Isolation, genetic characterization, and pathogenicity of the porcine epidemic diarrhea virus S-INDEL strain EJS6 in China

Abstract Porcine epidemic diarrhea virus (PEDV) is a highly infectious intestinal coronavirus that poses a significant threat to the pig industry because of its strong virulence and propensity for mutation and recombination. PEDV is classified into three major genotypes based on the spike (S) gene sequence: G1 (classical), G2 (variant), and S-INDEL (characterized by nucleotide insertions/deletions in the S gene). Both the G1 and G2 genotypes have been frequently detected in China, whereas the S-INDEL strain has rarely been reported or isolated. In this study, we isolated a PEDV S-INDEL strain, designated EJS6, from a pig farm experiencing severe diarrhea in Jiangsu Province, China. Genetic evolution analysis revealed that the Chinese S-INDEL strains represented by EJS6 presented sequence differences from other S-INDEL strains isolated in Europe and the United States, forming a new branch within the S-INDEL genotype. Compared with the G2 strain EHuB4, EJS6 presented a lower viral titer, smaller plaque size, and reduced syncytium-forming ability in Vero cells. We also compared the pathogenicity of EJS6 and EHuB4 in 5-day-old suckling piglets. Both strains exhibited similar levels of fecal virus shedding in the infected piglets; however, the histopathological and mortality results indicated that the pathogenicity of the EJS6 strain was weaker than that of the EHuB4 strain. In summary, we successfully isolated the first Chinese PEDV S-INDEL strain and characterized its genetic evolution and pathogenicity, thereby enhancing our understanding of the prevalence of PEDV in China.