Detection and spike gene characterization in porcine deltacoronavirus in China during 2016–2018

Abstract

A B S T R A C TPorcine deltacoronavirus (PDCoV) has been emerging in several swine-producing countries for years. In our study, 719 porcine diarrhoea samples from 18 provinces in China were collected for PDCoV and porcine epidemic diarrhoea virus (PEDV) detection. The epidemiological survey revealed that the positive rates of PDCoV, PEDV and coinfection were 13.07%, 36.72% and 4.73%, respectively. The entire spike (S) genes of eleven detected PDCoV strains were sequenced. Phylogenetic analysis showed that the majority of PDCoVs could be divided into three lineages: the China lineage, the USA/Japan/South Korea lineage and the Viet Nam/Laos/ Thailand lineage. The China and the Viet Nam/Laos/Thailand lineages showed much greater genetic divergences than the USA/Japan/South Korea lineage. The present study detected one new monophyletic branch that contained three PDCoVs from China, and this branch was separated from the China lineage but closely related to the Viet Nam/Laos/Thailand lineage. The strain CH-HA2-2017, which belongs to this new branch, had a possible recombination event between positions 27 and 1234. Significant amino acid substitutions of PDCoV S proteins were analysed and displayed with a three-dimensional cartoon diagram. The visual spatial location of these substitutions gave a conformational-based reference for further studies on the significance of critical sites on the PDCoV S protein.

Genetic characterization and phylogenetic analysis of porcine deltacoronavirus (PDCoV) in Shandong Province, China

“…Compared with the USA/Japan/South Korea lineage and Vietnam/ Laos/Thailand lineage strains, the China lineage strains have 3-nt TAA deletions (52 N), leading to the lack of an asparagine in the S gene. This may be the most important feature of the Chinese lineage strains, except for CH/Jiangsu/2014 (Zhang et al, 2019d). Sequence analysis showed that 27 aa mutations were detected in S1 (Fig.…”

“…After nucleotide homology comparison and screening, 29 representative strains were selected from 102 strains for molecular evolutionary analyses (Tables 2 and S1). In addition, these strain sequences have been previously published as reference sequences (Suzuki et al, 2018;Zhang et al, 2019a, c;Zhang et al, 2019d). To obtain the sequence, the complete S protein, N protein and partial ORF1a genes were amplified in 10 PDCoV-positive samples ( Table 1).…”

“…The PDCoV S protein is a glycoprotein of approximately 1383 amino acids aa with an apparent molecular mass of 180 kDa. Studies of genomic sequences analyses using S protein genes have shown that PDCoV can be further divided into three lineages: the China lineage, USA/Japan/South Korea lineage and Vietnam/Laos/Thailand lineage Zhang et al, 2019d). The Vietnam/Laos/Thailand lineage has been detected in Southeast Asia (Janetanakit et al, 2016;Lorsirigool et al, 2017Lorsirigool et al, , 2016Saeng-Chuto et al, 2017).…”

Characterization, pathogenicity and protective efficacy of a cell culture-derived porcine deltacoronavirus

“…Most of the reported Chinese strains were isolated from the eastern and central regions of China (Dong et al, 2016;Dong et al, 2015;Wang et al, 2015;Zhang et al, 2019c). Besides, PDCoV isolate, CHN-SC2015, was isolated from Sichuan Province in southwest China .…”

Quantitative Proteomic Analysis of Porcine Intestinal Epithelial Cells Infected with Porcine Deltacoronavirus Using iTRAQ-Coupled LC-MS/MS

“… 3 Since then, the virus has been detected in many other countries, including Canada, mainland China, South Korea, Thailand, Laos, Vietnam, Japan, Mexico, and so on. 4 , 5 Clinically, PDCoV-infected pigs often present with diarrhea and/or vomiting, dehydration, and death of neonatal piglets. 6 The outbreak of PDCoV infection in numerous countries has resulted in considerable economic losses to the global swine industry.…”