count was normal at 5.8×10⁶/mL (46% neutrophils), but a few atypical lymphocytes were present. The animal clinically worsened, with lethargy, >20% weight loss, abnormally low body temperature, and dyspnea. A nasal swab collected at the time was positive for MSSA, but cultures of bronchoalveolar lavage fluid and blood were negative for MSSA. Although also treated aggressively with intravenous fluids, oxygen, and antibiotics, he was humanely euthanized three days later after developing muscle spasticity (opisthotonus), 5 days after onset of symptoms and at 21 days of age.
On necropsy, the lungs revealed a bronchointerstitial pneumonia with prominent areas of congestion (edema) and consolidation. Inflammatory neutrophilic infiltrates were evident in the major airways with extension into the interstitium and alveolar spaces. Intranuclear inclusions were evident in epithelial cells and subtracheal gland epithelium, and excess inflammatory cells were visualized in mediastinal lymph nodes. Other tissues were negative for histologic lesions, with the exception of medullary necrosis of the thymus consistent with stress. Gram stain and cultures of lung tissue were negative for bacteria or fungi, although rare WBCs were seen. A respiratory viral culture of the lung tissue was positive for AdV, and the isolate was also untypeable by neutralization testing.
Two other animals in the room were noted to be sneezing and coughing around the same time cases B1 and B2 presented with fatal pneumonia (FIG. 1B, B3 and B5). A nasal swab collected from one of these two symptomatic individuals was culture-positive for an adenovirus (FIG. 1B, BaAdV₃). Nasal swabs were also collected from the sole remaining asymptomatic baboon in the same room as the symptomatic cases (FIG. 1B, Room 1, B4) and from asymptomatic baboons in a nearby but separate room (FIG. 1B, Room 2). From these nasal swabs, 3 additional AdV isolates were obtained (FIG. 1B, BaAdV₁, BaAdV₂, and BaAdV₄). The two symptomatic baboons in Room 1, cases B3 and B5, were quarantined and recovered completely within 1 week with supportive care including intravenous fluids, oxygen administration, and empiric antibiotics. None of the 4 baboon AdV isolates (BaAdV_1,2,3,4) was typeable as HAdV species A-F or SAdV-A by neutralization testing done at this time.

Example 3

Cell Culture Tropism of Novel Baboon Adenoviruses (BaAdV-1 Through BaAdV-4)

The 4 adenoviruses isolated from sick and asymptomatic baboons during the first outbreak were cultured in a variety of human and monkey cell lines. The majority of cells and cell lines tested resulted in productive infection as determined by magnitude of cytopathic effect (CPE) (Table 1).

TABLE 1

Tropism of 4 novel baboon adenoviruses in human and monkey cell.

Virus	Source	Name of	Cell Type	Growth

BaAdV₁	Human	A549	human epithelial lung adenocarcinoma	+++
		HFDL	human fetal diploid lung	−
		HFDK	human fetal diploid kidney	−
	Monkey	PMK	primary rhesus monkey kidney (Old World	+++
		B95a	marmoset monkey lymphoblastoid (New World	−
		Vero	African green monkey kidney (Old World	+++
		CyMK	Cynomolgus monkey kidney (Old World monkey)	+++
BaAdV_2,4	Human	A549	human epithelial lung adenocarcinoma	+++
		HFDL	human fetal diploid lung	−
		HFDK	human fetal diploid kidney	−
	Monkey	PMK	primary rhesus monkey kidney (Old World	+++
		B95a	marmoset monkey lymphoblastoid (New World	−
		Vero	African green monkey kidney (Old World	+++
		CyMK	Cynomolgus monkey kidney (Old World monkey)	+++
BaAdV₃	Human	A549	human epithelial lung adenocarcinoma	+++
		HFDL	human fetal diploid lung	++
		HFDK	human fetal diploid kidney	++
	Monkey	PMK	primary rhesus monkey kidney (Old World	+++
		B95a	marmoset monkey lymphoblastoid (New World	−
		Vero	African green monkey kidney (Old World	+++
		CyMK	Cynomolgus monkey kidney (Old World monkey)	+++

+++, strong cytopathic effect (CPE);
++, moderate CPE;
−, no CPE

All 4 baboon adenoviruses were successfully propagated in cells from other Old World monkey species (rhesus, cynomolgus, African green monkeys). The BaAdVs were tested for growth in human cell lines; all 4 grew efficiently in the human lung adenocarcinoma A549 cell line, which is commonly employed in isolation of human AdVs (Lipson et al., 1993, FEMS Microbiol Lett 113: 175-18) Notably, unlike the other 3 AdV strains, BaAdV₃was also successfully cultured from two additional human cell lines. No growth was observed in lymphoblastoid B95a cells from marmosets, which are New World monkeys.

Example 4

De Novo Assembly and Whole-Genome Phylogenetic Analysis of Novel Baboon Adenoviruses (BaAdV-1 Through BaAdV-4)

The 4 adenoviruses isolated from baboons were further characterized by whole-genome sequencing and phylogenetic analysis. The sequences of the adenovirus hexon, polymerase, and fiber were initially recovered by Sanger sequencing. To sequence the entire genome, early passaged cultures corresponding to isolates BaAdV-1 through BaAdV-4 were subjected to unbiased deep sequencing on an Illumina HiSeq2000 (FIG. 2). Out of 32.9-45.2 million raw reads, from 61.3%-93.1% of the genome was assembled de novo for each of the 4 adenovirus strains; the remainder of the genome was then assembled manually from the deep sequencing reads with Sanger sequencing used to fill in the gaps.
Scanning nucleotide pairwise identity plots across the assembled genomes revealed that all 4 baboon adenoviral strains retained the major core adenoviral proteins and, similar to AdVs in species SAdV-B, F, and G, all 4 strains contained two fiber proteins, a long fiber and a short fiber (FIG. 3). BaAdV₁, the strain isolated from an asymptomatic baboon in the outbreak room (FIG. 1B, B4), was found to be closely related to a previously described SAdV-B species AdV isolated from stool from a captive rhesus monkey (SAdV-A1335, GENBANK® accession number JN880456, 97.8% identity) (FIG. 3A)) (Roy et al., 2009, PLoS Pathog 5: e1000503). Strains BaAdV₂and BaAdV₄, both isolated from asymptomatic baboons housed away from the outbreak location in a separate room (FIG. 1B, B8 and B9), were 100% identical to each other, while strain BaAdV₃, isolated from a symptomatic baboon positioned near the two baboons who died from adenoviral pneumonia (FIG. 1B, B5), was 91.2% identical to strains BaAdV_2,4(FIG. 3B). The closest relatives to BaAdV_2,4and BaAdV₃were members of adenoviral species F and G (FIGS. 3B and 4A-D). Phylogenetic analysis of the individual hexon, penton base, DNA polymerase, and fiber proteins and amino acid pairwise identity comparisons revealed that BaAdV₁is a member of the SAdV-B species group (FIGS. 4A-D and 5A), while BaAdV_2,4and BaAdV₃appear to be members of a new species intermediate between F and G, provisionally named “species H” (FIGS. 4A-D and 5B). Repeat serological testing in 2012 using sera containing neutralizing antibodies against human AdVs in species A-G (Table 2) revealed only a low level of cross-neutralizing activity to species F AdVs with BaAdV₁(SAdV-B) and BaAdV_2,4(species H). No cross-neutralization with human AdVs in species A-G was observed with BaAdV₃.
Notably, despite sharing 91.2% overall nucleotide identity across the genome (FIG. 3B), the sequence of BaAdV₃, the only AdV among the 4 that had been isolated from a symptomatic baboon, diverged significantly from that of BaAdV_2,4in the short fiber region. While the other major adenoviral proteins were >90% identical, the short fiber of BaAdV₃shared only 58% amino acid identity relative to that of BaAdV_2,4(FIG. 5B). This strongly suggested the possibility of a recombination event involving BaAdV_2,4and the short fiber of BaAdV₃. Similarity and bootscanning plots of BaAdV₃relative to BaAdV_2,4(species H) and related AdVs in species SAdV-A, F, and G confirmed the likelihood of a recombination event (FIG. 6A). However, since the short fiber of BaAdV₃was found to lack any closely related phylogenetic neighbors (˜58% to BaAdV_2,4and ≦50% amino acid identity to other sequenced fiber proteins in GENBANK®), the presumptive AdV donor strain for the short fiber has yet to be identified.

Example 5

Seroprevalence of BaAdV₁, BaAdV₃, and BaAdV_2,4in Baboons and Humans

Of note, many staff members had anecdotally reported experiencing “flu-like” symptoms around the time of onset of this baboon outbreak. To investigate the possibility that a cross-species transmission event, either zoonotic (from baboon to human) or anthroponotic (from human to baboon), may have occurred, pre-outbreak and post-outbreak sera from potentially exposed human staff personnel at the TBRI (Table 2, H1-H6) were tested for antibodies to BaAdV₁, BaAdV₃, and BaAdV_2,4by virus neutralization in a blinded fashion. As additional controls for baseline seroprevalence, sera from a random selection of 5 human children less than 5 years of age and available sera from 10 baboons born approximately the same time as affected baboons with pneumonia, but not part of the outbreak, were tested. Significantly, 5 of 6 (83%) and 6 of 6 (100%) personnel, while seronegative prior to the outbreak, had evidence of neutralizing antibody titers to BaAdV₁and BaAdV_2,4, respectively, after the outbreak. The greatest magnitude of neutralizing antibody response, ≧1:80, corresponded to the researcher in closest contact with sick baboons during the outbreak (Table 2, H1). Interestingly, no neutralization to BaAdV₃was observed in any of the staff personnel. The specificity of the neutralization assays was further confirmed by the screening of 5 epidemiologically unassociated children under 5 years of age, all of whom were negative for neutralizing antibodies to BaAdV₁, BaAdV_2,4, and BaAdV₃(Table 2, H8-H12). Among 10 healthy baboons in the colony who were not part of this outbreak, 4 of 10 (40%) and 3 of 10 (30%) harbored antibodies to BaAdV₁and BaAdV_2,4, respectively (Table 2, B100-B110). Very little to no neutralization was observed to BaAdV₃; neutralizing antibody at 1:10 titer was detected in only one baboon, B107, with high existing titers of 1:80 to closely related strain BaAdV_2,4.

TABLE 2

Neutralizing antibody titers to BaAdV₁, BaAdV_2,4, and BaAdV₃in rabbit
neutralizing sera to HAdV species A-F, laboratory staff (H1-H6), young children (H8-H12),
and baboons currently housed (B100-B110). No cross-reactivity with HAdV species A-F is
observed except for a low level of cross-neutralization of BaAdV₁and BaAdV_2/4, but not
BaAdV₃, with rabbit neutralizing sera against HAdV species F. There was also no evidence of
cross-reactivity to a species G adenovirus HAdV-52 in an indirect neutralization assay with a
baboon serum sample reactive to BaAdV₁, BaAdV₃, and BaAdV_2,4(B107).

Serum Sample	Identification	BaAdV₁	BaAdV2,4	BaAdV3

Rabbit neutralizing sera	N/A	Only HAdV-F	Only HAdV-	—
to HAdVs (A-F), 7		pool, 1:20	F pool, 1:20
pools
Rabbit neutralizing sera	N/A	1:20	1:20	—
to HAdV-F (HAdV-40
and HAddV-41)
	primate
H1 (pre-outbreak)	primate	—	—	—
H1 (post-outbreak)	primate	≧1:80	≧1:80	—
H2 (pre-outbreak)	primate	—	—	—
H2 (post-outbreak)	primate	1:80	1:80	—
H3 (pre-outbreak)	primate	—	—	—
H3 (post-outbreak)	primate	1:80	1:80	—
H4 (pre-outbreak)	primate	—	—	—
H4 (post-outbreak)	primate	1:40	1:40	—
H5 (pre-outbreak)	primate	—	—	—
H5 (post-outbreak)	primate	—	1:80	—
H6 (pre-outbreak)	primate	—	—	—
H6 (post-outbreak)	primate	1:80	1:80	—
H8	child <5 years of age	—	—	—
H9	child <5 years of age	—	—	—
H10	child <5 years of age	—	—	—
H11	child <5 years of age	—	—	—
H12	child <5 years of age	—	—	—
B100	primate	—	—	—
B101 (earlier)	primate	—	—	—
B101 (later)	primate	1:10	—	—
B102	primate	—	1:10	—
B103	primate	—	—	—
B104	primate	—	—	—
B105	primate	—	—	—
B106	primate	—	—	—
B107	primate	1:10	1:80	1:10
B108	primate	1:10	1:10	—
B109	primate	—	—	—
B110	primate	1:10	—	—

Abbreviations:
N/A, not applicable.

Thus, an outbreak of rapidly fatal adenovirus pneumonia in infant baboons occurred. The diagnosis of primary AdV infection was supported by the presence of atypical lymphocytes in the peripheral circulation, hemorrhagic and necrotic lesions in the lung and liver, and intranuclear inclusions in bronchial epithelium, with subsequent confirmation by direct isolation of AdV from lung tissue. Two of four baboons presenting with acute respiratory infection (50%) died in the outbreak. Although numbers are low, the case fatality rate of 50% is high for AdV infections, which typically cause much lower mortality rates in susceptible human children of <15% (Hong et al., 2001, Clin Infect Dis 32: 1423-1429; Siminovich et al., 2011, Pediatr Dev Pathol 14: 214-217; Murtagh et al., 2009, Pediatr Pulmonol 44: 450-456). One explanation for the high death rate may be the concurrent identification of bacteria such as MSSA in at least one of the 2 baboons, which may have predisposed AdV-infected baboons with severe and potentially fatal bacterial superinfections of the lung (Bakaletz, 1995, Trends Microbiol 3: 110-114). It is also possible that newborn baboons are highly susceptible in general to severe infection from AdVs, which can cause more severe disease in immunocompromised, elderly, or very young individuals (Wold W, Horwitz M (2007) Adenoviruses. In: Fields B N, Knipe D M, Howley P M, editors. Fields Virology. 5th ed. Philadelphia: Wolters Kluwer Health/Lippincott Williams & Wilkins. pp. 2395-24361 Echavarria, 2008, Clin Microbiol Rev 21: 704-715).
The AdV strains isolated from lung tissue from the two baboons who died from pneumonia were untypeable by virus neutralization testing for AdVs in HAdV species A-F and SAdV-A, including HAdVs in species B, C, and E that are typically associated with human respiratory disease and pneumonia (Echavarria et al., 2006, J Clin Microbiol 44: 625-627). This finding raised the possibility that the causative agent of the outbreak may be a novel AdV strain of unknown pathogenicity. Since tissue and primary cultures from the two fatal cases had been sent out to outside laboratories and were unavailable for further analysis, AdVs isolated from other symptomatic and/or asymptomatic baboons (BaAdVs) involved in the outbreak were characterized. Four AdV isolates (BaAdV_1,2,3,4) had been successfully cultured from nasal swabs, of which only one, BaAdV₃, was derived from a surviving baboon with acute respiratory symptoms. Similar to the two AdV strains from dead baboons, the 4 isolates were untypeable at the time of the outbreak for HAdV species A-F and SAdV-A by virus neutralization testing (although subsequent repeat neutralization testing against HAdV species A-G found a low level of serological cross-reactivity between BaAdV₁or BaAdV_2,4and the species F HAdVs) (Table 2).
To further characterize these untypeable AdVs, the genomes corresponding to all 4 isolates were recovered by a combined deep sequencing, traditional Sanger sequencing, and de novo assembly approach (FIG. 2). BaAdV₁was found to be a member of the recently described SAdV-B species (Roy et al., 2012, Emerg Infect Dis 18: 1081-1088), but BaAdV₂, BaAdV₃, and BaAdV₄(identical to BaAdV₂) were found to represent members of a potentially novel species (FIGS. 3B and 4). Both BaAdV_2,4and BaAdV₃meet one of the two ICTV criteria for a new AdV species by exhibiting >10% phylogenetic distance from their nearest AdV neighbors, members of species F and G (FIG. 3B). The other criterion, lack of cross-neutralization with other AdVs, appears to be satisfied by at least BaAdV₃(Table 2). Since it is currently unclear whether these new AdVs are human or simian in origin, the designation “species H” has been proposed for members of this new species.
Interestingly, BaAdV₃, despite being a species H AdV with 91.2% overall nucleotide identity to BaAdV_2,4(FIG. 3B), exhibits little to no cross-reactivity with BaAdV_2,4in testing of both human and baboon sera (Table 2). The basis for this serological specificity may be the sequence of the short fiber, which diverges significantly in BaAdV₃relative to both BaAdV_2,4and all other sequenced AdVs (58% identity at the amino acid level) (FIG. 5B). Bootscan analysis suggests that BaAdV₃may have arisen from a recombination event involving a species H AdV such as BaAdV_2,4and an as-yet unidentified donor strain harboring the divergent BaAdV₃short fiber (FIG. 6). Since productive infection by BaAdV₃, but not BaAdV_2,4, was observed in two human fetal cell lines (Table 1), this donor strain may potentially be a human adenovirus, or at least human-tropic.
Anecdotal reports of “flu-like” symptoms in staff members around the time of the baboon outbreak precipitated an investigation of serological responses to BaAdV₁, BaAdV_2,4, and BaAdV₃in baboons currently in the colony and potentially exposed staff personnel. Neutralizing antibody titers to BaAdV₁(species SAdV-B) and BaAdV_2,4(species H), were detected in both baboons and humans (Table 2). Although it is possible that these titers may reflect borderline cross-reactivity with human species F AdVs (Table 1), it is far more likely that BaAdV₁(species SAdV-B) and BaAdV_2,4(species H) are serologically distinct from HAdV-F, given the low protein homology with the species F AdVs (FIG. 5), and the high rates of seroconversion and magnitude of antibody titer rise in exposed staff personnel over a relatively brief period (Table 2). Thus, the serological results likely provide the first glimpse of zoonotic transmission of a presumptive simian AdV in the species SAdV-B lineage, BaAdV₁, to exposed humans. The observed seroconversion in exposed staff personnel to BaAdV_2,4also raises concerns regarding the pathogenicity of novel species H AdV infection in humans. As the origin and host reservoir of the species H AdVs remain unknown, it is unclear whether the direction of transmission for BaAdV_2,4was zoonotic or anthroponotic. These findings continue to underscore the threat from potentially pathogenic AdVs with capacity for cross-species transmission between monkeys and humans.
In a previous outbreak of respiratory and enteric illness in baboons (Eugster et al., 1969, Arch Gesamte Virusforsch 26: 260-270), the cause was found to be SAdV-20, a species SAdV-A AdV which had been originally isolated as strain V340 in association with an outbreak of pneumoenteritis in vervet monkeys (Kim et al., J Infect Dis 117: 292-300, 1967). The data presented herein indicate that BaAdV₃, a novel species H AdV, is the most likely cause of this pneumonia outbreak. BaAdV₃was the only sequenced AdV among recovered species H and SAdV-B AdVs that was isolated from the sick baboon, and the two baboons who died from pneumonia had previously tested negative at the time of the outbreak for HAdV species A-F and SAdV-A. Collectively with the serological testing showing little to no seroreactivity to BaAdV₃in currently captive baboons and human staff, these data suggest that BaAdV₃may be a rare pathogenic species H recombinant whose emergence precipitated the outbreak.

Example 6

Annotated Sequence Information

The locations of the open reading frames (coding sequence, CDS) in SEQ ID NOs: 1-4 are provided below, along with information on the identities of the encoded proteins. The location of the terminal repeats (ITRs) is also provided.


BaAdV-2 (SEQ ID NO: 1)

LOCUS	BaAdV-2_final_an 34391 bp DNA linear
DEFINITION	.
ACCESSION	urn.local...1357154693134.16
VERSION	urn.local...1357154693134.16
KEYWORDS	.
SOURCE
ORGANISM
	.

FEATURES	Location/Qualifiers
misc_feature	1..87
	/label=“ITR repeat”
CDS	order(982..1199,444..903)
	/label=“E1A CDS”
CDS	1320..1820
	/label=“E1B 19K CDS”
CDS	1625..3049
	/label=“E1B 55K CDS”
CDS	3056..3535
	/label=“IX CDS”
CDS	order(complement(5190..5202),complement(3581..4911))
	/label=“IVa2 CDS”
CDS	order(complement(13081..13089),complement(4684..8232))
	/label=“pol CDS”
CDS	order(complement(13081..13089),complement(8031..9968))
	/label=“pTP CDS”
CDS	10187..11314
	/label=“52K CDS”
CDS	11335..13059
	/label=“pIIIa CDS”
CDS	13135..14646
	/label=“III (penton) CDS”
CDS	14649..15194
	/label=“pVII CDS”
CDS	15251..16303
	/label=“pV CDS”
CDS	16323..16532
	/label=“pX CDS”
CDS	16564..17403
	/label=“pVI CDS”
CDS	17490..20273
	/label=“II (hexon) CDS”
CDS	20146..20898
	/label=“protease CDS”
CDS	complement(20948..22333)
	/label=“DBP CDS”
CDS	22357..24642
	/label=“100K protein CDS”
CDS	order(24344..24664,24944..25144)
	/label=“33K protein CDS”
CDS	24344..24886
	/label=“22K protein CDS”
CDS	25203..25904
	/label=“pVIII CDS”
CDS	25904..26218
	/label=“E3 12.5K CDS”
CDS	26175..26648
	/label=“E3 CR1-alpha CDS”
CDS	26645..27517
	/label=“E3 CR1-beta CDS”
CDS	27531..27803
	/label=“E3 RID-alpha CDS”
CDS	27791..28132
	/label=“E3 RID-beta CDS”
CDS	28125..28490
	/label=“E3 14.7 CDS”
CDS	complement(28504..28665)
	/label=“U exon CDS”
CDS	28676..29866
	/label=“IV (fiber 1) CDS”
CDS	29697..31535
	/label=“IV (fiber 2) CDS”
CDS	order(complement(32509..32652),complement(31559..31777))
	/label=“E4 ORF 6/7 CDS”
CDS	complement(31795..32652)
	/label=“E4 34K CDS”
CDS	complement(32585..32947)
	/label=“E4 ORF4 CDS”
CDS	complement(32949..33299)
	/label=“E4 ORF3 CDS”
CDS	complement(33296..33688)
	/label=“E4 ORF2 CDS”
CDS	complement(33703..34083)
	/label=“E4 ORF1 CDS”
misc_feature	34305..34391
	/label=“ITR repeat”

BaAdV-4 (SEQ ID NO: 2)

LOCUS	BaAdV-4_final_an 34391 bp DNA linear
DEFINITION	.
ACCESSION	urn.local...1357154692931.12
VERSION	urn.local...1357154692931.12
KEYWORDS	.
SOURCE
ORGANISM
	.

FEATURES	Location/Qualifiers
misc_feature	1..87
	/label=“ITR repeat”
CDS	order(444..903,982..1199)
	/label=“E1A CDS”
CDS	1320..1820
	/label=“E1B 19K”
CDS	1625..3049
	/label=“E1B 55K CDS”
CDS	3056..3535
	/label=“IX CDS”
CDS	order(complement(3581..4911),complement(5190..5202))
	/label=“IVa2 CDS”
CDS	order(complement(13081..13089),complement(4684..8232))
	/label=“pol CDS”
CDS	order(complement(13081..13089),complement(8031..9968))
	/label=“pTP CDS”
CDS	10187..11314
	/label=“52K CDS”
CDS	11335..13059
	/label=“pIIIa CDS”
CDS	13135..14646
	/label=“III (penton) CDS”
CDS	14649..15194
	/label=“pVII CDS”
CDS	15251..16303
	/label=“pV CDS”
CDS	16323..16532
	/label=“pX CDS”
CDS	16564..17403
	/label=“pVI CDS”
CDS	17490..20273
	/label=“II (hexon) CDS”
CDS	20281..20898
	/label=“protease CDS”
CDS	complement(20948..22333)
	/label=“DBP CDS”
CDS	22357..24642
	/label=“100K protein CDS”
CDS	order(24876..25151,24344..24664)
	/label=“33K protein CDS”
CDS	24344..24886
	/label=“22K protein CDS”
CDS	25203..25904
	/label=“pVIII CDS”
CDS	25904..26178
	/label=“E3 12.5K CDS”
CDS	26175..26648
	/label=“E3-CR-1-alpha CDS”
CDS	26645..27517
	/label=“E3 CR1-beta CDS”
CDS	27531..27803
	/label=“E3 RID-alpha CDS”
CDS	27791..28132
	/label=“E3 RID-beta CDS”
CDS	28125..28490
	/label=“E3 14.7 protein CDS”
CDS	complement(28504..28665)
	/label=“U exon CDS”
CDS	28676..29866
	/label=“IV (fiber1)”
CDS	29697..31535
	/label=“IV (fiber 2) CDS”
CDS	order(complement(31559..31735),complement(32509..32652))
	/label=“E4 ORF 6/7”
CDS	complement(31795..32652)
	/label=“E4 34K CDS”
CDS	complement(32585..32947)
	/label=“E4 ORF4 CDS”
CDS	complement(32949..33299)
	/label=“E4 ORF3 CDS”
CDS	complement(33296..33688)
	/label=“E4 ORF2 CDS”
CDS	complement(33703..34083)
	/label=“E4 ORF1 CDS”
misc_feature	34305..34391
	/label=“ITR repeat”

BaAdV-3 (SEQ ID NO: 3)

LOCUS	BaAdV-3_final_an 34402 bp DNA linear
DEFINITION	.
ACCESSION	urn.local...1350955631692.388
VERSION	urn.local...1350955631692.388
KEYWORDS	.
SOURCE
ORGANISM
	.

FEATURES	Location/Qualifiers
misc_feature	1..124
	/label=“ITR repeat”
CDS	order(1024..1241,487..949)
	/label=“E1A CDS”
CDS	1364..1858
	/label=“E1B 19K”
CDS	1669..3087
	/label=“E1B 55K CDS”
CDS	3092..3571
	/label=“pIX CDS”
CDS	order(complement(3608..4938),complement(5217..5229))
	/label=“IVa2 CDS”
CDS	order(complement(13105..13113),complement(4711..8259))
	/label=“pol CDS”
CDS	order(complement(13105..13113),complement(8058..9989))
	/label=“pTP CDS”
CDS	10208..11335
	/label=“52K CDS”
CDS	11356..13080
	/label=“pIIIa CDS”
CDS	13159..14676
	/label=“III (penton)”
CDS	14679..15230
	/label=“pVII CDS”
CDS	15288..16328
	/label=“pV CDS”
CDS	16342..16557
	/label=“pX CDS”
CDS	16496..17422
	/label=“pVI CDS”
CDS	17509..20301
	/label=“II (hexon)”
CDS	20156..20926
	/label=“protease CDS”
CDS	complement(20976..22361)
	/label=“DBP CDS”
CDS	22385..24661
	/label=“100K protein CDS”
CDS	order(24366..24683,24895..25163)
	/label=“33K protein CDS”
CDS	24366..24905
	/label=“22K protein CDS”
CDS	25222..25923
	/label=“pVIII CDS”
CDS	25920..26231
	/label=“E3 12.5K CDS”
CDS	26179..26724
	/label=“E3-CR-1-alpha CDS”
CDS	26721..27533
	/label=“E3 CR1-beta CDS”
CDS	27547..27819
	/label=“E3 RID-alpha CDS”
CDS	27816..28145
	/label=“E3 RID-beta CDS”
CDS	28138..28503
	/label=“E7 14.7 protein CDS”
CDS	complement(28506..28667)
	/label=“U exon CDS”
CDS	28678..29811
	/label=“IV (fiber)”
CDS	29687..31480
	/label=“IV (fiber 2) CDS”
CDS	order(complement(32482..32625),complement(31504..31680))
	/label=“E4 ORF 6/7 CDS”
CDS	complement(31774..32625)
	/label=“E4 34K CDS”
CDS	complement(32558..32920)
	/label=“E4 ORF4 CDS”
CDS	complement(32922..33272)
	/label=“E4 ORF3 CDS”
CDS	complement(33269..33661)
	/label=“E4 ORF2 CDS”
CDS	complement(33675..34055)
	/label=“E4 ORF1 CDS”
misc_feature	34279..34402
	/label=“ITR repeat”

BaAdV-1 (SEQ ID NO: 4)

LOCUS	BaAdV-1_final_an 35537 bp DNA linear UNA
DEFINITION	.
ACCESSION	urn.local...1357154805381.28
VERSION	urn.local...1357154805381.28
KEYWORDS	.
SOURCE
ORGANISM
	.

FEATURES	Location/Qualifiers
misc_feature	1..215
	/label=“ITR repeat region”
CDS	order(1171..1451,528..1101)
	/label=“E1A CDS”
CDS	1579..2124
	/label=“E1B 19K”
CDS	1884..3362
	/label=“E1B55K CDS”
CDS	3429..3878
	/label=“IX CDS”
CDS	order(complement(3916..5255),complement(5534..5546))
	/label=“IVa2 CDS”
CDS	order(complement(13577..13585),complement(5025..8621))
	/label=“pol CDS”
CDS	order(complement(13577..13585),complement(8420..10405))
	/label=“pTP CDS”
CDS	10522..11736
	/label=“52K CDS”
CDS	11755..13551
	/label=“pIIIa CDS”
CDS	13636..15171
	/label=“III (penton) CDS”
CDS	15200..15754
	/label=“pVII CDS”
CDS	15803..16903
	/label=“pV CDS”
CDS	16925..17149
	/label=“pX CDS”
CDS	17204..17998
	/label=“pVI CDS”
CDS	18071..20833
	/label=“II (hexon) CDS”
CDS	20834..21451
	/label=“protease CDS”
CDS	complement(21499..22980)
	/label=“DBP CDS”
CDS	23018..25381
	/label=“100K CDS”
CDS	order(25071..25627,25806..25902)
	/label=“33K CDS”
CDS	25071..25775
	/label=“22K CDS”
CDS	25948..26649
	/label=“pVIII CDS”
CDS	26649..26975
	/label=“E3 12.5K CDS”
CDS	26920..28341
	/label=“E3 CR1 alpha-beta CDS”
CDS	28357..28629
	/label=“E3 RID-alpha CDS”
CDS	28536..28997
	/label=“E3 RID-beta CDS”
CDS	29000..29392
	/label=“E3 14.7K protein CDS”
CDS	complement(29409..29567)
	/label=“U exon CDS”
CDS	29586..31196
	/label=“IV (fiber 1) CDS”
CDS	31218..32474
	/label=“IV (fiber 2) CDS”
CDS	order(complement(32507..32716),complement(33481..33630))
	/label=“E4 ORF 6/7 CDS”
CDS	complement(32755..33630)
	/label=“E4 34K CDS”
CDS	complement(33563..33928)
	/label=“E4 ORF4 CDS”
CDS	complement(33933..34283)
	/label=“E4 ORF3 CDS”
CDS	complement(34294..34680)
	/label=“E4 ORF2 CDS”
CDS	complement(34705..35088)
	/label=“E4 ORF1 CDS”
misc_feature	35323..35537
	/label=“ITR repeat”

Example 7

Annotated Sequence Information

The table below provides identity of the molecules listed in the sequence listing.


SEQ
ID NO:	Baboon Adenovirus	Molecule

1	BaAdV-2	Viral genome
2	BaAdV-4	Viral genome
3	BaAdv-3	Viral genome
4	BaAdv-1	Viral genome
5	BaAdv-2	100K_protein_CDS_translation
6	BaAdv-2	22K_protein_CDS_translation
7	BaAdv-2	33K_protein_CDS_translation
8	BaAdv-2	52K_CDS_translation
9	BaAdv-2	DBP_CDS_translation
10	BaAdv-2	E1A_CDS_translation
11	BaAdv-2	E1B_55K_CDS_translation
12	BaAdv-2	E3_12.5K_CDS_translation
13	BaAdv-2	E3_14.7_CDS_translation
14	BaAdv-2	E3_CR1-alpha_CDS_translation
15	BaAdv-2	E3_CR1-beta_CDS_translation
16	BaAdv-2	E3_RID-alpha_CDS_translation
17	BaAdv-2	E3_RID-beta_CDS_translation
18	BaAdv-2	E4_34K_CDS_translation
19	BaAdv-2	E4_ORF_6/7_CDS_translation
20	BaAdv-2	E4_ORF1_CDS_translation
21	BaAdv-2	E4_ORF2_CDS_translation
22	BaAdv-2	E4_ORF3_CDS_translation
23	BaAdv-2	E4_ORF4_CDS_translation
24	BaAdv-2	II_(hexon)_CDS_translation
25	BaAdv-2	III_(penton)_CDS_translation
26	BaAdv-2	IV_(fiber_1)_CDS_translation
27	BaAdv-2	IV_(fiber_2)_CDS_translation
28	BaAdv-2	IVa2_CDS_translation
29	BaAdv-2	IX_CDS_translation
30	BaAdv-2	pIIIa_CDS_translation
31	BaAdv-2	pol_CDS_translation
32	BaAdv-2	protease_CDS_translation
33	BaAdv-2	pTP_CDS_translation
34	BaAdv-2	pV_CDS_translation
35	BaAdv-2	pVI_CDS_translation
36	BaAdv-2	pVII_CDS_translation
37	BaAdv-2	pVIII_CDS_translation
38	BaAdv-2	pX_CDS_translation
39	BaAdv-2	U_exon_CDS_translation
40	BaAdV-4	U_exon_CDS_translation
41	BaAdV-4	pX_CDS_translation
42	BaAdV-4	pVIII_CDS_translation
43	BaAdV-4	pVII_CDS_translation
44	BaAdV-4	pVI_CDS_translation
45	BaAdV-4	pV_CDS_translation
46	BaAdV-4	pTP_CDS_translation
47	BaAdV-4	protease_CDS_translation
48	BaAdV-4	pol_CDS_translation
49	BaAdV-4	pIIIa_CDS_translation
50	BaAdV-4	IX_CDS_translation
51	BaAdV-4	IVa2_CDS_translation
52	BaAdV-4	IV_(fiber1)_CDS_translation
53	BaAdV-4	IV_(fiber_2)_CDS_translation
54	BaAdV-4	III_(penton)_CDS_translation
55	BaAdV-4	II_(hexon)_CDS_translation
56	BaAdV-4	E4_ORF4_CDS_translation
57	BaAdV-4	E4_ORF3_CDS_translation
58	BaAdV-4	E4_ORF2_CDS_translation
59	BaAdV-4	E4_ORF1_CDS_translation
60	BaAdV-4	E4_ORF_6/7_translation
61	BaAdV-4	E4_34K_CDS_translation
62	BaAdV-4	E3_RID-beta_CDS_translation
63	BaAdV-4	E3_RID-alpha_CDS_translation
64	BaAdV-4	E3_CR1-beta_CDS_translation
65	BaAdV-4	E3_CR1-alpha_CDS_translation
66	BaAdV-4	E3_14.7_protein_CDS_translation
67	BaAdV-4	E3_12.5K_CDS_translation
68	BaAdV-4	E1B_55K_CDS_translation
69	BaAdV-4	E1A_CDS_translation
70	BaAdV-4	DBP_CDS_translation
71	BaAdV-4	52K_CDS_translation
72	BaAdV-4	33K_protein_CDS_translation
73	BaAdV-4	22K_protein_CDS_translation
74	BaAdV-4	100K_protein_CDS_translation
75	BaAdv-3	100K_protein_CDS_translation
76	BaAdv-3	22K_protein_CDS_translation
77	BaAdv-3	33K_protein_CDS_translation
78	BaAdv-3	52K_CDS_translation
79	BaAdv-3	DBP_CDS_translation
80	BaAdv-3	E1A_CDS_translation
81	BaAdv-3	E1B_55K_CDS_translation
82	BaAdv-3	E3_12.5K_CDS_translation
83	BaAdv-3	E3_14.7_protein_CDS_translation
84	BaAdv-3	E3_CR1-beta_CDS_translation
85	BaAdv-3	E3_RID-alpha_CDS_translation
86	BaAdv-3	E3_RID-beta_CDS_translation
87	BaAdv-3	E3-CR1-alpha_CDS_translation
88	BaAdv-3	E4_34K_CDS_translation
89	BaAdv-3	E4_ORF_6/7_CDS_translation
90	BaAdv-3	E4_ORF1_CDS_translation
91	BaAdv-3	E4_ORF2_CDS_translation
92	BaAdv-3	E4_ORF3_CDS_translation
93	BaAdv-3	E4_ORF4_CDS_translation
94	BaAdv-3	pII_(hexon)_translation
95	BaAdv-3	pII_(penton)_translation
96	BaAdv-3	pIV_(fiber_2)_CDS_translation
97	BaAdv-3	pIV_(fiber)_translation
98	BaAdv-3	pIVa2_CDS_translation
99	BaAdv-3	pIIIa_CDS_translation
100	BaAdv-3	pIX_CDS_translation
101	BaAdv-3	pol_CDS_translation
102	BaAdv-3	protease_CDS_translation
103	BaAdv-3	pTP_CDS_translation
104	BaAdv-3	pV_CDS_translation
105	BaAdv-3	pVI_CDS_translation
106	BaAdv-3	pVII_CDS_translation
107	BaAdv-3	pVIII_CDS_translation
108	BaAdv-3	pX_CDS_translation
109	BaAdv-3	U_exon_CDS_translation
110	BaAdv-1	100K_CDS_translation
111	BaAdv-1	22K_CDS_translation
112	BaAdv-1	33K_CDS_translation
113	BaAdv-1	52K_CDS_translation
114	BaAdv-1	DBP_CDS_translation
115	BaAdv-1	E1A_CDS_translation
116	BaAdv-1	E1B_55K_CDS_translation
117	BaAdv-1	E3_12.5K_CDS
118	BaAdv-1	E3_14.7K_protein_CDS_translation
116	BaAdv-1	E3_CR1_alpha-beta_CDS_translation
1120	BaAdv-1	E3_RID-alpha_CDS_translation
121	BaAdv-1	E3_RID-beta_CDS_translation
122	BaAdv-1	E4_34K_CDS_translation
123	BaAdv-1	E4_ORF_6/7_CDS_translation
124	BaAdv-1	E4_ORF1_CDS_translation
125	BaAdv-1	E4_ORF2_CDS_translation
126	BaAdv-1	E4_ORF3_CDS_translation
127	BaAdv-1	E4_ORF4_CDS_translation
128	BaAdv-1	II_(hexon)_CDS_translation
129	BaAdv-1	III_(penton)_CDS_translation
130	BaAdv-1	IV_(fiber_1)_CDS_translation
131	BaAdv-1	IV_(fiber_2)_CDS_translation
132	BaAdv-1	IVa2_CDS_translation
133	BaAdv-1	pIIIa_CDS_translation
134	BaAdv-1	pIX_CDS_translation
135	BaAdv-1	pol_CDS_translation
136	BaAdv-1	protease_CDS_translation
137	BaAdv-1	pTP_CDS_translation
138	BaAdv-1	pV_CDS_translation
139	BaAdv-1	pVI_CDS_translation
140	BaAdv-1	pVII_CDS_translation
141	BaAdv-1	pVIII_CDS_translation
142	BaAdv-1	pX_CDS_translation
143	BaAdv-1	U_exon_CDS_translation

It will be apparent that the precise details of the methods or compositions described may be varied or modified without departing from the spirit of the described invention. We claim all such modifications and variations that fall within the scope and spirit of the claims below.

Claims

1. An isolated recombinant nucleic acid molecule comprising a nucleic acid sequence at least 100 nucleotides in length that has at least 90% sequence identity over its length to SEQ ID NO:1, SEQ ID NO: 2, SEQ ID NO: 3, or the complement thereof, wherein the recombinant nucleic acid is:

(a) a cDNA;

(b) attached to a detectable label; or

(c) operably linked to a heterologous nucleic acid.

2. An isolated recombinant isolated nucleic acid molecule comprising:

(a) a nucleic acid sequence at least 90% identical to nucleotides 1-29685 and 29867-34391 of the nucleic acid sequence set forth as SEQ ID NO: 1;

(b) a nucleic acid sequence at least 90% identical to nucleotides 1-29865 and 29867-34391 of the nucleic acid sequence set forth as SEQ ID NO: 2;

(c) a nucleotide sequence at least 90% identical to the nucleotide sequence set forth as nucleotides 1-28677 and 29812-34402 of SEQ ID NO: 3.

3. The isolated recombinant nucleic acid molecule of claim 2, comprising the nucleic acid sequence set forth as SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 or a degenerate variant thereof.

4. A cDNA comprising a nucleic acid sequence at least 90% identical to an open reading frame of SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3.

5. The cDNA of claim 4, comprising an open reading frame of the nucleic acid sequence set forth as SEQ ID NO: 1, SEQ ID NO: 2 or SEQ ID NO: 3.

6. An isolated polypeptide encoded by the nucleic acid sequence of claim 4.

7. The isolated polypeptide of claim 6, comprising an amino acid sequence at least 90% identical to the amino acid sequence set forth as one of SEQ ID NOs: 5-109.

8. An isolated polypeptide comprising the amino acid sequence encoded by the nucleotide sequence of claim 5.

9. An isolated antibody that specifically binds to the polypeptide of claim 6.

10. The isolated antibody of claim 9, wherein the antibody is a monoclonal antibody.

11. The isolated antibody of claim 9, wherein the antibody is labeled.

12. A composition comprising an effective amount of the nucleic acid of claim 1, a polypeptide encoded by the nucleic acid, a vector comprising the nucleic acid, a host cell comprising the vector, an adenovirus comprising the nucleic acid, molecule or antibody that specifically binds the polypeptide, and a pharmaceutically acceptable carrier.

13. A method of detecting a Baboon adenovirus (BaAdV)-3 or a BaAdV-2/4 adenovirus, comprising

(a) contacting a sample suspected of comprising an adenoviral nucleic acid with the nucleic acid of claim 1 under stringent conditions; and

(b) detecting the presence or absence of hybridization of the nucleotide sequence to the sample, wherein the presence of hybridization detects the BaAdV-3 or a BaAdV-2/4 adenovirus.

14. A method of detecting a Baboon adenovirus (BaAdV)-3 or BaAdV-2/4 nucleic acid, the method comprising the steps of:

(a) contacting a sample suspected of comprising an adenoviral nucleic acid with at least one primer that hybridizes under stringent conditions to the nucleotide sequence set forth as SEQ ID NO:1, SEQ ID NO: 2, and/or SEQ ID NO: 3;

(b) performing a PCR reaction to amplify cDNA; and

(c) detecting presence or absence of the cDNA, wherein the presence of the cDNA detects the BaAdV-3 or a BaAdV-2/4 adenovirus.

15. A method of detecting a baboon adenovirus BaAdV-3 or a BaAdV-2/4 infection in a subject, comprising:

(a) contacting a sample from the subject suspected of having an infection caused by the BaAdV-3 or the BaAdV-2/4 with the antibody of claim 9; and

(b) detecting binding of the antibody to a polypeptide in the sample, wherein binding of the antibody to the polypeptide detects the presence of the BaAdV-3 or the BaAdV-2/4 infection.

16. A kit, comprising

a container comprising the isolated recombinant nucleic acid molecule of claim 1, a polypeptide encoded by the nucleic acid or an immunogenic fragment of the polypeptide, a vector comprising the nucleic acid, a host cell comprising the vector, an adenovirus comprising the nucleic acid, or an antibody that specifically binds the polypeptide, or a primer that hybridizes to the nucleotide sequence set forth SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3 under highly stringent conditions; and

instructions for using the kit.

17. A kit, comprising

the polypeptide of claim 6, and

instructions for the detection of the presence of antibodies that specifically bind Baboon adenovirus (BaAdV)-3 or BaAdV-4 in a sample from a subject.

18. A kit comprising

the antibody of any claim 9; and

instructions for the detection of the presence of a Baboon adenovirus (BaAdV)-3 or BaAdV-4 polypeptide in a sample from a subject.

19. An isolated polypeptide comprising the amino acid sequence set forth as one of SEQ ID NOs: 5-109.

20. The isolated polypeptide of claim 20, consisting of the amino acid sequence set forth as one of SEQ ID NOs: 5-109.

21. An adenovirus comprising the polypeptide of claim 20.

22. The method of claim 15, wherein the antibody specifically binds the amino acid sequence set forth as one of SEQ ID NOs: 5-109.