Genetic Characteristics and Pathogenicity of a Novel Porcine Deltacoronavirus Southeast Asia-Like Strain Found in China

Hejie Wang; Yibin Qin; Wu Zhao; Tingting Yuan; Chunjie Yang; Xue Mi; Ping Zhao; Ying Lu; Bingxia Lu; Zhongwei Chen; Ying He; Cui Yang; Xianfeng Yi; Zhuyue Wu; Ying Chen; Zuzhang Wei; Weijian Huang; Kang Ouyang

doi:10.3389/fvets.2021.701612

Genetic Characteristics and Pathogenicity of a Novel Porcine Deltacoronavirus Southeast Asia-Like Strain Found in China

Front Vet Sci. 2021 Jul 16:8:701612. doi: 10.3389/fvets.2021.701612. eCollection 2021.

Authors

Hejie Wang¹, Yibin Qin², Wu Zhao², Tingting Yuan¹, Chunjie Yang¹, Xue Mi¹, Ping Zhao¹, Ying Lu¹, Bingxia Lu², Zhongwei Chen², Ying He², Cui Yang³, Xianfeng Yi³, Zhuyue Wu³, Ying Chen¹, Zuzhang Wei¹, Weijian Huang¹, Kang Ouyang¹

Affiliations

¹ College of Animal Science and Technology, Guangxi University, Nanning, China.
² Department of Virology, Guangxi Veterinary Research Institute, Nanning, China.
³ Guangxi Key Laboratory of Livestock Genetic Improvement, Guangxi Institute of Animal Science, Nanning, China.

Abstract

Farmers involved in the lucrative pork trading business between China and Southeast Asian countries should be aware of a recently discovered novel porcine deltacoronavirus (PDCoV) in Guangxi province, China. A PDCoV strain, CHN/GX/1468B/2017, was isolated from the small intestinal contents of piglets with diarrhea from this region, with a titer of 1 × 10^8.0 TCID₅₀/mL on LLC-PK cells. The full-length genome sequence consists of 25,399 nt as determined by next-generation sequencing and this was deposited in the GenBank (accession number MN025260.1). Genomic analysis showed that CHN/GX/1468B/2017 strain had 96.9~99.4% nucleotide homology with other 87 referenced PDCoV strains from different areas, and contained 6 and 9-nt deletions at positions 1,733~1,738 and 2,804~2,812, respectively, in the ORF1a gene. Phylogenetic analyses based on the whole gene sequence as well as S protein and ORF1a/1b protein sequences all showed that this strain was closely related to the Southeast Asia strain. When 7-day-old piglets were inoculated orally with the CHN/GX/1468B/2017 strain, they developed severe diarrhea, with a peak of fecal viral shedding at 4 days post-infection. Although no death or fever were observed, the CHN/GX/1468B/2017 strain produced a wide range of tissue tropism, with the main target being the intestine. Importantly, the VH:CD ratios of the jejunum and ileum in infected piglets were significantly lower than controls. These results indicate that CHN/GX/1468B/2017, isolated in China, is a novel PDCoV Southeast Asia-like strain with distinct genetic characteristics and pathogenicity. This finding enriches the international information on the genetic diversity of PDCoV.

Keywords: diarrhea; genomic characteristics; pathogenicity; piglets; porcine deltacoronavirus; virus isolation.