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.