Objective Evolution and recombination of ORF3, gene of the sole accessory protein of the decades-long serious world-wide disease-causing porcine epidemic diarrhea virus (PEDV), were studied.

Method Randomly selected from the GenBank, data on 144 PEDV strains collected from 26 provincial administrative regions in China from 2013 to 2023 were used for the study. A phylogenetic tree of the genes was constructed by the neighbor-joining method with MEGA.11, and the nucleotide homology compared using the MegAlign tool in DNAstar. Subsequently, amino acid sequence alignment was determined with PowerPoint software, and evolution tree and recombination pattern of the genes analyzed by RDP4.0 software that employed 7 methods including RDP, Chimaera, BootSscan, 3Seq, GENE CONV, MaxChi, and SiScan.

Result The sampled PEDV strains belonged to the PEDV-1 and PEDV-2 subtypes. The more widely distributed PEDV-2 was further divided into PEDV-2a and PEDV-2b. The sequence similarity of ORF3 in the 144 strains was between 85.1% and 100%. Located in the V3 hypervariable region between the S and E of PEDV, ORF3 had amino acid sequences encoded with 6 major regions of mutation points without base deletion or insertion. The mutation sites in varied viral subtypes were specific, and there were one confirmed and three uncertain recombination events in the 144 strains.

Conclusion The mutations in the subtypes of the prevalent PEDV strains in China were numerous. The nucleotide sequence homology of ORF3 was high within a subtype. Gene recombination was not the main cause of the mutation. Development of a PEDV-2-targeted vaccine would be a practical approach in studying and dealing with the devastating disease on pigs in China.