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

Substitutions observed in pandemic A/H1N1 virus strains classified by gene segment, year of circulation and description.

<p>Substitutions observed in pandemic A/H1N1 virus strains classified by gene segment, year of circulation and description.</p

Frequency of SSc-associated autoantibodies in our SSc patients.

<p>dcSSc: diffuse cutaneous systemic sclerosis, lcSSc: limited cutaneous systemic sclerosis, Anti-RNA Pol III: anti-RNA polymerase I/III.</p><p>Frequency of SSc-associated autoantibodies in our SSc patients.</p

Demographic data and organ damage according to the modified Medsger’s Severity Scale.

<p>dcSSc: diffuse cutaneous systemic sclerosis, lcSSc: limited cutaneous systemic sclerosis, ILD: interstitial lung disease; PAH: pulmonary arterial hypertension.</p><p>Demographic data and organ damage according to the modified Medsger’s Severity Scale.</p

HLA Class I and II Blocks Are Associated to Susceptibility, Clinical Subtypes and Autoantibodies in Mexican Systemic Sclerosis (SSc) Patients

<div><p>Introduction</p><p>Human leukocyte antigen (HLA) polymorphism studies in Systemic Sclerosis (SSc) have yielded variable results. These studies need to consider the genetic admixture of the studied population. Here we used our previously reported definition of genetic admixture of Mexicans using HLA class I and II DNA blocks to map genetic susceptibility to develop SSc and its complications.</p><p>Methods</p><p>We included 159 patients from a cohort of Mexican Mestizo SSc patients. We performed clinical evaluation, obtained SSc-associated antibodies, and determined HLA class I and class II alleles using sequence-based, high-resolution techniques to evaluate the contribution of these genes to SSc susceptibility, their correlation with the clinical and autoantibody profile and the prevalence of Amerindian, Caucasian and African alleles, blocks and haplotypes in this population.</p><p>Results</p><p>Our study revealed that class I block HLA-C*12:03-B*18:01 was important to map susceptibility to diffuse cutaneous (dc) SSc, HLA-C*07:01-B*08:01 block to map the susceptibility role of HLA-B*08:01 to develop SSc, and the C*07:02-B*39:05 and C*07:02-B*39:06 blocks to map the protective role of C*07:02 in SSc. We also confirmed previous associations of HLA-DRB1*11:04 and –DRB1*01 to susceptibility to develop SSc. Importantly, we mapped the protective role of DQB1*03:01 using three Amerindian blocks. We also found a significant association for the presence of anti-Topoisomerase I antibody with HLA-DQB1*04:02, present in an Amerindian block (DRB1*08:02-DQB1*04:02), and we found several alleles associated to internal organ damage. The admixture estimations revealed a lower proportion of the Amerindian genetic component among SSc patients.</p><p>Conclusion</p><p>This is the first report of the diversity of HLA class I and II alleles and haplotypes Mexican patients with SSc. Our findings suggest that HLA class I and class II genes contribute to the protection and susceptibility to develop SSc and its different clinical presentations as well as different autoantibody profiles in Mexicans.</p></div

HLA class II genes associations with specific autoantibodies in SSc.

<p>anti-RNAP I/III: anti-RNA polymerase I/III.</p><p>HLA class II genes associations with specific autoantibodies in SSc.</p

Principal component analysis (PCA) plot reveals a close genetic relationship of Mexican admixed SSc patients and healthy controls (HC) from Mexico City to Native American groups.

<p>Native American populations are represented in the upper left of the graphic and Caucasian components in the right bottom area of the graphic. Amerindian components are represented in the left bottom area. Red and blue dots represent difusse and limited SSc patients respectively and the total group in represented in green. The different populations included in the PCA analysis were: Ire: Ireland, Eng: England, Ger: Germany, Aus: Austria; Spa: Spain, Ita: Italy, UK: United Kingdom, Fra: France, Azo: Azores, Sao: São Tomé Island, Cam: Cameroon, Mal: Mali, Zam: Zambia, KLu: Luo from Kenia, KNa: Nandi from Kenia, Sen: Senegal, Gui: Guinea Bissau, Tar: Tarahumara, Gil: Native Americans from Gila River, Yup: Yu’pik from Alaska, Mit: Mixtec from Oaxaca, Zap: Zapotec from Oaxaca, Mix: Mixe from Oaxaca, Ser: Seri from Sonora, Nav: Navajo from New Mexico, HC: “Mexican Admixed controls” [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0126727#pone.0126727.ref026" target="_blank">26</a>].</p

Clinical and demographic characteristics of the studied patients.

<p>Clinical and demographic characteristics of the studied patients.</p