The present disclosure discloses a whole avian-origin reverse genetic manipulation system and its use in producing a recombinant H7N9 avian influenza vaccine. The whole avian-origin reverse genetic manipulation system is an eight-plasmid reverse genetic manipulation system based on H5N2 subtype avian influenza D7 virus strain, which is comprised of 8 recombinant plasmids respectively containing PB2, PB1, PA, HA, NP, NA, M and NS gene fragments derived from H5N2 subtype avian influenza D7 virus strain. The genome of the recombinant H7N9 subtype avian influenza vaccine of the present disclosure is comprised of an NA gene and a modified HA gene derived from a highly pathogenic H7N9 subtype avian influenza virus strain, as well as PB2, PB1, PA, NP, M and NS genes derived from H5N2 subtype avian influenza D7 virus strain.

Methods of producing a pathogen with reduced replicative fitness are disclosed, as are attenuated pathogens produced using the methods. In particular examples, the method includes deoptimizing one or more codons in a coding sequence, thereby reducing the replicative fitness of the pathogen. Methods of using the attenuated pathogens as immunogenic compositions are also disclosed.

The subject invention pertains to attenuated influenza viruses, and related vaccines and methods, comprising a genetically modified viral genome. The genetically modified viral genome comprises a disruption in the non-structural (NS1) coding segment and one or more base substitution in the matrix membrane protein coding segment. The genetic modifications result in viruses that lose NS1 functionality, yet remain replication competent.

Disclosed herein are compositions and methods related to mutant viruses, and in particular, mutant influenza viruses. The mutant viruses disclosed herein include a mutant M2 sequence, and are useful in immunogenic compositions, e.g., as vaccines. Also disclosed herein are methods, compositions and cells for propagating the viral mutants, and methods, devices and compositions related to vaccination.

Methods of producing a pathogen with reduced replicative fitness are disclosed, as are attenuated pathogens produced using the methods. In particular examples, the method includes deoptimizing one or more codons in a coding sequence, thereby reducing the replicative fitness of the pathogen. Methods of using the attenuated pathogens as immunogenic compositions are also disclosed.

The invention relates to defective interfering viruses and defective interfering virus RNAs that are effective as antiviral agents. The invention also relates to methods for identifying defective interfering virus RNAs that can be used as effective antiviral agents.

The present invention provides, among other things, a novel and improved method for generating “mosaic” influenza antigenic polypeptides including hemagglutinin (HA) and neuraminidase (NA) polypeptides based on unique combination of epitope patterns that maximize exposure to epitopes present across multiple HA or NA sequences and therefore improved influenza strain coverage. In particular, the present invention provides engineered H1N1 influenza hemagglutinin (HA) polypeptides that are comprised of novel combinations of protective epitopes and antigenic regions from multiple H1N1 viral strains. Such engineered HA polypeptides have improved properties over HA polypeptides developed through conventional approaches that rely on consensus alignments of viral sequences.

Disclosed are compositions and methods comprising one or more recombinant influenza viruses. Recombinant influenza viruses with mutated polymerases and/or rearranged genomes are disclosed. Constructs comprising different influenza nucleic acid sequences are also provided. Methods of inducing protecting immunity with the recombinant influenza viruses are disclosed. Also disclosed are methods of plasmid-free production of influenza virus comprising amplicons comprising one or more of influenza genes.

Mutation of adenosine methylation sites in nucleic acids encoding influenza virus hemagglutinin are provided that result in increases in vRNA, mRNA, and protein expression over time and increases in infectious titers when produced in mammalian cells.

Recombinant constructs, influenza viral genomes including the recombinant constructs, influenza viruses including the constructs, and vaccine formulations formed thereof for inducing or increasing an immune response against influenza virus are provided. The compositions typically include a nucleic acid having a nucleic acid sequence encoding IgA-inducing protein (IGIP) polypeptide that can positively regulate IgA expression operably linked to expression of a hemagglutinin or a neuraminidase. When the nucleic acid is expressed by recombinant influenza virus in infected cells, it preferably enhances IgA production against influenza virus. Live attenuated virus expressing IGIP, and methods of use thereof for treating and preventing influenza infections are also provided.