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

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

doi:10.3389/fvets.2021.701612

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 × 108.0 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.

Highlights

In recent years, enteric coronaviruses have been deemed to be one of the most serious pathogens that can endanger the healthy development of the farmed pig
Obvious cytopathic effects (CPEs) were observed from fourth passage cells at 24 h post inoculated (HPI)
Contrary to most of the China strains, the 3-nt (TAA) deletion at position 19,471∼19,473 of the S gene was not present in the CHN/GX/1468B/2017 strain as well as in the strains from the USA, Japan, and South Korea. This deletion was located in the S1 subunit which is responsible for the binding of viral receptors [15]

Summary

Introduction

Enteric coronaviruses have been deemed to be one of the most serious pathogens that can endanger the healthy development of the farmed pig. Examples include PEDV [1], TGEV [2], swine acute diarrhea syndrome coronavirus (SADS-CoV) called swine enteric alphacoronavirus (SeACoV) and porcine deltacoronavirus (PDCoV) [3]. PDCoV causes acute diarrhea, vomiting, dehydration and even death in suckling piglets [5, 6]. ORF1a/1b encode polyproteins pp1a and pp1ab and subsequently auto-proteolyzed into 15 non-structural proteins (Nsp to Nsp). The remaining ORFs encode at least four structural proteins: spike protein (S), envelope protein (E), membrane protein (M), nucleocapsid protein (N) [9]. The S protein interacts with the host cell receptor to mediate fusion of the virus envelope with the host cell membrane, which is a crucial step for virus entry into cells [10]. The N protein is highly conserved and plays a key role in the encapsulation of viral RNA [13, 14]

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