Title
Authors
Abstract
Introduction and objectives: During the Influenza A pH1N1 2009 pandemics in Brazil, the most affected state was Rio Grande do Sul (RS), with 3,585 confirmed cases, 298 deaths. While no pH1N1cases were confirmed in 2010, since 2011 pH1N1 has been circulating in RS. This study investigated genomes of pH1N1 virus from pandemic and post-pandemic periods in RS, Southern Brazil.
Materials and Methods: RNA was extracted from nasopharyngeal aspirates of influenza A pH1N1-infected patients, analyzed by RT-qPCR and submitted to whole-genome sequencing. Genomic segments and genes of 6 pH1N1 samples were aligned with other influenza A sequences (Influenza Research Database). Amino acid substitutions were inspected using the sequences of archetype strains California/07/2009 and California/07/2009 as reference. Phylogenetic trees were constructed using maximum likelihood method. Detection of adaptive evolution was assessed, and vaccine efficiency was estimated based on antigenic distances of five epitopes of hemagglutinin of samples in relation to those of strain California/07/2009.
Results: Phylogenetic analyses demonstrated that at least two pH1N1 lineages co-circulated in RS during the pandemic period; the post-pandemic virus composes a distinct clade. All six isolates presented amino acid substitutions in their proteins in relation to reference strains. The 2011 isolates present more amino acid substitutions and most of their genes were under purifying selection. The predicted vaccine efficacy against the 2011 isolates was 31.44% (dominant epitope D), while against the pandemic isolates was 39.84% (dominant epitope E).
Conclusions: Genomic analyses of circulating viruses are fundamental to understand viral evolution and to support vaccine development against influenza.
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