Sentinel surveillance and whole genome evolution of influenza A (H1N1) pdm09 in Hunan, 2009–2018

ObjectiveTo analyze the sentinel surveillance results of influenza A (H1N1) pdm09 and understand the whole genome evolution or molecular characteristics of the virus strains isolated in Hunan province from 2009 to 2018.

MethodsInfluenza surveillance was carried out in 23 sentinel hospitals in all 14 cities in the province. In every sentinel hospital, 5–20 throat swabs were collected from influenza-like illness (ILI) cases in outpatients every week for the nucleic acid test and/or isolation of influenza virus. The isolated strains were sequenced for whole genome, and the gene phylogenetic trees were constructed by using Bayesian method and BEAST software. The gene sequences of the strains were aligned with vaccine strain.

ResultsDuring 2009–2018, a total of 190 289 samples of ILI cases were collected in Hunan. Among them, 8 014 were positive for influenza A (H1N1) pdm09 virus (4.21%). Seven epidemics were observed, the incidence peak was in 2009. The cases mainly occurred in age group 1–5 years, accounting for 25.13% of the total, and in age group 5–15 years, accounting for 32.83%. The male to female ratio of the cases was 1.23∶1. The whole genome of 60 strains of influenza A (H1N1) pdm09 virus from Hunan during 2009–2018 was analyzed. Compared with the vaccine strain, the homology of the whole genome sequence was between 97.2% and 99.9%. The Bayesian phylogenetic tree showed a step-like growth shape. It was estimated that the earliest public ancestor appeared in 2 009.177, and the estimated average evolution rate was 2.695×10⁻³ substitutions/site/year. Bayesian skyline plot analysis showed that the population dynamics of influenza A (H1N1) pdm09 virus remained basically stable from 2009 to 2018. The surface protein selection pressure analysis showed that the values of dN/dS were 0.201 and 0.219. The main mutation sites of the hemagglutinin molecules were L8M, S91R, S160G, S181T, A214T, and I312V. Two strains had the drug resistance mutation of H275Y in neuraminidase molecule.

ConclusionDuring 2009–2018, the positive rate and proportion of influenza A (H1N1) pdm09 virus in Hunan varied with year. The incidence peak occurred in winter. The cases were mainly children and adolescents. The virus genes continued to evolve and the population dynamic was stable.