Abstract: 【Objective】 In order to investigate the genotypes and genetic variation of Porcine epidemic diarrhea virus (PEDV) strains spreading in parts of Southwest China.【Method】 200 anal swabs of diarrhea porcine which were collected in different regions of Sichuan and Yunnan from 2020 to 2021 were detected by RT-PCR methods.Then, the S and ORF3 genes of PEDV in positive samples were cloned and sequenced.MegAlign software was used for variability analysis, Mega 7.0 software was used for system evolution analysis, and RDP4 software was used for gene recombination analysis.【Result】 The positive rates of PEDV in all samples were 15.50%(31/200) and the positive rate of population was 100%(8/8).The PEDV S and ORF3 genes sequences of 8 isolates were 90.5%-99.4% and 92.9%-100%, respectively.Phylogenetic analysis based on the S gene showed that 8 PEDV strains were distributed in three subgroups, G2a, G2b, and G2c.Among them, the Sichuan SCWJSWUN02 strain was closed to Fujian CH/FJXM/1/2012 strain, Yunnan YNKMSWUN01 strain and Vietnamese strain were clustered in a separate group.It indicated that the current PEDV epidemic in Southwest China was characterized by inter-regional transmission.Compared with the previously circulating strains and vaccine strains, the amino acid of the S protein of 8 PEDV isolates were changed on different levels.However, ORF3 protein was relatively conserved.The continuous amino acid insertions and deletions were found in the S protein of parts of PEDV strains.Such as, 4 continuous amino acid deletions were found in 59-62 aimo acid of SCMYSWUN03 strain S protein.5 amino acid insertions and deletions were found in 78-82 and 84-88 aimo acid of YNKMSWUN01 strain, respectively.Some amino acid mutations were present in the identified receptor binding domains of the S protein.In addition, the recombination analysis showed that SCMYSWUN03 strain might have gene recombination events, with a probability of 98.2% (P<0.01).【Conclusion】 This study found that the current popular PEDV strains in Southwest China included three subgroups of G2a, G2b and G2c.The genotypes of the strains were diverse, and the variability among different strains was large, which enriched the molecular epidemiological investigation data of PEDV in Sichuan and Yunnan, and revealed the molecular genetic variation law and evolutionary characteristics of 8 PEDV strains prevalent in Southwest China, It provided a theoretical basis for the formulation of prevention and control measures of porcine diarrhea in this region.

Key words: Porcine epidemic diarrhea virus (PEDV); S gene; ORF3 gene; phylogenetic analysis