A menu of mutations was developed that is useful in fine-tuning the attenuation and growth characteristics of dengue virus vaccines.

Aspects of the disclosure relate to attenuated flaviviruses for use in vaccines and immunogenic compositions. Embodiments include methods for treating or preventing one or more conditions, for example flavivirus infection, using an attenuated flavivirus. In some embodiments, the disclosed methods and compositions involve one or more attenuated flaviviruses that are capable of inducing a protective immune response.

The present disclosure relates to Zika vaccines. In certain embodiments, this disclosure relates to vaccine compositions for use in methods of protecting a human subject against Zika disease or infection, wherein said composition comprises a vaccinal for Zika such as a live attenuated or inactivated chimeric Zika virus; live attenuated Zika virus; an inactivated Zika virus; a replication-defective pseudo-infectious Zika virus; a Zika virus-like particle (VLP), a Zika protein or combinations thereof. In certain embodiments, the Zika vaccinal comprises or encodes altered polypeptide sequences disclosed herein.

Chimeric proteins that comprise one or more amino acid sequences of an insect-specific flavivirus and one or more other immunogenic proteins are provided. The chimeric proteins are suitably capable of forming virus particles. The chimeric protein and/or virus particle may be suitable for delivery to a subject to elicit an immune response to a pathogen and/or for diagnosis or detection of a pathogen. Also provided are nucleic acids and vectors encoding the chimeric proteins, and isolated chimeric insect-specific flaviviruses comprising the chimeric proteins and/or nucleic acids.

The present invention provides for modified Flavivirus such as a modified dengue virus type 1, 2, 3, 4, a combination of these, or a tetravalent combination of these. The modification according to various aspects of the invention results in reduced viral protein expression compared to a parent virus, wherein the reduction in expression is the result of recoding one or more regions of the virus. For example, the prM, or envelope (E) region can be recoded. In various embodiments one or more regions are recoded by reducing the codon pair bias or codon usage bias of the protein-encoding sequence. These modified Flaviviruses are used as vaccine compositions to provide a protective immune response.

Certain embodiments are directed to a stable recombinant flavivirus nucleic acid having a heterologous reporter cassette, the reporter cassette having a 5′ end, a nucleotide segment encoding a reporter, and a 3′ end; the 5′ end of the reporter cassette encoding 25 to 38 amino acids of a flavivirus capsid protein; the 3′ end of the reporter cassette encoding 25 to 38 amino acids of a flavivirus capsid protein.

Modified genomes of an organism comprising at least one coding sequence comprising at least one mutation, wherein the mutation generates an underrepresented sequence that is underrepresented in the unmodified genome of the organism are provided. Organism and cells comprising the modified genomes of the invention, pharmaceutical compositions comprising the organisms and cells of the invention, as well as methods of making the modified genomes are also provided.

The present disclosure relates to Zika vaccines. In certain embodiments, this disclosure relates to vaccine compositions for use in methods of protecting a human subject against Zika disease or infection, wherein said composition comprises a vaccinal for Zika such as a live attenuated or inactivated chimeric Zika virus; live attenuated Zika virus; an inactivated Zika virus; a replication-defective pseudo-infectious Zika virus; a Zika virus-like particle (VLP), a Zika protein or combinations thereof. In certain embodiments, the Zika vaccinal comprises or encodes altered polypeptide sequences disclosed herein.

The invention relates to polynucleotides comprising the sequence of a flavivirus preceded by a sequence encoding an N terminal part of a flavivirus Capsid protein, an immunogenic protein, or a part thereof comprising a an immunogenic peptide, and a 2A cleaving peptide, and to the virus encoded by such sequences. The invention further relates to the use of such polynucleotides and viruses as vaccines.

The present disclosure relates to compositions and methods for investigating Zika virus (ZIKV) biology and pathogenicity. The present disclosure provides genetically stable viral vectors to produce functional RNA transcripts of ZIKV cDNAs. In particular, the present disclosure provides full-length infectious cDNAs as bacterial artificial chromosomes for spatiotemporally distinct and genetically divergent ZIKVs. The present disclosure also provides methods of generating a genetically engineered attenuated ZIKV using the genetically stable viral vectors described herein.