Genome Sequencing and Analysis of a Porcine Delta Coronavirus from Eastern China

Yang D,Ge F,Sun Q,Zhu J,Liu J,Liu P,Bai Y,Li X,Wang J,Ju H,Zhou J,Yang Xc

doi:10.21767/2248-9215.100025

Abstract

Porcine delta coronavirus (PDCoV) has been reported in many countries, including the United States, Canada, South Korea, China, Thailand, Vietnam and Laos. In December 2016, clinical diarrhea similar to that caused by porcine epidemic diarrhea virus (PEDV), but with a lower mortality rate, was reported on a swine farm in Shanghai, China. 6 Intestine samples were collected from dead suckling piglets (<3 weeks old) with clinical diarrhea, and they were assayed for the presence of swine enteric coronaviruses. Polymerase chain reaction results were positive for PDCoV (6/6), but negative for PEDV (0/6), transmissible gastroenteritis virus (TGEV) (0/6) and porcine rotavirus group A (Rota A) (0/6). The full-length genome sequence of the PDCoV strain SHJS/SL/2016 was determined. Phylogenetic trees demonstrated that PDCoV strain SHJS/SL/2016 belongs to the Chinese clade, which might share a common evolutionary ancestor with United States and South Korean clades, but it clustered separately from Thai and Laotian PDCoV strains. This report describes the complete genome sequence of SHJS/SL/2016, and the data will promote a better understanding of the molecular epidemiology and genetic diversity of PDCoV isolates in China.

Highlights

Porcine deltacoronavirus (PDCoV) is an enveloped, singlestranded, positive-sense RNA virus that is taxonomically classified within the family Coronaviridae, genus Deltacoronavirus [1]
The PCR results demonstrated that all samples were positive for Porcine delta coronavirus (PDCoV) (6/6), and none were PCR positive for porcine epidemic diarrhea virus (PEDV) (0/6), transmissible gastroenteritis virus (TGEV) (0/6) or rotavirus group A (Rota A) (0/6)
A subsequent sequence alignment showed that seven PDCoV strains, including three Thai PDCoV strains, two Vietnamese PDCoV strains, one Laotian PDCoV strain, and one Chinese PDCoV strain, contain a 6-nt (TTTGAA) deletion and a 9nt deletion (CCGGTTGGT) in ORF1a, while the SHJS/SL/2016 and CHN/Tianjin/2016 PDCoV strains only have a 6-nt deletion in ORF1a (Figure 1)

Summary

Introduction

Porcine deltacoronavirus (PDCoV) is an enveloped, singlestranded, positive-sense RNA virus that is taxonomically classified within the family Coronaviridae, genus Deltacoronavirus [1]. The complete genomic sequence of PDCoV (SHJS/SL/2016) was subsequently determined from extracted RNA by RT-PCR amplification of 16 regions covering the PDCoV genome as described previously [3]. The full-length genome sequence of a PDCoV strain (SHJS/SL/2016) was determined.

Results

Conclusion