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.

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.

A protocol has been developed for genetically engineering an attenuated pathogen such as the influenza virus that can grow in cells without interferons but has suppressed growth in cells with the interferons. The protocol comprises systematically identifying immune evasion functions on the pathogen's genome, then eliminating the immune evasion functions while maintaining a certain replication fitness of the pathogen. The resulting attenuated pathogen causes a strong immunologic response and can be used in a live attenuated vaccine.

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 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.

This disclosure provides attenuated swine influenza strains, particularly those produced via a reverse genetics approach, compositions comprising same, and methods of production and use thereof.

A recombinant virus is obtained by mutating a codon that encodes a tyrosine residue at position 385 of NP protein in the genome of influenza A virus to a codon of phenylalanine residue. The virus WSN-Y385F is a temperature-sensitive virus that can normally replicate and survive at 37 C., and cannot normally replicate and cannot survive at 33 C. Phosphorylation of a NP protein of influenza A virus can be inhibited by mutating an amino acid residue at position 385 from N terminal of the NP protein of influenza A virus, from a tyrosine to a phenylalanine. The recombinant virus can be used in analyzing mechanisms of infection by influenza virus, and in connection with methods of prevention and treatment of infection by influenza virus.

Disclosed herein are compositions and methods related to mutant viruses, and in particular, mutant influenza viruses. The mutant viruses disclosed herein include a mutant BM2 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.

Live attenuated viruses for protection against the novel coronavirus Sars-CoV-2 are provided. The live attenuated chimeric virus strains are based on a live attenuated influenza A or B virus (LAIVA/B), used a master backbone, which includes deletion of the viral virulence element, the NS1 (non-structural protein 1) (DeLNS1), engineered to express one or more antigens of the Sars-CoV-2 (herein, CoV2Ag). The chimeric virus strain is referred to generally herein, as DelNS1-A/B-Sars-CoV-2-CoV2Ag. The DelNS1-A/B-Sars-CoV-2-CoV2Ag strain preferably shows spontaneous cold adaption with preference to grow at 30-33 C. Compositions including the chimeric virus also provided as a co-composition with a LAIVA/B. The DelNS1-A/B-Sars-CoV-2-CoV2Ag strain can be used to protect a subject in need thereof, against a challenge of Sars-CoV-2. The co-compositions can be used to protect a subject in need thereof, against a challenge of Sars-CoV-2 and influenza A and/or B.

A protocol has been developed for genetically engineering an attenuated pathogen such as the influenza virus that can grow in cells without interferons but has suppressed growth in cells with the interferons. The protocol comprises systematically identifying immune evasion functions on the pathogen's genome, then eliminating the immune evasion functions while maintaining a certain replication fitness of the pathogen. The resulting attenuated pathogen causes a strong immunologic response and can be used in a live attenuated vaccine.