Abstract: 【Objective】 This study was aimed to investigate the genome characteristics and variation of Porcine epidemic diarrhea virus (PEDV).【Method】 The small intestine tissues of 3 diarrhea piglets were used as templates,the pathogen was detected by RT-PCR.Using the RNA of the positive intestine tissue,RT-PCR technology was used to amplify the whole genome of PEDV. DNAStar software was used to edit and splice of the amplified sequence and perform similarity alignment.Mega X 10.0.5 software was used to construct phylogenetic trees of the whole genome and S gene of PEDV strain. RDP4 software was used to analyze the potential recombination events of PEDV strain.【Result】 PCR results showed that PEDV was detected in all the three sick piglets.The whole genome of PEDV strain was successfully obtained by RT-PCR fragmented amplification,named HB/HEBEU/2020.The virus genome size was 28 038 bp and it contained 7 open reading frames (ORF) which encoded replicase polyprotein 1a,replicase polyprotein 1b,spike (S),ORF3,envelope (E),membrane (M),and nucleoprotein (N) gene in 5' to 3' orientation.The similarity alignment of the complete genome as well as S gene between HB/HEBEU/2020 and PEDV variant strains,such as SNJ-P,USA/Colorado/2013 and HB2018 were 97.8%-99.3% and 95.7%-98.8%,respectively.Among all the commercially available vaccines,AJ1102 shared the highest similarity with HB/HEBEU/2020 strain,the nucleotide similarity between the complete genome as well as S gene of HB/HEBEU/2020 and AJ1102 were 98.3% and 97.3%,respectively.Genome-wide evolution results showed that 21 PEDV strains were classified into G1 genogroup and G2 genogroup,G1 genogroup was divided into G1a subgroup and G1b subgroup,G2 genogroup was divided into G2a subgroup and G2b subgroup,HB/HEBEU/2020 belonged to G2a subgroup.All the PEDV strains that belonged to G2 genogroup in the study were emerged after 2010.Among all the commercially available vaccines,AJ1102 had the nearest genetic relation with HB/HEBEU/2020,LW/L was second,the genetic distances between HB/HEBEU/2020 and CV777 as well as attenuated CV777 were far.3 possible recombination events were identified in the genome of HB/HEBEU/2020 strain.The recombinant regions of the three possible recombination events were 15 918-22 119,100-734 and 2 214-2 729 bp,respectively.The first two recombination events had high probability of occurrence.【Conclusion】 HB/HEBEU/2020 was a variant recombinant PEDV,which harbored distant phylogenetic relationships with classic PEDV strain CV777,but was closed related to the variant strains occurred in China after 2010.The results would provide theoretical and practical reference for postponing natural selection and evolution as well as formulating the vaccination procedure of PEDV.

Key words: Porcine epidemic diarrhea virus; whole genome; genetic variation; recombination analysis