ARS | Publication request: Frequency of genomic reassortment of influenza A virus in North American swine, 1998-2011

Submitted to: Journal of General Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 17, 2012
Publication Date: December 1, 2012
Citation: Nelson, M.I., Detmer, S.E., Wentworth, D.E., Tan, Y., Schwartzbard, A., Halpin, R.A., Stockwell, T.B., Lin, X., Vincent, A.L., Gramer, M.R., Holmes, E.C. 2012. Genomic reassortment of influenza A virus in North American swine, 1998-2011. Journal of General Virology. 93(Pt 12):2584-2589.

Interpretive Summary: Influenza A viruses (IAV) evolve genetically by mutation or change at the nucleic acid (RNA) level. The IAV genome includes 8 segments that code for the major surface glycoproteins hemagglutinin (HA) and neuraminidase (NA), as well as 6 gene segments encoding "internal" proteins (PB2, PB1, PA, NP, M, and NP). The HA and NA are important for subtyping or categorizing IAV (17 HA and 9 NA subtypes). One way change can occur is through exchange of gene segments from one influenza virus with another, known as reassortment, when 2 viruses infect the same cell in an infected host (ie., pig). Revealing the frequency that reassortment occurs in swine is fundamental to understanding basic aspects of the biology and evolution of influenza virus. To provide a comparison of the frequency 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, representing the H3N2, H1N1, and H1N2 subtypes and seven distinct HA phylogenetic groups. There were high frequencies of reassortment overall, notably between H3 and the internal gene segments (PB2, PB1, PA, NP, M, and NS), while the lowest reassortment frequencies were observed among the H1gamma, H1pdm, and NA segments, particularly N1. Strikingly, there was a negative association between reassortment frequency and the prevalence of specific HA-NA combinations, suggesting that some genome constellations are evolutionarily more stable.

Technical Abstract: Revealing the frequency and determinants of reassortment among RNA genome segments is fundamental to understanding basic aspects of the biology and evolution of influenza virus. To provide a quantitative comparison of the frequency 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 frequencies 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 H1', H1pdm, and NA segments, particularly N1. Strikingly, there was a negative association between reassortment frequency and the prevalence of specific HA-NA combinations, suggesting that some genome constellations are evolutionarily more stable.