Phylodvnamics Of 2009 Pandemic Influenza A(H1N1) Virus In China:2009～2019

Seasonal influenza epidemics are a major public health burden,causing significant morbidity and mortality all over the world.Currently,seasonal influenza～associated deaths were estimated to be 291,000～645,000 per year.In the past 100 years,there have been four outbreaks of influenza A virus in the world,each of which caused millions of deaths.After 2009,a triple recombination of swine～origin 2009 pandemic influenza A(H1N1)(A/H1N1pdm)emerged in the Mexico and rapidly spread worldwide,causing great panic.At present,two subtypes of influenza A virus(A(H1N1)and A(H3N2)),and two lineages of influenza B virus(Victoria and Yamagata)are major causative agents responsible for the seasonal influenza epidemics,and often co～circulatingSince its first introduction into China in 2009,influenza A/H1N1pdm virus has undergone a rapid expansion and replaced the classical seasonal A(H1N1)virus.To characterize the ongoing evolution and national transmission dynamics of this virus,a total of 1,205 patient samples of influenza～like illness in Shanghai were collected in this study.Positive samples of influenza A and B viruses were determined by one～step fluorescence quantitative PCR.Then 1 00 samples were randomly selected from influenza A positive of samples.The 1 00 samples were constructed for amplicon DNA library and high～throughput sequencing.We obtained 66 influenza A(H1N1)pdm09 virus sequences and 33 H3N2 virus sequences.The sequencing results were dispoted to the GISAID database.All available sequences with clear sampling dates and locations were downloaded from the GENEBANK and GISAID databases,removing 100%identical sequences.Finally,we analysis 335 complete genome,1259 HA,and 1043 NA sequences of the A/H1N1pdm strains isolated from China.The best nucleic acid substitution model was selected by Jmodeltest.And we analysis dN/dS value of eight genomic segments of A/H1N1pdm by CODEML and analysis spatiotemporal dynamics of the A/H1N11pdm virus in China from 2009 to 2019 by Bayesian methodWe found that the dN/dS value and relative genetic diversity of the A/H1N1pdm virus experienced a decrease from 2009 to 2017,and then a rapid increase during 2018～2019.Importantly,elevated relative genetic diversity was observed in the A/H1N1pdm and the A(H3N2)viruses,as well as two lineages(Victoria and Yamagata)of influenza B virus during 2018～2019,suggesting the simultaneous changes of these viruses in terms of genetic diversity were associated with the recent large outbreak of seasonal influenza epidemic in China during 2018～2019.Fifteen amino acid mutations were found to be fixed along the main trunks of both HA and NA phylogenetic trees,and some of them are located in the antigen binding site or the receptor binding site.A sequential accumulation of mutations relative to the 2009～vaccine strain was observed in the circulating A/H1N1pdm strains during 2009～2016,while a rapid accumulation of mutations relative to the 2015～vaccine strain appeared in the emerging variants in 2017 shortly after the release of the vaccine.Multiple introductions of the A/H1N1pdm lineages into China were observed during 2009～2019,and East China and South China were found to serve as two major epicenters responsible for the national migration of the virus.In summary,these data provide important insights into the understanding of the evolution,epidemiology and transmission of the A/H1N1pdm virus,and highlight the importance of strengthening influenza surveillance in East China and South China.