Prevalence analysis and genome characteristics of PEDV in China
In the PEDV positive farms, 115 clinical samples were found to be positive for PEDV based on the RT-PCR results. The positive rates of PEDV collected from pig farms was 10.77% to 25.10% from March 2020 to March 2021. Among them, the S genes of 91 PEDV positive samples obtained in 17 different provinces in China from 2020 to 2021 were successfully amplied and sequenced. This epidemiological survey covered the major pig-raising provinces in China (Figure 1A). During the period of this study, PEDV could be detected every month of the year. However, the number of positive samples was significantly different in each month (p < 0.05), with two epidemic peak of infection identified. The epidemic waves occurred in October and December (Figure 1B), in line with the epidemic characteristics of PEDV(specially spread in winter or the turn of autumn and winter)(Jung, Saif, & Wang, 2020).
The length of S genes of 91 field strains was 4,149–4,176 nucleotides (nt), which encoded proteins of 1383–1392 amino acids. A phylogenetic analysis based on the sequenced S genes and 24 reference strains indicated that PEDV can be divided into two genotypes (GI and GII) and further classified into five subgroups, including GI-a, GI-b, GI-c, GII-a, and GII-b (Figure 1C). The GI-a clade comprised classical strains, such as CV777, CH/S, and DR13.The classical vaccine strains attenuated from CV777 and DR13 belonged to GI-b subgroup. Notably, 92.3% (84 out of 91) of the strains identified from 2020 to 2021 were belonged to genotype GII. CH/HBTS/202010, CH/SCMY/202012, CH/GXLB/202005, and CH/GXLP/202007 were categorized as GII-a and other 80 belonged to GII-b subgroup. Meawhile, CH/JSXZ/202012, CH/SCYB/202012, CH/SCGA/202103, CH/SCST/202004, CH/HNBR/202101, CH/JXXG/202101, and CH/HNSQ/202102 were located in the GI-c clade and closely related to PEDV S-INDEL strains found in the US (OH851), Korea (KNU-1406-1), and China (ZL29). They were distributed in four provinces of China (Figure 1A). However, the sequenced S-INDEL like strains were not clustered together with reference S-INDEL strains, indicating that the origin of these PEDV strains may be different.