Laboratory findings

After preliminary confirmation of the PEDV pathogen by the pig farm laboratory, fecal samples, milk and serum of 20 sows, as well as the feces and intestines of three infected piglets were sent to South China Agriculture University for sequence analysis and serological testing. In order to reveal the molecular characteristics of the virus and determine the relationship between the current epidemic strains in China and other subtype strains, the Bootstrap method of MEGA6.0 software was used to analyze the evolutionary tree of domestic isolates and reference strains from different sources at different times, which indicated that the strain formed a new and unique branch in the PEDV genotype II (Figure 2), which had the closest genetic distance to the genotype I strain. The S1 gene homology comparative analysis of this strain showed that it had 98.1%-100% homology with 59 epidemic strains uploaded by NCBI in the past year, 91.8% homology with CV777 strain, 97.8 homology with the AJ1102 vaccine strain, and 97.3%-98.1% homology with the 89 strains prevalent in 2014-2015 measured by our laboratory (Table 1), indicating that the PEDV of the current outbreak had mutated. Please see Supplementary Figure 1 for specific similarities. The similarity with the 2020 strain was also poorer by 1-2% compared to the 2014-2015 strain, indicating that PEDV had continuously mutated.

To evaluate the immunizing effect of the PED vaccine in this farm, 20 diseased sows in farrowing season were randomly selected before the immunization with autogenous inactivated vaccines and numbered 1-20. Colostrum, feces, and serum were collected respectively to test the levels of PED antigen and IgA antibody in colostrum, as well as the levels of PED antigen in feces and specific IgG antibody in serum. The results showed that the pigs had a good immune response after immunization with the PED vaccine, with high levels of IgA and IgG antibodies. However, for the three sows numbered 8, 11, and 20, despite the high levels of IgA in milk and serum IgG antibodies, there were still detectable PED antigens (Table 2). PED antigens were detected in feces of more sows, indicating that the antibody levels produced by the existing commercial vaccines cannot completely neutralize the new epidemic strain of PEDV.

To evaluate the fecal virus shedding of sows during the disease course, we conducted a two-week monitoring of virus shedding on 7 diseased sows. The results showed that the affected sows had intermittent virus shedding within two weeks after delivery. Some of the sows shed a great load of virus due to individual differences (Table 3).