China Animal Husbandry and Veterinary Medicine ›› 2020, Vol. 47 ›› Issue (1): 209-220.doi: 10.16431/j.cnki.1671-7236.2020.01.025

• Preventive Veterinary Medicine • Previous Articles     Next Articles

Sequencing and Genetic Variation Analysis of the Whole Gene of Epidemic Strain of PEDV in Pengzhou,Sichuan Province

XIANG Meng, ZHANG Huanrong, REN Yupeng, ZHANG Keke   

  1. College of Life Science and Technology of Southwest Minzu University, Chengdu 610041, China
  • Received:2019-08-12 Online:2020-01-20 Published:2020-01-17

Abstract: In order to study the genomic characteristics and genetic variation of porcine epidemic diarrhea virus (PEDV) strains infected by a pig farm immunized with PEDV vaccine in Pengzhou,Sichuan province,RT-PCR was used to screen the positive samples of PEDV,named SCXM strain.The whole genome sequence was cloned and sequenced to obtain the whole genome sequence,and the main structural genes were analyzed for genetic variation and phylogenetic analysis.The results showed that the genetic variation of SCXM strain was mainly concentrated in S gene,the homologies were 90.4%-99.2% compared with 71 strains and 93.8% compared with CV777.Compared with common vaccine strains in China,amino acid mutations were found in 5 linear epitopes (P1,S1P2,S1P3,SS5 and SS6) and 1 neutralizing epitope (SID).The analysis of genetic evolution showed that SCXM strain belonged to the G2b subtype of PEDV,which was the same branch with HBXY3 strain in Hubei province and Vietnam strain.In addition,the analysis of ORF3,M and N genes showed that there were a certain number of amino acid mutations in SCXM compared with the vaccine strain,but the degree of variation was relatively small,and did not cause the change of antigenicity prediction value.The results showed that PEDV SCXM strain was a new variant strain,and its S gene was mutated to a large extent.The mutation and antigenicity change of multiple amino acids in S gene might be one of the reasons for the failure of vaccine immunization in pig farms.This study enriched the genetic data of PEDV,discussed the genetic variation and evolution characteristics of PEDV of SCXM strain,and laid a foundation for the molecular evolution of PEDV.

Key words: porcine epidemic diarrhea virus (PEDV); genome; structural gene; failure immunization

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