Analysis Of Complete Genome Sequences Of H3N2 And H1N1 Subtype Swine Influenza Virus In Guangxi

Swine respiratory epithelium has the ability to infect both human and avian influenza virus receptors,so pigs are considered "mixing vessel" of influenza viruses.Once the new reassortant virus is produced,it will pose a potential threat to human health.In our previous study(2013-2015),novel reassortant influenza viruses(H1N1 and H3N2 subtypes)with different genotypes have been isolated and obtained from several regions in Guangxi.Therefore,in our study,we continues to continuously monitor the epidemiology of influenza viruses in pig farms in Guangxi,and isolated one H1N1 and one H3N2 subtype of swine influenza virus(SIV),which were subtyped and named A/Swine/Guangxi/JG24/2019(H1N1)(abbreviated as JG24 strain)and A/Swine/Guangxi/JG13/2019(H3N2)(abbreviated as JG13 strain).It was found that the surface genes HA and NA of JG13 strain were derived from human-like H3N2 lineage(Human-Like,HL),while the surface gene HA of JG24 strain and NA were derived from the Eurasian Avian-like(EA).Their internal genes NP,M,PA,PB1 and PB2 were derived from the 2009H1N1 pandemic lineage(pdm09/H1N1),and the NS gene was derived from the classical H1N1 Swine(CS)through the amplification of complete genome and genetic evolution analysis of the two strains.Interestingly,the surface genes of the new isolated JG13/2019 had begun to undergo antigenic drift,and their nucleotide homology with the HA and NA genes of the H3N2 strain obtained in2013 and 2014 years is only 95.2%-95% and 93.5%-93.7%,respectively.The JG24/2019 strain had the highest homology with A/swine/Guangxi/NNLX/2014,and the homology between HA and NA gene nucleotide were 97.5% and 97.9%,respectively.The sequence analysis of the newly isolated strains and the strains obtained in recent years showed that both strains were low pathogenic attenuated strains,and the HA protein cleavage regions were single basic amino acid cleavage sites.JG13/2019 not only maintained the early sites that can bind to SA?-2,6-Gal receptor of human influenza virus(190D,226I and 228S),but also occurred the amino acid mutations at the new sites of 223I and 227S;None of the NA protein had a deletion in the stem region,and no mutations such as E119V/I,H274Y,and R292K have occurred at typical sites that have been reported.The internal genes of JG13/2019 showed changes in the R356K(PA protein)and I588T(PB2 protein)sites compared to the early strain.In addition,the HA protein of the JG24/2019 strain remained at the receptor binding sites of190 D,225E and 226Q,while the internal gene PB2 protein also retained the molecular characteristics of 590S/591R and 627E.After several years of genetic evolution,whether these amino acid changes will affect the ability to pathogenicity,replication and cross-species transmission remains to be further studied in the future.