Revealing the frequency and determinants of reassortment among RNA genome segments is fundamental to understanding basic aspects of the biology and evolution of the influenza virus. To estimate the extent of genomic reassortment in influenza viruses circulating in North American swine, we performed a phylogenetic analysis of 139 whole-genome viral sequences sampled during 1998–2011 and representing seven antigenically distinct viral lineages. The highest amounts of reassortment were detected between the H3 and the internal gene segments (PB2, PB1, PA, NP, M and NS), while the lowest reassortment frequencies were observed among the H1γ, H1pdm and neuraminidase segments, particularly N1. Less reassortment was observed among specific haemagglutinin–neuraminidase combinations that were more prevalent in swine, suggesting that some genome constellations may be evolutionarily more stable.
BaoY., BolotovP., DernovoyD., KiryutinB., ZaslavskyL., TatusovaT., OstellJ., LipmanD.2008; The influenza virus resource at the National Center for Biotechnology Information. J Virol 82:596–601 [View Article][PubMed]
Centers for Disease Control and Prevention2012; Evaluation of rapid influenza diagnostic tests for influenza A (H3N2)v virus and updated case count – United States, 2012. MMWR Morb Mortal Wkly Rep 61:619–621[PubMed]
ChenL. M., DavisC. T., ZhouH., CoxN. J., DonisR. O.2008; Genetic compatibility and virulence of reassortants derived from contemporary avian H5N1 and human H3N2 influenza A viruses. PLoS Pathog 4:e1000072 [View Article][PubMed]
ImaiM., KawaokaY.2012; The role of receptor binding specificity in interspecies transmission of influenza viruses. Curr Opin Virol 2:160–167 [View Article][PubMed]
KarasinA. I., CarmanS., OlsenC. W.2006; Identification of human H1N2 and human-swine reassortant H1N2 and H1N1 influenza A viruses among pigs in Ontario, Canada (2003 to 2005). J Clin Microbiol 44:1123–1126 [View Article][PubMed]
KimbleJ. B., SorrellE., ShaoH., MartinP. L., PerezD. R.2011; Compatibility of H9N2 avian influenza surface genes and 2009 pandemic H1N1 internal genes for transmission in the ferret model. Proc Natl Acad Sci U S A 108:12084–12088 [View Article][PubMed]
LiC., HattaM., NidomC. A., MuramotoY., WatanabeS., NeumannG., KawaokaY.2010; Reassortment between avian H5N1 and human H3N2 influenza viruses creates hybrid viruses with substantial virulence. Proc Natl Acad Sci U S A 107:4687–4692 [View Article][PubMed]
LorussoA., VincentA. L., HarlandM. L., AltD., BaylesD. O., SwensonS. L., GramerM. R., RussellC. A., SmithD. J.other authors2011; Genetic and antigenic characterization of H1 influenza viruses from United States swine from 2008. J Gen Virol 92:919–930 [View Article][PubMed]
NelsonM. I., LemeyP., TanY., VincentA., LamT. T., DetmerS., ViboudC., SuchardM. A., RambautA.other authors2011; Spatial dynamics of human-origin H1 influenza A virus in North American swine. PLoS Pathog 7:e1002077 [View Article][PubMed]
NelsonM. I., VincentA. L., KitikoonP., HolmesE. C., GramerM. R.2012; Evolution of novel reassortant A/H3N2 influenza viruses in North American swine and humans, 2009–2011. J Virol 86:8872–8878 [View Article][PubMed]
SorrellE. M., WanH., ArayaY., SongH., PerezD. R.2009; Minimal molecular constraints for respiratory droplet transmission of an avian-human H9N2 influenza A virus. Proc Natl Acad Sci U S A 106:7565–7570 [View Article][PubMed]
VincentA. L., MaW., LagerK. M., JankeB. H., RichtJ. A.2008; Swine influenza viruses a North American perspective. Adv Virus Res 72:127–154 [View Article][PubMed]
XuR., ZhuX., McBrideR., NycholatC. M., YuW., PaulsonJ. C., WilsonI. A.2012; Functional balance of the hemagglutinin and neuraminidase activities accompanies the emergence of the 2009 H1N1 influenza pandemic. J Virol 86:9221–9232 [View Article][PubMed]
ZhouN. N., SenneD. A., LandgrafJ. S., SwensonS. L., EricksonG., RossowK., LiuL., YoonK., KraussS., WebsterR. G.1999; Genetic reassortment of avian, swine, and human influenza A viruses in American pigs. J Virol 73:8851–8856[PubMed]
ZhouB., DonnellyM. E., ScholesD. T., St GeorgeK., HattaM., KawaokaY., WentworthD. E.2009; Single-reaction genomic amplification accelerates sequencing and vaccine production for classical and swine origin human influenza A viruses. J Virol 83:10309–10313 [View Article][PubMed]