Whole genome characteristics of H3N2 influenza virus in Wuxi City from 2018 to 2022
Objective To investigate the evolutionary and variation characteristics of H3N2 influenza virus in Wuxi City in recent years.Methods Nasopharyngeal swab specimens from influenza-like illness(ILI)cases were detected and genotyped using fluores-cent,quantitative,real-time,reverse-transcription PCR(RT-qPCR)assay.Specimens tested positive for H3N2 influenza virus nuclear acid were cultured in cells,and virus isolates with 1∶8 and higher titers of red blood cell haemagglutination assay were used for amplifi-cation of whole genomes.The library was constructed and sequenced on a MiSeq sequencing system,and the sequencing data were ana-lyzed using the software CLC Genomics Workbench version 23 with NC_007366.1 as the reference strain.Phylogenetic tree was built using the software MEGA version 7.0,and the N-glycosylation sites were predicted using NetNGlyc 1.0 Server.Results A total of 10 440 nasopharyngeal swab specimens were collected from ILI cases during the period from 2018 through 2022,and the proportion of positive influenza virus nuclear acid was 9.60％,with 285 H3N2 influenza virus isolates(28.44％).Whole-genome sequencing of 19 H3N2 influenza virus isolates showed the lowest nucleotide and amino acid homology in the HA gene(97.43％to 100.00％and 96.37％to 100.00％),and the highest nucleotide and amino acid homology in theM gene(98.23％to 100.00％and 100.00％).There were significant differences in the proportions of nucleotide(Mgene vs.HA gene:3.05％vs.7.05％;x2=41.26,P＜0.05)and amino acid variations(PB2 vs.NA:1.54％vs.7.45％;x2=86.12,P＜0.05).The minimal genetic evolutionary distance was seen in the NS gene(0.000 to 0.028),and the maximum distance was measured in the HA gene(0.000 to 0.065).The prevalent H3N2 influ-enza virus isolate was a 3C.2a cladein 2018(January to March),a 3C.2alb.2 clade between 2018 and 2020,and a 3C.2alb.2a.la.1 clade in 2022(April to December).Mutational sites were found in 8 gene fragments of 19 H3N2 influenza virus isolates,with more sites in HA(51)and NA genes(40),and few sites in the M gene(6).In addition,specific mutational sites were found across the five-year study period,with 9 to 12 potential N-glycosylation sites in the HA gene and 6 potential N-glycosylation sites in the NA gene.Conclu-sions Continuous evolution of prevalent H3N2 influenza virus isolates is found in Wuxi City;however,the virus isolates match well with vaccine candidate isolates.Intensified influenza surveillance and understanding of trends in epidemiological features of influenza vi-rus are required to formulate the influenza control strategy.
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