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  • C12N2770/00011—Details
  • C12N2770/24011—Flaviviridae
  • C12N2770/24111—Flavivirus, e.g. yellow fever virus, dengue, JEV
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  • C12N2770/24011—Flaviviridae
  • C12N2770/24111—Flavivirus, e.g. yellow fever virus, dengue, JEV
  • C12N2770/24134—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
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  • C12N2770/00011—Details
  • C12N2770/24011—Flaviviridae
  • C12N2770/24111—Flavivirus, e.g. yellow fever virus, dengue, JEV
  • C12N2770/24161—Methods of inactivation or attenuation
  • C12N2770/24162—Methods of inactivation or attenuation by genetic engineering
• • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
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  • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
  • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

• This invention provides highly attenuated flaviviruses and particularly, attenuated dengue viruses and vaccines.
• the attenuated viruses provide protective immunity from challenge by virus of the same lineage, as well as cross protection against heterologous viruses.
• Dengue vims is a single-stranded positive-sense RNA vims belonging to the Flaviviridae family, in the same genus (Flavivims) that includes Zika vims (ZIKV), West Nile vims (WNV), and yellow fever vims (YFV).
• ZIKV Zika vims
• WNV West Nile vims
• YFV yellow fever vims
• DENV is closely related phylogenetically to ZIKV and shares a common mosquito vector, Aedes aegypti, with both ZIKV and Chikungunya vims (an alphavims).
• Aedes aegypti The vector for DENV, Aedes aegypti, is found throughout the southern U.S.
• Aedes albopictus, the Asian tiger mosquito is also competent for transmitting DENV. If DENV enters A. albopictus populations in the U.S., it will have a vastly expanded range extending into the American Midwest and Northeast.
• ADE Antibody-Dependent Enhancement
• ADE occurs when prior infection with one flavivims predisposes an individual to an enhanced severity of disease upon re-infection with a different serotype.
• antibodies against the first vims bind, but do not neutralize the second vims, instead increasing its infectivity.
• DENV is prevalent in many countries, thus any vaccine strategy should consider the impact on a population with established dengue immunity. It is worth noting that people with underlying DENV immunity could experience increased adverse events from a live DENV vaccine, since their DENV immunity could enhance infectivity of the DENV vaccine strain, leading to increased adverse events.
• Dengue vims comprised four serotypes (DENV 1-4) of the mosquito-borne Flavivimses in the family Flaviviridae.
• Dengue vimses are enveloped vimses with an icosahedral virion comprised of C (Core), M(Membrane), and E (Envelope) glycoproteins that is 40-65 nanometers in diameter.
• the Dengue virus genome is a single positive-strand RNA molecule of 10,000-11,000 bases in length encoding structural (C, prM, E) and nonstructural (NS1, NS2, NS3, NS4, and NS5) proteins.
• Dengue viruses transcribe and replicate their genome in the cell cytoplasm, with the genome translated into a single polypeptide that is cleaved and processed by both host and viral proteins.
• Dengue vims is an emerging agent of international concern in the tropics and the individual serotypes are genetically as well as antigenically distinct viruses.
• various embodiments of the invention provides an attenuated dengue vims in which expression of viral proteins is reduced through codon-pair deoptimization of the E coding regions.
• E is the only vims protein coding regions targeted.
• the reduction is small compared to the reduction of E.
• reduction in expression of vims proteins of the invention is accomplished by changes in protein encoding sequence, for example by lowering the codon pair bias of the protein-encoding sequence, substituting rare codons, modifying G+C content, modifying CG and/or TA (or UA) dinucleotide content, or combinations. Reduced expression can also be accomplished by modifications to the regulatory sequences of the proteins.
• reducing the codon-pair bias can comprise identifying a codon pair in the parent protein-encoding sequence having a codon-pair score that can be reduced, and reducing the codon-pair bias by substituting the codon pair with a codon pair that has a lower codon-pair score.
• reducing the codon-pair bias comprises rearranging the codons of a parent protein-encoding sequence.
• the E protein-encoding sequence has a codon pair bias less than -0.1, or less than -0.2, or less than -0.3, or less than -0.4. Codon pair bias of a protein-encoding sequence (i.e., an open reading frame) is calculated as described in Coleman et al., 2000 and herein.
• expression of the E protein-encoding sequence is reduced by replacing one or more codons with synonymous codons that are less frequent in the host.
• the E protein-encoding sequence DENV serotype are present in a background from a different strain of the same DENV serotype or the homologous strain.
• the invention also provides a dengue vaccine composition for inducing a protective immune response in a subject, wherein the vaccine composition comprises vims in which viral translation is reduced while maintaining at least 90% antigenic identity with wt vims.
• the viral translation is reduced while maintaining at least 95, 96, 97, 98 or 99% antigenic identity with wt vims.
• the viral translation is reduced while maintaining 100% antigenic identity with wt vims.
• the invention also provides a method of eliciting a protective immune response in a subject comprising administering to the subject a prophylactically or therapeutically effective dose of a vaccine composition comprising an attenuated dengue vims, wherein expression of viral proteins is reduced by at least 10%. In various embodiments, the expression of viral proteins is reduced by at least 15%, at least 20% or at least 25%. In an embodiment of the invention, an immune response is elicited that is effective against dengue vims of the same lineage as the attenuated vims of the vaccine. In another embodiment, an immune response is elicited that is effective against a heterologous dengue vims.
• the invention also provides a method of making an attenuated dengue vims genome comprising a) obtaining the genomic nucleotide b) recoding the envelope-encoding nucleotide sequence to reduce expression and recoding the nonstmctural protein 3-encoding nucleotide sequence to reduce expression, and substituting the recoded nucleotide sequences into a dengue vims genome to make an attenuated dengue vims genome.
• only the E region is targeted.
• expression of another vims protein encoding region is also reduced.
• the invention also provides a method of constructing template dengue vims DNA sequences for transcription of infectious viral RNA genomes by T7 polymerase using overlapping PCR. All dengue genomes with homologous backbone were divided into three fragments starting from 5’ end (fragment 1: ntl-3596; fragment 2: nt3030-6959, and fragment 3: nt: nt6851-end) and chemically/biochemically synthesized. Instead of constructing an infectious cDNA clone, a long overlap extension PCR strategy was used to obtain full-length dengue genome (or: the syn-wt and min dengue genomes simultaneously).
• the first 2.5 Kb fragments containing the DENV2 16681 5’UTR, C domain and the prM/M, E (wildtype or deoptimized) domain from individual DENV serotype and a small fraction of the DENV2 16681 NS1 domain, were synthesized.
• the 8 Kb DENV2 16681 backbone containing all NS domains and the 3’UTR were obtained from infectious clones encoding wildtype or deoptimized DENV2 16681.
• the 2.5 Kb and 8 Kb fragments were fused together using an asymmetric-fusion PCR method.
• a modified dengue vims comprising a recoded prM protein, a recoded envelope (E) protein, or both, wherein the recoded prM protein has a reduced codon pair bias compared to its parent prM protein encoding sequence, or has at least 5 codons substituted with synonymous codons less frequently used, or has an increased number of CpG or UpA di-nucleotides compared its parent prM protein encoding sequence, and wherein the recoded E protein has a reduced codon pair bias compared to its parent E protein encoding sequence, or has at least 5 codons substituted with synonymous codons less frequently used, or has an increased number of CpG or UpA di-nucleotides compared its parent E protein encoding sequence.
• the expression of the prM protein or E protein or both can be reduced compared to its parent dengue vims.
• the recoded prM protein has a reduced codon pair bias compared to its parent prM protein encoding sequence.
• the recoded prM protein can have at least 5 codons substituted with synonymous codons less frequently used.
• the recoded prM protein can have an increased number of CpG or UpA di-nucleotides compared its parent prM protein encoding sequence.
• the recoded E protein can have a reduced codon pair bias compared to its parent E protein encoding sequence.
• the recoded E protein can have at least 5 codons substituted with synonymous codons less frequently used. In various embodiments, the recoded E protein can have an increased number of CpG or UpA di-nucleotides compared its parent E protein encoding sequence. In various embodiments, each of the recoded prM or E protein-encoding sequence can have a codon pair bias of less than -0.05. In various embodiments, the codon pair bias of each of the recoded prM or E protein-encoding sequence can be reduced by at least 0.05.
• the modified dengue virus can be selected from type 1, type 2, type 3, type 4 or a combination thereof.
• the modified dengue vims is a modified tetravalent dengue vims.
• a dengue vaccine composition for inducing a protective immune response in a subject, comprising a modified dengue vims as described above and herein, and a pharmaceutically acceptable excipient or carrier.
• Various embodiments of the invention provide a method of eliciting an immune response in a subject, comprising: administering to the subject an effective dose of a composition comprising a modified dengue vims as described above and herein, and a pharmaceutically acceptable excipient or carrier.
• the immune response can be a protective immune response, and a prophylactically effective or therapeutically effective dose of a vaccine composition of claims can be administered.
• the immune response can be cross-protective against a heterologous dengue vims.
• the method can further comprise administering to the subject at least one adjuvant.
• Various embodiments of the present invention provide for a method of eliciting an immune response in a subject in need thereof, comprising: administering a prime dose of (i) an attenuated dengue vims produced by a method other than codon-pair deoptimization or codon deoptimization, or increasing of CpG or UpA di-nucleotides, or (ii) a modified dengue vims comprising a recoded prM protein, a recoded envelope (E) protein, or both, wherein the recoded prM protein has a reduced codon pair bias compared to its parent prM protein encoding sequence, or has at least 5 codons substituted with synonymous codons less frequently used, or has an increased number of CpG or UpA di-nucleotides compared its parent prM protein encoding sequence, and wherein the recoded E protein has a reduced codon pair bias compared to its parent E protein encoding sequence, or has at least 5
• a first of the one or more boost dose can be administered about 2 weeks after the prime dose.
• the expression of the prM protein or E protein or both can be reduced compared to its parent dengue vims.
• the recoded prM protein can have a reduced codon pair bias compared to its parent prM protein encoding sequence. In various embodiments, the recoded prM protein can have at least 5 codons substituted with synonymous codons less frequently used. In various embodiments, the recoded prM protein can have an increased number of CpG or UpA di-nucleotides compared its parent prM protein encoding sequence. In various embodiments, the recoded E protein can have a reduced codon pair bias compared to its parent E protein encoding sequence. In various embodiments, the recoded E protein can have at least 5 codons substituted with synonymous codons less frequently used.
• the recoded E protein can have an increased number of CpG or UpA di-nucleotides compared its parent E protein encoding sequence.
• each of the recoded prM or E protein-encoding sequence has a codon pair bias of less than -0.05.
• the codon pair bias of each of the recoded prM or E protein-encoding sequence is reduced by at least 0.05.
• the modified dengue vims is selected from type 1, type 2, type 3, type 4 or a combination thereof. In various embodiments, the modified dengue vims is a modified tetravalent dengue vims.
• Various embodiments of the present invention provide for a method of making a modified dengue vims genome comprising: obtaining a nucleotide sequence encoding the envelope protein of a dengue vims; recoding the envelope encoding nucleotide sequence to reduce protein expression, and substituting a nucleic acid having the recoded envelope-encoding nucleotide sequence into a parent dengue vims genome to make a modified dengue vims genome; whereby expression of the recoded envelope-encoding nucleotide sequence is reduced compared to the parent vims.
• FIG. 1 depicts rapid construction of SAVE-deoptimized, live-attenuated dengue vaccine candidate with growth in Vero cells under animal component-free conditions. Codon pair bias of the dengue prM/E genes and their SAVE-deoptimized counterparts in relation to the human ORFeome. Codon-Pair Bias (CPB) is expressed as the average codon pair score of a given gene’s open reading frame (ORF). Positive and negative CPB value signifies the predominance of statistically over- or under-represented codon-pairs, respectively in an ORF. Red circles indicate the CPB of each of the 14,795 human ORFs, representing the majority of the known, annotated human genes at the time of our analysis (ORFeome).
• CPB Codon-Pair Bias
• the CPB of wild-type E gene fall within the normal range of human host cell’s genes. Following codon pair‘deoptimization’ via SAVE, the resulting deoptimized prM/E gene segments were now encoded predominately by under-represented human codon-pairs as evident by their extremely negative CPB, and are drastically different from any human gene.
• B cDNA genomes of wild-type and synthetically ‘de-optimized’ chimeric dengue vaccine variants.
• the SAVE- deoptimized synthetic E were synthesized c/e novo and using overlapping PCR subcloned individually into the WT DENV genomes - yielding eight independent cDNA genomes each containing a synthetically‘de optimized’ ffagment(s).
• FIG. 2 depicts diagram of subcloning strategies for decreasing attenuation or increasing immunogenicity by reducing the length of deoptimized sequence in the E encoding region.
• the second generation of dengue vaccine candidates leverages the flexibility of the SAVE platform to reduce the deoptimized region from full-length (E-min) to approximately half of the length (W-E-Min) while keeping the amino acid sequence 100% identical.
• FIG. 3 depicts growth of heterologous backbone dengue vaccine candidates in Vero cells under animal component-free conditions.
• DENV 1-4 E-Min were used to infect Vero cells under animal-component free conditions at a MOI of 0.01 and supernatant titrated daily in a multiple-step growth curve over the course of 10 days post-infection.
• DENV2, DENV3, and DENV4 candidates reached titers of 1-2 x 10 5 FFU/ml while DENV1 E-Min titer was reduced by ⁇ 1 logio compared to the others.
• FIG. 4A-4C depicts multiple step growth curves that were conducted in Vero cells for synthetic DENV1 WT vims in a full-length DENV1 backbone (FIG. 4A) and attenuated live vaccine candidates DENV1 E-W/MIN (FIG. 4B) and E-MIN (FIG. 4C) derived from DENV1 WT.
• Synthetic DENV1 WT grows well in Vero cells at 33 ° C and 37 ° C. Typical of DENV, a transient reduction in vims yield was observed at 39 ° C, however, titers recovered to 37 ° C levels by 7 dpi.
• DENV1 E-W/MIN reached serviceable titers ⁇ 10- fold lower than DENV1 WT at both 33 ° C and 37 ° C.
• DENV1 E-MIN was highly attenuated in Vero cells and only reached detectable titers at 33 ° C starting on days 10-14 post-infection.
• FIG. 5 depicts multiple step growth curves that were conducted in Vero cells for synthetic DENV2 WT vims (in a full-length DENV2 backbone) and attenuated live vaccine candidates DENV2 E-W/MIN and E-MIN derived from DENV2 WT.
• DENV2 E-W/MIN and E-MIN were both attenuated in vitro with a 1-2 logio FFU/ml reduction for E-W/MIN and a more pronounced 2-3 logio FFU/ml reduction for DENV2 E-MIN ( Figure 3). While growth kinetics were delayed, with regular medium replacement every 1-2 days vims titers reached >10 6 FFU/ml for DENV2 E-W/MIN.
• DENV3 E-W/MIN was more temperature sensitive at 39 ° C than the WT with a significantly greater difference observable on days 3, 4, 5, and 7 post-infection.
• DENV3 E-MIN had minimal levels of replication in Vero cells at 39 ° C, the difference in vims yield from 37 ° C to 39 ° C were as high as 10 7 FFU/ml.
• DENV3 E-MIN reached high titers which is promising for cGMP manufacture.
• FIG. 7 depicts multiple step growth curves that were conducted in Vero cells for synthetic DENV4 WT vims (in a full-length DENV4 backbone) and attenuated live vaccine candidates DENV4 E-W/MIN and E-MIN derived from DENV4 WT.
• DENV4 WT and E-W/MIN grew to high titers in Vero cells, with the peak DENV4 E-W/MIN titers approximately 10-fold lower but still high ( ⁇ 10 7 FFU/ml) at 33 ° C and 37 ° C.
• Both vimses were partially restricted at 39 ° C, but not to the extent seen with DENV1-3.
• DENV4 E-MIN was attenuated in Vero cells with peak titers 100-fold lower than WT.
• DENV4 E-MIN replication at 33 ° C and 37 ° C was similar, however, DENV4 E-MIN was not viable at 39 ° C with no detectable vims on days 1-14 post infection.
• FIG. 8A-8B depicts evaluation of the attenuation, immunogenicity, and efficacy of DENV2 vaccine candidates in AG129 mice.
• DENV-2 E-min based on a DENV2 16681 backbone was tested in an immunogenicity/dose escalation study in AG 129 mice lacking interferon alpha or gamma receptors. Animals were immunized with DENV-2 E-min or DENV-2 16681 at two different concentrations. Resultant neutralizing antibody titers were determined, and the protective efficacy afforded evaluated against a mouse-adapted lethal strain of DENV2, D2S10.
• FIG. 9 depicts constructed D2-E-min and D2-l/2-E-min with E sequence derived from DENV- 2/NI/BID-V533/2005 in the heterologous DENV2 16681 backbone to improve the clinical relevance of our DENV2 candidate.
• D2-l/2-E-min with the E region consisting of half wt DENV-2/NI/BID- V533/2005 sequence and half CPD, to improve the immunogenicity of our vims.
• FIG. 10A-10B depicts AG129 mice used to test the immunogenicity and protective efficacy of DENV-3 vaccine candidate DENV D2/D3-E-min, which comprises the DENV-2 strain 16681 backbone with a codon-deoptimized prME cassette from DENV-3/VE/BID-V2268/2008.
• DENV-3 vaccine candidate DENV D2/D3-E-min which comprises the DENV-2 strain 16681 backbone with a codon-deoptimized prME cassette from DENV-3/VE/BID-V2268/2008.
• This study was designed to evaluate the immunogenicity and efficacy of this candidate vaccine against challenge with virulent DENV3 CO360/94. The first immunization was well tolerated by all of the animals with no major associated weight loss and none of the animals developed clinical signs.
• FIG. 11A-11B depicts AG129 mice used to test the immunogenicity and protective efficacy of DENV-4 vaccine candidates DENV D2/D4-E-min and D2/D4-l/2-E-min, which comprise the DENV-2 strain 16681 backbone with a codon-deoptimized prME cassette from DENV4.
• Each vaccine candidate was immunogenic at 35 DPI with vaccination with D2/D4-E-min (GMT 332.9) and D2/D4-l/2-E-min (GMT 738.4) lower than vaccination with D2/D4-WTE (GMT 1640).
• DPC D2/D4-E-min
• viremia levels were below the limit of detection of the assay (500 genome equivalents/ml).
• DENV-4 703/4 challenge produced rapid progressive infection with universal lethality in the media control group.
• three animals immunized with D2/D4-E-min experienced lethal infection with the other animals in this group remaining healthy for the duration of the study. Importantly, no lethality or evidence of morbidity as determined by weight loss was seen in any of the D2/D4-l/2-E-min immunized animals after DENV-4 703/4 challenge.
• FIG. 12 depicts tested DENV1-4 WT as well as vaccine candidates for DENV2-4 for immunogenicity in IFNa receptor knockout mice .
• All WT viruses were highly immunogenic in these mice, with neutralizing antibody titers >1024.
• DENV2-E-W/MIN was equally immunogenic to DENV2 WT vims at both a 10 6 and 10 4 FFU dose.
• Immunogenicity of DENV3 viruses waned with decreasing dose and increased deoptimization, however, DENV3 E-W/MIN was still highly immunogenic at a 10 4 FFU dose (-1024 FRNT50).
• FIG. 13 depicts immunogenicity and efficacy of tetravalent vaccination in AG129 mice against lethal challenge with DENV3 C0360/94.
• mice On day 35, all remaining mice were challenged with 10 7 IFU DENV3 C0360/94 delivered by the intraperitoneal route. As anticipated, animals in the media control group developed a rapid progressive infection that was lethal in 8/9 (89%) animals with the mean day of death (MDD) among the animals that died of 4.1 ⁇ 0.4 days. Immunization with monovalent DENV D2/D3-E-min or the tetravalent vaccine provided significant protection with no lethality or morbidity (as measured by > 10% weight loss) among the animals in either group.
• FIG. 14 depicts attenuation of homologous backbone viruses - focus size of vaccine strains vs wt - vaccine viruses spread less in vitro as compared to wt.
• Individual foci areas (mm 2 ) were calculated for Vero cells infected with DENV 1-4 WT, E-W/MIN, or E-MIN and incubated for 3 days at temperatures of 33 ° C, 37 ° C, or 39 ° C.
• FFU focus-forming unit
• FIG. 15 depicts in vivo immunogenicity data for tetravalent homologous backbone vaccine
• Tetravalent and monovalent homologous backbone dengue vaccine candidates were immunogenic in IFNa receptor knockout mice after vaccination with 10 6 or 10 4 FFU delivered by the subcutaneous route on day 0 and 21.
• Neutralizing antibodies were tested using a focus-reduction neutralization 50% test at days 0, 21, and 35 post-vaccination against each strain of DENV 1-4 wt.
• the term“about” when used in connection with a referenced numeric indication means the referenced numeric indication plus or minus up to 5% of that referenced numeric indication, unless otherwise specifically provided for herein.
• the language“about 50%” covers the range of 45% to 55%.
• the term“about” when used in connection with a referenced numeric indication can mean the referenced numeric indication plus or minus up to 4%, 3%, 2%, 1%, 0.5%, or 0.25% of that referenced numeric indication, if specifically provided for in the claims.
• Codon-Pair Bias is expressed as the average codon pair score of a given gene’s open reading frame (ORF).
• A“subject” means any animal or artificially modified animal.
• Animals include, but are not limited to, humans, non-human primates, cows, horses, sheep, pigs, dogs, cats, rabbits, ferrets, rodents such as mice, rats and guinea pigs, and birds.
• Artificially modified animals include, but are not limited to, SCID mice with human immune systems.
• the subject is a human.
• Embodiments of birds are domesticated poultry species, including, but not limited to, chickens, turkeys, ducks, and geese.
• A“viral host” means any animal or artificially modified animal, or insect that the vims can infect.
• Animals include, but are not limited to, humans, non-human primates, cows, horses, sheep, pigs, dogs, cats, rabbits, ferrets, rodents such as mice, rats and guinea pigs, and birds.
• Artificially modified animals include, but are not limited to, SCID mice with human immune systems.
• the viral host is a human.
• Embodiments of birds are domesticated poultry species, including, but not limited to, chickens, turkeys, ducks, and geese.
• Insects include, but are not limited to mosquitos.
• A“prophylactically effective dose” is any amount of a vaccine that, when administered to a subject prone to viral infection or prone to affliction with a virus-associated disorder, induces in the subject an immune response that protects the subject from becoming infected by the virus or afflicted with the disorder.“Protecting” the subject means either reducing the likelihood of the subject’s becoming infected with the virus, or lessening the likelihood of the disorder’s onset in the subject, by at least two-fold, preferably at least ten-fold, 25-fold, 50- fold, or 100-fold.
• a“therapeutically effective dose” is any amount of a vaccine that, when administered to a subject afflicted with a disorder against which the vaccine is effective, induces in the subject an immune response that causes the subject to experience a reduction, remission or regression of the disorder and/or its symptoms. In preferred embodiments, recurrence of the disorder and/or its symptoms is prevented. In other preferred embodiments, the subject is cured of the disorder and/or its symptoms.
• the present invention relates to attenuated dengue vimses and the production of attenuated dengue vimses that can be used to protect against viral infection and disease.
• a basic premise in vaccination is adequate delivery of protective antigens to vaccine recipients assuming that a very high dose (“Peptide or Vims-Like Particle”) or a dose corresponding to live viral infection (“ChimeriVax”) of these traditionally dominant antigenic polypeptides alone are sufficient for adequate vaccine efficacy.
• a very high dose (“Peptide or Vims-Like Particle”) or a dose corresponding to live viral infection (“ChimeriVax”) of these traditionally dominant antigenic polypeptides alone are sufficient for adequate vaccine efficacy.
• Those expectations aside, the present invention benefits from a contrary approach.
• the invention provides attenuated dengue vimses in which expression of viral proteins is reduced, which have excellent growth properties useful to vaccine production, yet possess an extraordinary safety profile and enhanced protective characteristics.
• the attenuated vimses proliferate nearly as well as wild type virus, have highly attenuated phenotypes, as revealed by LD50 values, are unusually effective in providing protective immunity against challenge by dengue vims of the same strain, and also provide protective immunity against challenge by dengue vims of other strains.
• the attenuated dengue vimses of the invention comprise a recoded pre-membrane (prM)/Envelope (E) encoding region.
• prM pre-membrane
• E envelopee
• the C, NS1, NS2, NS3, NS4, or NS5 protein encoding regions are not recoded does not exclude mutations and other variations in those sequences, but only means that any mutations or variations made in those sequences have little or no effect on attenuation.
• Little or no effect on attenuation includes one or both of the following: 1) The mutations or variations in the C, NS 1, NS2, NS3, NS4, or NS5 encoding regions do not reduce viral replication or viral infectivity more than 20% when the variant C, NS 1, NS2, NS3, NS4, or NS5 encoding region is the only variant in atest dengue vims; 2) Mutations or variations in any ofthe C, NS1, NS2, NS3, NS4, orNS5 encoding regions represent fewer than 10% of the nucleotides in that coding sequence if specifically provided for in the claims, little or no effect on attenuation includes one or both of the following: 1) The mutations or variations in the C, NS 1, NS2, NS3, NS4, or NS5 encoding regions do not reduce viral replication or viral infectivity more than 10% when the variant C, NS 1, NS2, NS3, NS4, or NS5 encoding region is the only variant in a test dengue vims; 2)
• vimses of the invention are attenuated.
• the vimses are at least 10 fold attenuated, at least 50 fold attenuated, or at least 100 fold attenuated, or at least 200 fold attenuated, or at least 500 fold attenuated, or at least 1000 fold attenuated, of at least 2000 fold attenuated in the AG 129 mouse model compared to a wild type vims having proteins of the same amino acid sequence but encoded by a different nucleotide sequence.
• the attenuated vimses are also highly protective against wild type vims of the same strain.
• the protective dose (PD50) of the vimses is, when measured by a mouse model, such as exemplified herein.
• the attenuated vimses of the invention also exhibit a large margin of safety (i.e., the difference between LD50 and PD50), thus have high safety factors, defined herein as the ratio of LD50/PD50.
• the safety factor is at least 10 2 , or at least 10 3 , or at least 10 4 , or at least 10 5 , or at least 2 x 10 5 , or at least 3 c 10 5 , or at least 4 c 10 5 or at least 5 c 10 5 , or at least 10 6 , or at least 2 c 10 6 , or at least 3 c 10 6 , or at least 4/ 10 6 , or at least 5 c 10 6 .
• the safety factor is from 10 2 to 10 3 , or from 10 3 to 10 4 , or from 10 4 to 10 5 , or from 10 5 to 10 6 .
• the attenuated vimses of the invention are also highly protective against heterologous strains of the dengue vims within the same serotype.
• the protective dose (PD50) of an attenuated vims of the invention is less than 1000 PFU, or less than 750 PFU, or less than 500 PFU, or less than 200 PFU, or less than 100 PFU, or less than 50 PFU when measured by a mouse model, such as exemplified herein.
• the recoding of E protein encoding sequences of the attenuated viruses of the invention have been made or can be made by one of skill in the art in light of disclosure discussed herein.
• nucleotide substitutions are engineered in multiple locations in the E coding sequence, wherein the substitutions introduce a plurality of synonymous codons into the genome.
• the synonymous codon substitutions alter codon bias, codon pair bias, the density of infrequent codons or infrequently occurring codon pairs, RNA secondary structure, CG and/or TA (or UA) dinucleotide content, C+G content, translation ffameshift sites, translation pause sites, the presence or absence of microRNA recognition sequences or any combination thereof, in the genome .
• the codon substitutions may be engineered in multiple locations distributed throughout the E coding sequence, or in the multiple locations restricted to a portion of the E coding sequence. Because of the large number of defects (i.e., nucleotide substitutions) involved, the invention provides a means of producing stably attenuated viruses and live vaccines.
• a virus coding sequence is recoded by substituting one or more codon with synonymous codons used less frequently in the dengue host (e.g., mammals, humans, mosquitoes).
• a vims coding sequence is recoded by substituting one or more codons with synonymous codons used less frequently in the dengue vims.
• the number of codons substituted with synonymous codons is at least 5.
• at least 10, or at least 20 codons are substituted with synonymous codons.
• the number of codons substituted with synonymous codons is at least 30, or at least 40, or at least 50, or at least 75, or at least 100, or at least 125, or at least 150, or at least 175.
• vims codon pairs are recoded to reduce (i.e., lower the value of) codon-pair bias.
• codon-pair bias is reduced by identifying a codon pair in an E coding sequence having a codon-pair score that can be reduced and reducing the codon-pair bias by substituting the codon pair with a codon pair that has a lower codon-pair score.
• this substitution of codon pairs takes the form of rearranging existing codons of a sequence.
• a subset of codon pairs is substituted by rearranging a subset of synonymous codons.
• codon pairs are substituted by maximizing the number of rearranged synonymous codons. It is noted that while rearrangement of codons leads to codon-pair bias that is reduced (made more negative) for the vims coding sequence overall, and the rearrangement results in a decreased CPS at many locations, there may be accompanying CPS increases at other locations, but on average, the codon pair scores, and thus the CPB of the modified sequence, is reduced.
• recoding of codons or codon-pairs can take into account altering the G+C content of the E coding sequence. In some embodiments, recoding of codons or codon-pairs can take into account altering the frequency of CG and/or TA dinucleotides in the E coding sequence.
• the recoded E protein-encoding sequence has a codon pair bias less than -0.05, or less than -0.06, or less than -0.07, or less than -0.08, or less than -0.09, or less than -0.1, or less than -0.11, or less than -0.12, or less than -0.13, or less than -0.14, or less than -0.15, or less than -0.16, or less than -0.17, or less than -0.18, or less than -0.19, or less than -0.2, or less than -0.25, or less than -0.3, or less than -0.35, or less than -0.4, or less than -0.45, or less than -0.5.
• the codon pair bias of the recoded E protein encoding sequence is reduced by at least 0.05, or at least 0.06, or at least 0.07, or at least 0.08, or at least 0.09, or at least 0.1, or at least 0.11, or at least 0.12, or at least 0.13, or at least 0.14, or at least 0.15, or at least 0.16, or at least 0.17, or at least 0.18, or at least 0.19, or at least 0.2, or at least 0.25, or at least 0.3, or at least 0.35, or at least 0.4, or at least 0.45, or at least 0.5, compared to the parent E protein encoding sequence from which it is derived. In certain embodiments, it is in comparison to an E protein encoding sequence from which the calculation is to be made; for example, the E protein encoding sequence of a wild type virus.
• rearrangement of synonymous codons of the E protein-encoding sequence provides a codon-pair bias reduction of at least 0.05, or at least 0.06, or at least 0.07, or at least 0.08, or at least 0.09, or at least 0.1, or at least 0.11, or at least 0.12, or at least 0.13, or at least 0.14, or at least 0.15, or at least 0.16, or at least 0.17, or at least 0.18, or at least 0.19, or at least 0.2, or at least 0.25, or at least 0.3, or at least 0.35, or at least 0.4, or at least 0.45, or at least 0.5, compared to the parent E protein encoding sequence from which it is derived. In certain embodiments, it is in comparison to an E protein encoding sequence from which the calculation is to be made; for example, the E protein encoding sequence of a wild type virus.
• substitutions and alterations are made and reduce expression of the encoded virus proteins without altering the amino acid sequence of the encoded protein.
• the invention also includes alterations in the E coding sequence that result in substitution of non-synonymous codons and amino acid substitutions in the encoded protein, which may or may not be conservative. In various embodiments, there are up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 nucleotide substitutions.
• Most amino acids are encoded by more than one codon. See the genetic code in Table 1. For instance, alanine is encoded by GCU, GCC, GCA, and GCG. Three amino acids (Leu, Ser, and Arg) are encoded by six different codons, while only Trp and Met have unique codons.“Synonymous” codons are codons that encode the same amino acid. Thus, for example, CUU, CUC, CUA, CUG, UUA, and UUG are synonymous codons that code for Leu. Synonymous codons are not used with equal frequency.
• codons in a particular organism are those for which the cognate tRNA is abundant, and the use of these codons enhances the rate and/or accuracy of protein translation. Conversely, tRNAs for the rarely used codons are found at relatively low levels, and the use of rare codons is thought to reduce translation rate and/or accuracy. Table 1. Genetic Code
• the first nucleotide in each codon encoding a particular amino acid is shown in the left-most column; the second nucleotide is shown in the top row; and the third nucleotide is shown in the right-most column.
• a“rare” codon is one of at least two synonymous codons encoding a particular amino acid that is present in an mRNA at a significantly lower frequency than the most frequently used codon for that amino acid.
• the rare codon may be present at about a 2-fold lower frequency than the most frequently used codon.
• the rare codon is present at least a 3 -fold, more preferably at least a 5 -fold, lower frequency than the most frequently used codon for the amino acid.
• a“frequent” codon is one of at least two synonymous codons encoding a particular amino acid that is present in an mRNA at a significantly higher frequency than the least frequently used codon for that amino acid.
• the frequent codon may be present at about a 2-fold, preferably at least a 3 -fold, more preferably at least a 5 -fold, higher frequency than the least frequently used codon for the amino acid.
• human genes use the leucine codon CTG 40% of the time, but use the synonymous CTA only 7% of the time (see Table 2).
• CTG is a frequent codon
• CTA is a rare codon.
• TCT and TCC are read, via wobble, by the same tRNA, which has 10 copies of its gene in the genome, while TCG is read by a tRNA with only 4 copies. It is well known that those mRNAs that are very actively translated are strongly biased to use only the most frequent codons. This includes genes for ribosomal proteins and glycolytic enzymes. On the other hand, mRNAs for relatively non-abundant proteins may use the rare codons.
• the propensity for highly expressed genes to use frequent codons is called“codon bias.”
• a gene for a ribosomal protein might use only the 20 to 25 most frequent of the 61 codons, and have a high codon bias (a codon bias close to 1), while a poorly expressed gene might use all 61 codons, and have little or no codon bias (a codon bias close to 0). It is thought that the frequently used codons are codons where larger amounts of the cognate tRNA are expressed, and that use of these codons allows translation to proceed more rapidly, or more accurately, or both.
• the PV capsid protein for example, is very actively translated, and has a high codon bias.
• a given organism has a preference for the nearest codon neighbor of a given codon A, referred to a bias in codon pair utilization.
• a change of codon pair bias without changing the existing codons, can influence the rate of protein synthesis and production of a protein.
• Codon pair bias may be illustrated by considering the amino acid pair Ala-Glu, which can be encoded by 8 different codon pairs. If no factors other than the frequency of each individual codon (as shown in Table 2) are responsible for the frequency of the codon pair, the expected frequency of each of the 8 encodings can be calculated by multiplying the frequencies of the two relevant codons. For example, by this calculation the codon pair GCA-GAA would be expected to occur at a frequency of 0.097 out of all Ala-Glu coding pairs (0.23 x0.42; based on the frequencies in Table 2).
• Consensus CDS Consensus CDS
• This set of genes is the most comprehensive representation of human coding sequences.
• the frequencies of codon usage were re-calculated by dividing the number of occurrences of a codon by the number of all synonymous codons coding for the same amino acid.
• the frequencies correlated closely with previously published ones such as the ones given in Table 2.
• the codon pair is said to be overrepresented. If the ratio is smaller than one, it is said to be underrepresented. In the example, the codon pair GCA-GAA is overrepresented 1.65 fold while the coding pair GCC-GAA is more than 5-fold underrepresented.
• codon pairs show very strong bias; some pairs are under-represented, while other pairs are over-represented.
• codon pairs GCCGAA (AlaGlu) and GATCTG (AspLeu) are three- to six-fold under-represented (the preferred pairs being GCAGAG and GACCTG, respectively), while the codon pairs GCCAAG (AlaLys) and AATGAA (AsnGlu) are about two-fold over-represented.
• codon pair bias has nothing to do with the frequency of pairs of amino acids, nor with the frequency of individual codons.
• the under-represented pair GATCTG (AspFeu) happens to use the most frequent Feu codon, (CTG).
• codon pair bias takes into account the score for each codon pair in a coding sequence averaged over the entire length of the coding sequence. According to the invention, codon pair bias is determined by
• codon pair bias for a coding sequence can be obtained, for example, by minimized codon pair scores over a subsequence or moderately diminished codon pair scores over the full length of the coding sequence.
• Every individual codon pair of the possible 3721 non-“STOP” containing codon pairs (e.g., GTT- GCT) carries an assigned“codon pair score,” or“CPS” that is specific for a given“training set” of genes.
• the CPS of a given codon pair is defined as the log ratio of the observed number of occurrences over the number that would have been expected in this set of genes (in this example the human genome). Determining the actual number of occurrences of a particular codon pair (or in other words the likelihood of a particular amino acid pair being encoded by a particular codon pair) is simply a matter of counting the actual number of occurrences of a codon pair in a particular set of coding sequences.
• the expected number is calculated so as to be independent of both amino acid frequency and codon bias similarly to Gutman and Hatfield. That is, the expected frequency is calculated based on the relative proportion of the number of times an amino acid is encoded by a specific codon.
• a positive CPS value signifies that the given codon pair is statistically over-represented, and a negative CPS indicates the pair is statistically under-represented in the human genome.
• CCDS Consensus CDS
• P is a codon pair occurring with a frequency of No(Pi j ) in its synonymous group.
• Ciand Q are the two codons comprising P,,. occurring with frequencies F(C,) and F(Q) in their synonymous groups respectively.
• F( ) is calculated accordingly.
• No(X3 ⁇ 4 j ) is the number of occurrences of amino acid pair X,, throughout all coding regions.
• the codon pair bias score S(Pi j ) of Pi j was calculated as the log-odds ratio of the observed frequency N 0 (P,
• the codon pair bias of an entire coding region is thus calculated by adding all of the individual codon pair scores comprising the region and dividing this sum by the length of the coding sequence.
• CPS codon pair bias
• the expected number of occurrences of a codon pair requires additional calculation.
• this expected number to be independent both of amino acid frequency and of codon bias, similar to Gutman and Hatfield. That is, the expected frequency is calculated based on the relative proportion of the number of times an amino acid is encoded by a specific codon.
• a positive CPS value signifies that the given codon pair is statistically over-represented, and a negative CPS indicates the pair is statistically under-represented in the human genome.
• any coding region can then be rated as using over- or under represented codon pairs by taking the average of the codon pair scores, thus giving a Codon Pair Bias (CPB) for the entire gene.
• CPB Codon Pair Bias
• the CPB has been calculated for all annotated human genes using the equations shown and plotted (FIG. 1). Each point in the graph corresponds to the CPB of a single human gene. The peak of the distribution has a positive codon pair bias of 0.07, which is the mean score for all annotated human genes. Also, there are very few genes with a negative codon pair bias. Equations established to define and calculate CPB were then used to manipulate this bias.
• Recoding of protein-encoding sequences may be performed with or without the aid of a computer, using, for example, a gradient descent, or simulated annealing, or other minimization routine.
• An example of the procedure that rearranges codons present in a starting sequence can be represented by the following steps:
• step (8) • if yes-> go to step (5) or correct the design by replacing problematic regions with wildtype sequences and go to step (8).
• Attenuation of viruses by reducing codon pair bias is disclosed in WO 2008/121992 and WO 2011/044561, which are incorporated by reference.
• Methods of obtaining full-length Flavivirus or dengue genome sequence or codon pair deoptimized sequences embedded in a wild-type Flavivirus or dengue genome sequence can include for example, constructing an infectious cDNA clone, using an overlap extension PCR strategy, or long PCR-based fusion strategy.
• Various embodiments of the invention provide for a modified Flavivirus virus in which expression of viral proteins is reduced compared to a parent virus.
• the reduction in expression is the result of recoding the prM, or envelope (E) region or both.
• the parent vims is a wild type Flavivirus, and thus, comparisons are made to the wild-type vims or sequences in the wild-type vims.
• the E protein-encoding sequence is recoded by reducing the codon pair bias or codon usage bias of the protein-encoding sequence.
• reducing the codon-pair bias comprises identifying a codon pair in the parent protein-encoding sequence having a codon-pair score that can be reduced, and reducing the codon-pair bias by substituting the codon pair with a codon pair that has a lower codon-pair score.
• reducing the codon-pair bias comprises rearranging the codons of a parent protein-encoding sequence.
• each of the recoded prM/E protein-encoding sequence have a codon pair bias less than, -0.05, -0.1, or less than -0.2, or less than -0.3, or less than -0.4.
• the recoded prM protein-encoding sequence has a codon pair bias less than -0.05, or less than -0.06, or less than -0.07, or less than -0.08, or less than -0.09, or less than -0.1, or less than -0.11, or less than -0.12, or less than -0.13, or less than -0.14, or less than -0.15, or less than -0.16, or less than -0.17, or less than -0.18, or less than -0.19, or less than -0.2, or less than -0.25, or less than -0.3, or less than -0.35, or less than -0.4, or less than -0.45, or less than -0.5.
• the recoded E protein-encoding sequence has a codon pair bias less than -0.05, or less than -0.06, or less than -0.07, or less than -0.08, or less than -0.09, or less than -0.1, or less than -0.11, or less than -0.12, or less than -0.13, or less than -0.14, or less than -0.15, or less than -0.16, or less than -0.17, or less than -0.18, or less than -0.19, or less than -0.2, or less than -0.25, or less than -0.3, or less than -0.35, or less than -0.4, or less than -0.45, or less than -0.5.
• the codon pair bias of the recoded prM protein encoding sequence is reduced by at least 0.05, or at least 0.06, or at least 0.07, or at least 0.08, or at least 0.09, or at least 0.1, or at least 0.11, or at least 0.12, or at least 0.13, or at least 0.14, or at least 0.15, or at least 0.16, or at least 0.17, or at least 0.18, or at least 0.19, or at least 0.2, or at least 0.25, or at least 0.3, or at least 0.35, or at least 0.4, or at least 0.45, or at least 0.5, compared to the parent prM protein encoding sequence from which it is derived.
• the codon pair bias of the recoded E protein encoding sequence is reduced by at least 0.05, or at least 0.06, or at least 0.07, or at least 0.08, or at least 0.09, or at least 0.1, or at least 0.11, or at least 0.12, or at least 0.13, or at least 0.14, or at least 0.15, or at least 0.16, or at least 0.17, or at least 0.18, or at least 0.19, or at least 0.2, or at least 0.25, or at least 0.3, or at least 0.35, or at least 0.4, or at least 0.45, or at least 0.5, compared to the parent E protein encoding sequence from which it is derived. In certain embodiments, it is in comparison to an E protein encoding sequence from which the calculation is to be made; for example, the E protein encoding sequence of a wild type virus.
• the E protein-encoding sequence is recoded by increasing the number of CpG or UpA di nucleotides compared to its parent virus. In various embodiments, the E protein-encoding sequence is recoded by modifying G+C content compared to its parent virus.
• the E protein-encoding sequence is recoded by replacing one or more codons with synonymous codons that are less frequent in the viral host; for example, human.
• the E protein-encoding sequence is recoded by replacing one or more codons with synonymous codons that are less frequent in the virus itself.
• the number of codons substituted in the prM protein encoding sequence with synonymous codons is at least 5, or at least 10, or at least 30, or at least 30, or at least 40, or at least 50, or at least 75, or at least 100, or at least 150.
• the number of codons substituted in the E protein encoding sequence with synonymous codons is at least 5, or at least 10, or at least 30, or at least 30, or at least 40, or at least 50, or at least 75, or at least 100, or at least 125 or at least 150, or at least 175.
• the parent vims is a Flavivirus selected from the group consisting of dengue fever vims, West Nile vims, yellow fever vims, Japanese encephalitis vims, Spondweni vims, Zika vims, Saint Louis encephalitis vims, and Powassan vims.
• the parent vims is a natural isolate.
• the parent vims is a mutant of a natural isolate.
• a modified dengue vims in which expression of viral proteins is reduced compared to a parent vims, wherein the reduction in expression is the result of recoding the prM, or envelope (E) region, or both.
• a parent dengue vims is a wild-type dengue vims. As such, comparisons can be made in reference to a wild-type dengue vims.
• one or both of the E protein-encoding sequence is recoded by reducing the codon pair bias or codon usage bias of the protein-encoding sequence.
• reducing the codon-pair bias comprises identifying a codon pair in the parent protein-encoding sequence having a codon- pair score that can be reduced, and reducing the codon-pair bias by substituting the codon pair with a codon pair that has a lower codon-pair score.
• reducing the codon-pair bias comprises rearranging the codons of a parent protein-encoding sequence.
• a modified dengue vims comprising a recoded prM protein, a recoded envelope (E) protein, or both, wherein the recoded prM protein has a reduced codon pair bias compared to its parent prM protein encoding sequence, or has at least 5 codons substituted with synonymous codons less frequently used, or has an increased number of CpG or UpA di-nucleotides compared its parent prM protein encoding sequence, and wherein the recoded E protein has a reduced codon pair bias compared to its parent E protein encoding sequence, or has at least 5 codons substituted with synonymous codons less frequently used, or has an increased number of CpG or UpA di-nucleotides compared its parent E protein encoding sequence.
• “its parent protein encoding sequence” is“a wild-type dengue protein encoding sequence”, for example,“a wild-type dengue E protein encoding
• the expression of the prM protein or E protein or both are reduced compared to its parent dengue vims.
• the recoded prM protein has a reduced codon pair bias compared to its parent prM protein encoding sequence.
• the codon pair bias of the recoded prM encoding sequence is reduced by at least 0.05.
• the codon pair bias of the recoded prM protein encoding sequence of the dengue vims is reduced by at least 0.06, or at least 0.07, or at least 0.08, or at least 0.09, or at least 0.1, or at least 0.11, or at least 0.12, or at least 0.13, or at least 0.14, or at least 0.15, or at least 0.16, or at least 0.17, or at least 0.18, or at least 0.19, or at least 0.2, or at least 0.25, or at least 0.3, or at least 0.35, or at least 0.4, or at least 0.45, or at least 0.5, compared to the parent dengue vims’ prM protein encoding sequence from which it is derived. In certain embodiments, it is in comparison to a prM protein encoding sequence from which the calculation is to be made; for example, a prM protein encoding sequence of a wild-type dengue vims.
• the recoded prM protein has at least 5 codons substituted with synonymous codons less frequently used. In various embodiments, the recoded prM protein has at least 10, 20, 25, 30, 35, 40, 45, 50 or 55 codons substituted with synonymous codons less frequently used. In some embodiments, the substitution with synonymous codons less frequently used are one that are less frequently used in the viral host; for example, human, mosquitos. In some embodiments, the substitution with synonymous codons less frequently used are one that are less frequently used in the vims itself.
• the recoded prM protein has an increased number of CpG or UpA di nucleotides compared its parent prM protein encoding sequence. In various embodiments, the recoded prM protein has an increase of 15-55 CpG or UpA di-nucleotides compared its parent prM protein encoding sequence. In various embodiments, the recoded prM protein has an increase of about 15, 20, 25, 30, 35, 40, 45 or 55 CpG or UpA di-nucleotides compared its parent prM protein encoding sequence.
• the recoded E protein has a reduced codon pair bias compared to its parent
• the codon pair bias of E protein-encoding sequence is reduced by at least 0.05 compared to its parent E protein encoding sequence.
• the codon pair bias of the recoded E protein encoding sequence of the dengue vims is reduced by at least 0.06, or at least 0.07, or at least 0.08, or at least 0.09, or at least 0.1, or at least 0.11, or at least 0.12, or at least 0.13, or at least 0.14, or at least 0.15, or at least 0.16, or at least 0.17, or at least 0.18, or at least 0.19, or at least 0.2, or at least 0.25, or at least 0.3, or at least 0.35, or at least 0.4, or at least 0.45, or at least 0.5, compared to its parent dengue vims’ E protein encoding sequence from which it is derived. In certain embodiments, it is in comparison to an E protein encoding sequence from which the calculation is to be made; for example, the E
• the recoded E protein has at least 5 codons substituted with synonymous codons less frequently used. In various embodiments, the recoded E protein has at least 10, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, or 175 codons substituted with synonymous codons less frequently used. In some embodiments, the substitution with synonymous codons less frequently used are one that are less frequently used in the viral host; for example, human, mosquitos. In some embodiments, the substitution with synonymous codons less frequently used are one that are less frequently used in the vims itself.
• the recoded E protein has an increased number of CpG or UpA di nucleotides compared its parent E protein encoding sequence. In various embodiments, the recoded prM protein has an increase of 5-12 CpG or UpA di-nucleotides compared its parent E protein encoding sequence. In various embodiments, the recoded prM protein has an increase of about 5, 6, 7, 8, 9, 10 11 or 12 CpG or UpA di nucleotides compared its parent E protein encoding sequence.
• each of the recoded prM or E protein-encoding sequence has a codon pair bias of less than -0.05.
• the recoded prM protein encoding sequence has a codon pair bias of less than -0.05, or less than -0.06, or less than -0.07, or less than -0.08, or less than -0.09, or less than -0.1, or less than -0.11, or less than -0.12, or less than -0.13, or less than -0.14, or less than -0.15, or less than -0.16, or less than -0.17, or less than -0.18, or less than -0.19, or less than -0.2, or less than -0.25, or less than -0.3, or less than -0.35, or less than -0.4, or less than -0.45, or less than -0.5.
• the recoded E protein encoding sequence has a codon pair bias of less than -0.05, or less than -0.06, or less than -0.07, or less than -0.08, or less than -0.09, or less than -0.1, or less than -0.11, or less than -0.12, or less than -0.13, or less than -0.14, or less than -0.15, or less than -0.16, or less than -0.17, or less than -0.18, or less than -0.19, or less than -0.2, or less than -0.25, or less than -0.3, or less than -0.35, or less than -0.4, or less than -0.45, or less than -0.5.
• the modified dengue vims is selected from type 1, type 2, type 3, type 4 or a combination thereof.
• Additional examples are type 1 , type 2 and type 3 ; type 1 , type 3 and type 4; or type 2, type 3 and type 4.
• the modified dengue vims is a modified tetravalent dengue vims (i.e., type 1, type 2, type 3 and type 4).
• Various embodiments provide for a method of eliciting an immune response in a subject, comprising: administering to the subject an effective dose of a composition comprising a modified dengue vims of the present invention as described above and herein.
• the immune response is a protective immune response, and a prophylactically effective or therapeutically effective dose from 10 3 to 10 7 of a vaccine composition of claims is administered.
• the immune response is a protective immune response, and a prophylactically effective or therapeutically effective dose of 10 3 , 10 4 , 10 5 , 10 6 , or 10 7 of a vaccine composition of claims is administered.
• the method further comprises administering to the subject at least one adjuvant.
• the immune response is cross-protective against a heterologous dengue vims.
• Various embodiments provide for a method of eliciting an immune response in a subject in need thereof, comprising: administering a prime dose of (i) an attenuated dengue vims produced by a method other than codon-pair deoptimization or codon deoptimization, or increasing of CpG or UpA di-nucleotides, or (ii) a modified dengue vims comprising a recoded prM protein, a recoded envelope (E) protein, or both, wherein the recoded prM protein has a reduced codon pair bias compared to its parent prM protein encoding sequence, or has at least 5 codons substituted with synonymous codons less frequently used, or has an increased number of CpG or UpA di-nucleotides compared its parent prM protein encoding sequence, and wherein the recoded E protein has a reduced codon pair bias compared to its parent E protein encoding sequence, or has at least 5 codons substitute
• a first of the one or more boost dose is administered about 2 weeks after the prime dose.
• the expression of the prM protein or E protein or both are reduced compared to its parent dengue vims.
• the parent dengue vims is a wild-type dengue vims.
• the recoded prM protein has a reduced codon pair bias compared to its parent prM protein encoding sequence.
• the codon pair bias of the recoded prM encoding sequence is reduced by at least 0.05.
• the codon pair bias of the recoded prM protein encoding sequence of the dengue vims is reduced by at least 0.06, or at least 0.07, or at least 0.08, or at least 0.09, or at least 0.1, or at least 0.11, or at least 0.12, or at least 0.13, or at least 0.14, or at least 0.15, or at least 0.16, or at least 0.17, or at least 0.18, or at least 0.19, or at least 0.2, or at least 0.25, or at least 0.3, or at least 0.35, or at least 0.4, or at least 0.45, or at least 0.5, compared to the parent dengue vims’ prM protein encoding sequence from which it is derived. In certain embodiments, it is in comparison to a prM protein encoding sequence from which the calculation is to be made; for example, a prM protein encoding sequence of a wild-type dengue virus.
• the recoded prM protein has at least 5 codons substituted with synonymous codons less frequently used. In various embodiments, the recoded prM protein has at least 10, 20, 25, 30, 35, 40, 45, 50 or 55 codons substituted with synonymous codons less frequently used. In some embodiments, the substitution with synonymous codons less frequently used are one that are less frequently used in the viral host; for example, human, mosquitos. In some embodiments, the substitution with synonymous codons less frequently used are one that are less frequently used in the vims itself.
• the recoded prM protein has an increased number of CpG or UpA di nucleotides compared its parent prM protein encoding sequence. In various embodiments, the recoded prM protein has an increase of 15-55 CpG or UpA di-nucleotides compared its parent prM protein encoding sequence. In various embodiments, the recoded prM protein has an increase of about 15, 20, 25, 30, 35, 40, 45 or 55 CpG or UpA di-nucleotides compared its parent prM protein encoding sequence. In certain embodiments, it is in comparison to a prM protein encoding sequence from which the calculation is to be made; for example, a prM protein encoding sequence of a wild-type dengue vims.
• the recoded E protein has a reduced codon pair bias compared to its parent
• the codon pair bias of E protein-encoding sequence is reduced by at least 0.05 compared to its parent E protein encoding sequence.
• the codon pair bias of the recoded E protein encoding sequence of the dengue vims is reduced by at least 0.06, or at least 0.07, or at least 0.08, or at least 0.09, or at least 0.1, or at least 0.11, or at least 0.12, or at least 0.13, or at least 0.14, or at least 0.15, or at least 0.16, or at least 0.17, or at least 0.18, or at least 0.19, or at least 0.2, or at least 0.25, or at least 0.3, or at least 0.35, or at least 0.4, or at least 0.45, or at least 0.5, compared to its parent dengue vims’ E protein encoding sequence from which it is derived. In certain embodiments, it is in comparison to an E protein encoding sequence from which the calculation is to be made; for example, the E
• the recoded E protein has at least 5 codons substituted with synonymous codons less frequently used. In various embodiments, the recoded E protein has at least 10, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 125, 150, or 175 codons substituted with synonymous codons less frequently used. In some embodiments, the substitution with synonymous codons less frequently used are one that are less frequently used in the viral host; for example, human, mosquitos. In some embodiments, the substitution with synonymous codons less frequently used are one that are less frequently used in the vims itself.
• the recoded E protein has an increased number of CpG or UpA di nucleotides compared its parent E protein encoding sequence.
• the recoded prM protein has an increase of 5-12 CpG or UpA di-nucleotides compared its parent E protein encoding sequence.
• the recoded prM protein has an increase of about 5, 6, 7, 8, 9, 10 11 or 12 CpG or UpA di nucleotides compared its parent E protein encoding sequence. In certain embodiments, it is in comparison to an E protein encoding sequence from which the calculation is to be made; for example, the E protein encoding sequence of a wild-type dengue vims.
• each of the recoded prM or E protein-encoding sequence has a codon pair bias of less than -0.05.
• the recoded prM protein encoding sequence has a codon pair bias of less than -0.05, or less than -0.06, or less than -0.07, or less than -0.08, or less than -0.09, or less than -0.1, or less than -0.11, or less than -0.12, or less than -0.13, or less than -0.14, or less than -0.15, or less than -0.16, or less than -0.17, or less than -0.18, or less than -0.19, or less than -0.2, or less than -0.25, or less than -0.3, or less than -0.35, or less than -0.4, or less than -0.45, or less than -0.5.
• the recoded E protein encoding sequence has a codon pair bias of less than -0.05, or less than -0.06, or less than -0.07, or less than -0.08, or less than -0.09, or less than -0.1 , or less than -0.11, or less than -0.12, or less than -0.13, or less than -0.14, or less than -0.15, or less than -0.16, or less than -0.17, or less than -0.18, or less than -0.19, or less than -0.2, or less than -0.25, or less than -0.3, or less than -0.35, or less than -0.4, or less than -0.45, or less than -0.5.
• the modified dengue vims is selected from type 1, type 2, type 3, type 4 or a combination thereof.
• Additional examples are type 1 , type 2 and type 3 ; type 1 , type 3 and type 4; or type 2, type 3 and type 4.
• the modified dengue vims is a modified tetravalent dengue vims (i.e., type 1, type 2, type 3 and type 4).
• Various embodiments of the present invention provide for a method of making a modified Flavivims vims genome.
• the method comprises obtaining the nucleotide sequence encoding the envelope protein of a Flavivims vims and the nucleotide sequence encoding the nonstmctural 3 proteins of a Flavivims vims; recoding the envelope encoding nucleotide sequence to reduce protein expression and recoding the nonstmctural protein 3-encoding nucleotide sequence to reduce protein expression, and substituting a nucleic acid having the recoded envelope-encoding nucleotide sequence and a nucleic acid having the recoded nonstmctural protein 3 -encoding nucleotide sequence into a parent Flavivims vims genome to make a modified Flavivims vims genome; whereby expression of the recoded envelope-encoding nucleotide sequence and expression of the recoded nonstmctural protein 3-
• Various embodiments of the present invention provide for a method of making a modified dengue vims genome comprising: obtaining the nucleotide sequence encoding the envelope protein of a dengue vims and the nucleotide sequence encoding the nonstmctural 3 proteins of a dengue vims; recoding the envelope encoding nucleotide sequence to reduce protein expression and recoding the nonstmctural protein 3 -encoding nucleotide sequence to reduce protein expression, and substituting a nucleic acid having the recoded envelope encoding nucleotide sequence and a nucleic acid having the recoded nonstmctural protein 3 -encoding nucleotide sequence into a parent dengue vims genome to make a modified dengue vims genome; whereby expression of the recoded envelope-encoding nucleotide sequence and expression of the recoded nonstructural protein 3- encoding nucleotide sequence is reduced compared
• Various embodiments of the present invention provide for a method of making a modified dengue vims genome comprising: obtaining a nucleotide sequence encoding the envelope protein of a dengue vims; recoding the envelope encoding nucleotide sequence to reduce protein expression, and substituting a nucleic acid having the recoded envelope-encoding nucleotide sequence into a parent dengue vims genome to make a modified dengue vims genome; whereby expression of the recoded envelope-encoding nucleotide sequence is reduced compared to the parent vims.
• viral attenuation is accomplished by reducing expression viral proteins through codon pair deoptimization of E coding sequence.
• One way to reduce expression of the coding sequences is by a reduction in codon pair bias, but other methods can also be used, alone or in combination. While codon bias may be changed, adjusting codon pair bias is particularly advantageous. For example, attenuating a vims through codon bias generally requires elimination of common codons, and so the complexity of the nucleotide sequence is reduced. In contrast, codon pair bias reduction or minimization can be accomplished while maintaining far greater sequence diversity, and consequently greater control over nucleic acid secondary structure, annealing temperature, and other physical and biochemical properties.
• Codon pair bias of a protein-encoding sequence is calculated as set forth above and described in Coleman et ak, 2008.
• Viral attenuation and induction or protective immune responses can be confirmed in ways that are well known to one of ordinary skill in the art, including but not limited to, the methods and assays disclosed herein.
• Non-limiting examples include plaque assays, growth measurements, reduced lethality in test animals, and protection against subsequent infection with a wild type vims.
• the invention provides vimses that are highly attenuated, and induce immunity against a plurality of dengue types and/or subtypes.
• dengue vims varieties include vimses in serogroups 1, 2, 3, and 4. Examples of attenuated dengue protein coding sequences are provided below.
• a Flavivirus composition for inducing an immune response in a subject which comprises the modified Flavivirus of the present invention as described herein.
• a Flavivirus vaccine composition for inducing a protective immune response in a subject, which comprises the modified Flavivirus of the present invention as described herein.
• a modified dengue vims composition for inducing an immune response in a subject, comprising a modified dengue vims of the present invention as described above and herein, and a pharmaceutically acceptable excipient or carrier.
• a dengue vaccine composition for inducing a protective immune response in a subject, comprising a modified dengue vims of the present invention as described above and herein, and a pharmaceutically acceptable excipient or carrier.
• the modified dengue vims is selected from type 1, type 2, type 3, type 4 or a combination thereof.
• the modified dengue vims is a type 1 and type 2 modified dengue vims; a type 1 and type 3 modified dengue vims; a type 1 and type 4 modified dengue vims; a type 2 and type 3 modified dengue vims; a type 2 and type 4 modified dengue vims; a type 3 and type 4 modified dengue vims.
• the modified dengue vims is a type 1 , type 2 and type 3 modified dengue vims; a type 1, type 2 and type 4 modified dengue vims; a type 1, type 3 and type 4 modified dengue vims; or a type 2, type 3 and type 4 modified dengue vims.
• the modified dengue vims modified tetravalent dengue vims; (type 1, type 2, type 3 and type 4).
• Non-limiting examples of wild-type and modified dengue vimses are herein:

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