Genetic Structure of Human A/H1N1 and A/H3N2 Influenza Virus on Corsica Island: Phylogenetic Analysis and Vaccine Strain Match, 2006–2010

Abstract

BackgroundThe aim of this study was to analyse the genetic patterns of Hemagglutinin (HA) genes of influenza A strains circulating on Corsica Island during the 2006–2009 epidemic seasons and the 2009–2010 pandemic season.MethodsNasopharyngeal samples from 371 patients with influenza-like illness (ILI) were collected by General Practitioners (GPs) of the Sentinelles Network through a randomised selection routine.ResultsPhylogenetic analysis of HA revealed that A/H3N2 strains circulating on Corsica were closely related to the WHO recommended vaccine strains in each analyzed season (2006–2007 to 2008–2009). Seasonal Corsican influenza A/H1N1 isolated during the 2007–2008 season had drifted towards the A/Brisbane/59/2007 lineage, the A/H1N1 vaccine strain for the 2008–2009 season. The A/H1N1 2009 (A/H1N1pdm) strains isolated on Corsica Island were characterized by the S220T mutation specific to clade 7 isolates. It should be noted that Corsican isolates formed a separate sub-clade of clade 7 as a consequence of the presence of the fixed substitution D222E.The percentages of the perfect match vaccine efficacy, estimated by using the p epitope model, against influenza viruses circulating on Corsica Island varied substantially across the four seasons analyzed, and tend to be highest for A/H1N1 compared with A/H3N2 vaccines, suggesting that cross-immunity seems to be stronger for the H1 HA gene.ConclusionThe molecular analysis of the HA gene of influenza viruses that circulated on Corsica Island between 2006–2010 showed for each season the presence of a dominant lineage characterized by at least one fixed mutation. The A/H3N2 and A/H1N1pdm isolates were characterized by multiples fixation at antigenic sites. The fixation of specific mutations at each outbreak could be explained by the combination of a neutral phenomenon and a founder effect, favoring the presence of a dominant lineage in a closed environment such as Corsica Island.

Molecular Analysis of Genome of the Pandemic Influenza A(H1N1) 2009 Virus Associated with Fatal Infections in Gunma, Tochigi, Yamagata, and Yamaguchi Prefectures in Japan during the First Pandemic Wave

“…Alternatively, a D222E substitution was found in 1 of the isolates, A/Yamaguchi/247/2009, which was derived from a fatal infection. This substitution, however, seems to be unrelated to the disease severity of the A(H1N1)pdm09 as previously reported (4,8). Another V132E amino acid mutation in the receptor binding site was found in 2 isolates, a fatal casestrain (i.e., A/Tochigi/2/2010) and a mild case-strain (i.e., A/Yamaguchi/273/2009); however, the precise impact of this mutation is unclear.…”

Field seasonal influenza vaccine effectiveness

“…24 Corsican laboratoryconfirmed influenza cases were reported by Sentinelles GPs. 22,25 Nasopharyngeal swabs were collected through a randomized selection routine. GPs included the first patient of each week, of any age (Sentinelles protocol) or of a personally assigned age group among 0-4, 5-14, 15-64, and >65 y-old (GROG protocol).…”

Genetic changes in influenza A(H3N2) viruses circulating during 2011 to 2013 in northern India (Lucknow)

“…Majority of the Lucknow strains contained N402D mutation in the NA coding sequences which represents the loss of the N‐linked glycosylation site in the NA domain [Sobolev et al, ]. Variation in the N‐glycosylation sites at HA and NA domain may potentially alter the antigenic property of the glycoprotein and its function [Falchi et al, ]. Many studies reported the mutations associated with the NA protein (i.e.…”