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doi: 10.1186/1743-422X-6-198.

Evidence for a novel gene associated with human influenza A viruses

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Evidence for a novel gene associated with human influenza A viruses

Monica Clifford et al. Virol J..

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.

Conclusion: 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.

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Figures

Figure 1
Figure 1
Organization of the NS1 and NEP genes on genome segment 8. The genome segment is from the 1918 human influenza A virus H1N1. The 167 codon NEG8 ORF is shown as a solid red arrow; the 168-216 region of the 216 codon NEG8 ORF is shown as a dashed red arrow.
Figure 2
Figure 2
Neighbour-joining tree constructed from pre-1950 human influenza A virus NS1 proteins using software at NCBI. Blue bar indicates a single clade of viruses, which has no further descendents, that lack the 167 codon NEG8 ORF.
Figure 3
Figure 3
Predicted protein sequence for a human influenza A virus 216 codon NEG8 ORF. Consensus predictions, from multiple tools, for signal sequence and transmembrane domains are shown by colored letters. Red characters indicate the predicted signal sequence; Blue characters indicate the predicted transmembrane domains; Green characters indicate the polypeptide extension from 168 to 216 aa; the underlined characters indicate the functional CTL epitope.
Figure 4
Figure 4
Organization of negative strand ORFs in a 2009 swine-derived H1N1 influenza A virus. The NEG8-like open reading frames are shown as red arrows. Blue arrows indicate positions where single nucleotide changes are required to extend the 85 and 167 codon NEG8 ORFs. NS1 and NEP genes are shown in black.
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