Genetic Evolution Analysis Of H1N1 Subtype Swine Influenza Virus

Swine influenza(SI)is a highly contagious respiratory disease caused by the swine influenza virus(SIV).Pigs of different ages and genders are susceptible to infection,with symptoms of cough,dyspnea and fever.It is a common disease that is widespread and difficult to cure in today's large-scale pig farms.Pigs have been proposed as the mixing vessel of new reassortment virus for both having the receptors of avian and human.H1N1,H1N2 and H3N2 are the main subtypes of swine influenza viruses,whereas H1N1 subtype is the most common one.Therefore,it's essential to study the evolution of H1N1 subtype swine influenza viruses.In order to investigate the prevalence of SIV in pigs in west of Shandong province,a total of 1,500 samples of nasal swabs were collected from different farms and pig slaughterhouses in west of Shandong province during 2018.Five strains of H1N1 subtype SIV were isolated by 10 days embryonated eggs and identified by RT-PCR.Through the whole genome sequencing and genetic evolution analysis of the isolated strains,it was found that five virus genes showed two genotypes.The PB2,PB1,PA and NP genes of SW/SD/LC9/17 were derived from pdm/09 H1N1 viruses,HA,NA and M genes were derived from EA H1N1 virus,and NS gene was derived from CS H1N1 viruses.The other four strains of SW/SD/JN3/16,SW/SD/LC15/17,SW/SD/HZ18/18 and SW/SD/HZ22/18 have PB2,PB1,PA,NP and M genes from pdm/ 09 H1N1 viruses,HA and NA from EA H1N1 viruses,NS gene derived from CS H1N1 viruses.Which are derived from the reassortant strains formed by EA H1N1,pdm/09 H1N1 and CS H1N1 viruses.The key sites of the amino acid sequence of the 5 strains of SIV isolates were analyzed.It was found that the HA protein of the 3viruses exhibited the G225E(H3 Numbering)mutations indicating that they all could bind to the SAa-2,6-Gal receptor and their HA proteolytic cleavage site presented the R amino acid residue which is characteristic of the low pathogenic HA strains.