Abstract
Porcine epidemic diarrhea virus (PEDV), an enteric coronavirus, has
become the major causative agent of acute gastroenteritis in piglets
since 2010 in China. Given a raised interest in the mutation and
recombination of viral genomes, the genetic and antigenic
characteristics of PEDV should be continuously investigated. In the
current study, 91 complete spike (S) gene sequences were obtained from
PEDV positive samples collected from17 provinces in China from March
2020 to March 2021. A phylogenetic analysis showed that 92.3% (84 out
of 91) of the identified strains belonged to GII subtype, while 7.7 %
(7 out of 91) were categorized as S-INDEL like strains and grouped
within GI-c clade. Based on a recombination analysis, six of S-INDEL
like strains were recombinant strains originated from S-INDEL strain
FR/001/2014 and vaccine strain AJ1102. In addition, PEDV variant strains
carrying novel insertions (360QGRKS364 and 1278VDVF1281) in the S
protein were observed. Furthermore, the deduced amino acid sequences
analysis for the S protein showed that multiple amino acid substitutions
in the neutralizing domain (COE) and three neutralizing epitopes
(S1A, SS6, 2C10) were found as compared with the
vaccine strains (CV777 and AJ1102). The recombination of field and
vaccine strains, along with variation of antigenic epitopes, might
affect the virulence and antigenicity of PEDV, thus resulting in a
failure of immunization. In conclusion, these data provide novel
molecular evidences on the epidemiology and molecular diversity of PEDV
in 2020–2021. This information may help design a strategy for
controlling and preventing the prevalence of PEDV variant strains in
China.