Phylogenetic and evolutionary analysis of novel porcine epidemic diarrhea virus based on S gene

ABSTRACT

Recently, two novel subgroups of porcine epidemic diarrhea virus (PEDV) were identified in Tibetan pigs on the Qinghai-Tibet Plateau. We further investigated if the novel variant PEDV exists or had been prevalent in Sichuan region. One hundred and sixteen fecal and intestinal tissue samples collected in 2018-2019 from diarrheal pigs of Sichuan were detected for PEDV by RT-PCR, and the molecular characteristics of Spike genes (S) of PEDV were further investigated in this study. The results showed that the detection rate of PEDV was 42.2% (49/116, 95%CI=33.1%-51.8%) in diarrhea samples. Thirteen complete S gene sequences were obtained, and they were 4 149-4 170 bp in length, sharing 94.2%-99.9% identities with each other. Interestingly, SWUN-H3-CH-SCYA-2019 shared 97.0%-98.6% nucleotide sequence identities with those of the novel G1 subgroup of Tibetan Pig PEDVs. Phylogenetic and evolutionary analysis showed that the 13 S genes obtained in this study could be divided into G1 and G2 subgroups, one of which (SWUN-H3-CH-SCYA-2019 strain) fell into the novel G1 subgroup of Tibetan Pig PEDVs;the SWUN-19-CH-SCZY-2018, SWUN-4-CH-SCXC-2018, SWUN-1-CH-SCNJ-2019 and SWUN-3CH-CH-SCZG-2019 were clustered into an unique branch of G2 subgroup, and shared high sequence identities with the novel G2 subgroup of Tibetan Pig PEDVs. To further study the evolution process of 13 PEDVs, the BEAST software was used to estimate the divergence time. The results showed that the divergence time of SWUN-H3-CH-SCYA-2019 was about 2012.3 year, earlier than the earliest divergence time of the other novel G1 subgroup strains (2015.7 year), and the divergence time of SWUN-4-CH-SCXC-2018, SWUN-19-CH-SCZY-2018 and SWUN-3CH-CH-SCZG-2019 were about 2014.2 year, earlier than that of the novel G2 subgroup (2014.7 year). The divergence time of Tibetan pig PEDVs was later than that of strains identified in this study. Tibetan Pig PEDVs were first detected in Sichuan region, and we deduced a conclusion from different divergence time that the novel Tibetan Pig PEDVs were originated from Sichuan region. This study will provide the theoretical basis for monitoring the new variation of PEDV.