Molecular features of influenza A (H1N1)pdm09 prevalent in Mexico during winter seasons 2012-2014

<div><p>Since the emergence of the pandemic H1N1pdm09 virus in Mexico and California, biannual increases in the number of cases have been detected in Mexico. As observed in previous seasons, pandemic A/H1N1 09 virus was detected in severe cases during the 2011–2012 winter season and finally, during the 2013–2014 winter season it became the most prevalent influenza virus. Molecular and phylogenetic analyses of the whole viral genome are necessary to determine the antigenic and pathogenic characteristics of influenza viruses that cause severe outcomes of the disease. In this paper, we analyzed the evolution, antigenic and genetic drift of Mexican isolates from 2009, at the beginning of the pandemic, to 2014. We found a clear variation of the virus in Mexico from the 2011–2014 season due to different markers and in accordance with previous reports. In this study, we identified 13 novel substitutions with important biological effects, including virulence, T cell epitope presented by MHC and host specificity shift and some others substitutions might have more than one biological function. The systematic monitoring of mutations on whole genome of influenza A pH1N1 (2009) virus circulating at INER in Mexico City might provide valuable information to predict the emergence of new pathogenic influenza virus</p></div

Analysis of detected substitutions at or beside antigenic sites of HA, of Mexican isolates from 2011–12 and 2013–14.

<p>The analysis of substitutions at HA was made using sequence California/07/2009 as reference to establish the changes at the antigenic sites and in their neighboring positions. The antigenic sites are shaded and identified by colours. Blue is for Cb site, pink is for Sa site, Green is for Ca site and yellow is for Sb site. The amino acids in red represent changes detected in sequences of isolates from 2011–12 and white represent the changes detected in isolates from 2013–14.</p

Maximum likelihood (ML) phylogenetic tree for the HA segment.

<p>ML trees from 1200–1300 A(H1N1)pdm09 viruses deposited in GenBank from 2009 to 2014 were produced with 1,000 bootstrap replicates, for the indicated genetic segments as explained in the Methods section. Phylogenetic tree included 7–17 sequences from 2012 (PB2, 10; PB1, 8; PA, 7; HA, 10; NP, 11; NA, 8; M, 17 and NS, 17), 3 sequences from 2013 and 7 sequences from 2014; obtained for this study. Red dots at nodes show branches with 50% bootstrap support leading to the 2014 sequences described in this work. Trees for the rest of the viral genome segments can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0180419#pone.0180419.s002" target="_blank">S1</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0180419#pone.0180419.s008" target="_blank">S7</a> Figs (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0180419#pone.0180419.s002" target="_blank">S1 Fig</a> <b>NA</b>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0180419#pone.0180419.s003" target="_blank">S2 Fig</a> <b>PB2</b>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0180419#pone.0180419.s004" target="_blank">S3 Fig</a> <b>PB2</b>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0180419#pone.0180419.s005" target="_blank">S4 Fig</a> <b>PA</b>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0180419#pone.0180419.s006" target="_blank">S5 Fig</a> <b>M</b>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0180419#pone.0180419.s007" target="_blank">S6 Fig</a> <b>NP</b>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0180419#pone.0180419.s008" target="_blank">S7 Fig</a> <b>NS</b>). Colours for seasons: RED, 2009–2010; BRIGHT GREEN, 2010–2011; PURPLE, 2011–2012; BLUE SKY, 2012–2013; VIOLET, 2013–2014.</p