title: Evidence for a novel gene associated with human influenza A viruses.
abstract: BACKGROUND
  Influenza A virus genomes are comprised of 8 negative strand single-stranded RNA segments and are thought to encode 11 proteins, which are all translated from mRNAs complementary to the genomic strands. Although human, swine and avian influenza A viruses are very similar, cross-species infections are usually limited. However, antigenic differences are considerable and when viruses become established in a different host or if novel viruses are created by re-assortment devastating pandemics may arise.
  
  
  RESULTS
  Examination of influenza A virus genomes from the early 20th Century revealed the association of a 167 codon ORF encoded by the genomic strand of segment 8 with human isolates. Close to the timing of the 1948 pseudopandemic, a mutation occurred that resulted in the extension of this ORF to 216 codons. Since 1948, this ORF has been almost totally maintained in human influenza A viruses suggesting a selectable biological function. The discovery of cytotoxic T cells responding to an epitope encoded by this ORF suggests that it is translated into protein. Evidence of several other non-traditionally translated polypeptides in influenza A virus support the translation of this genomic strand ORF. The gene product is predicted to have a signal sequence and two transmembrane domains.
  
  
  CONCLUSIONS
  We hypothesize that the genomic strand of segment 8 of encodes a novel influenza A virus protein. The persistence and conservation of this genomic strand ORF for almost a century in human influenza A viruses provides strong evidence that it is translated into a polypeptide that enhances viral fitness in the human host. This has important consequences for the interpretation of experiments that utilize mutations in the NS1 and NEP genes of segment 8 and also for the consideration of events that may alter the spread and/or pathogenesis of swine and avian influenza A viruses in the human population.
authors.affiliation: Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada. mcliffor@uvic.ca
authors.forename: Monica
authors.initials: M
authors.lastname: Clifford
authors.forename: James
authors.initials: J
authors.lastname: Twigg
authors.forename: Chris
authors.initials: C
authors.lastname: Upton
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology; D005814:Genes, Viral; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000737:chemistry / Q000235:genetics*; D007251:Influenza, Human / Q000821:virology; D008969:Molecular Sequence Data; D009154:Mutation; D016366:Open Reading Frames; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D014764:Viral Proteins