Phylogenetic Classification of Global Porcine Deltacoronavirus (PDCoV) Reference Strains and Molecular Characterization of PDCoV in Taiwan.

Fu-Chun Hsueh,Chuen-Fu Lin,Ming-Tang Chiou,Chao-Nan Lin,Cheng-Yao Yang,Hsing-Chun Shih,Wei-Hao Lin,Feng-Yang Hsu,Yu-Hsuan Chen

doi:10.3390/v13071337

Abstract

Porcine deltacoronavirus (PDCoV), a highly transmissible intestinal pathogen, causes mild to severe clinical symptoms, such as anorexia, vomiting and watery diarrhea, in piglets and/or sows. Since the first report of PDCoV infection in Hong Kong in 2012, the virus has readily disseminated to North America and several countries in Asia. However, to date, no unified phylogenetic classification system has been developed. To fill this gap, we classified historical PDCoV reference strains into two major genogroups (G-I and G-II) and three subgroups (G-II-a, G-II-b and G-II-c). In addition, no genetic research on the whole PDCoV genome or spike gene has been conducted on isolates from Taiwan so far. To delineate the genetic characteristics of Taiwanese PDCoV, we performed whole-genome sequencing to decode the viral sequence. The PDCoV/104-553/TW-2015 strain is closely related to the G-II-b group, which is mainly composed of PDCoV variants from China. Additionally, various mutations in the Taiwanese PDCoV (104-553/TW-2015) strain might be linked to the probability of recombination with other genogroups of PDCoVs or other porcine coronaviruses. These results represent a pioneering phylogenetic characterization of the whole genome of a PDCoV strain isolated in Taiwan in 2015 and will potentially facilitate the development of applicable preventive strategies against this problematic virus.

Highlights

Porcine deltacoronavirus (PDCoV) belongs to the genus Deltacoronavirus, family Coronaviridae and order Nidovirales
Given that genetic insertions and deletions potentially altering the virulence or infectious pattern of porcine coronavirus have been discovered in Taiwan [13], analysis of the genetic composition of PDCoV might play a pivotal role in the development of preventive strategies to mitigate economic losses caused by outbreaks of this infectious disease
A total of 107 worldwide of porcine coronaviruses can be aligned and categorized by phyPDCoVGenetic variantsdiversities from different countries that had outbreaks of this virus were incorpologeny based on the whole genome and/or

Summary

Introduction

Porcine deltacoronavirus (PDCoV) belongs to the genus Deltacoronavirus, family Coronaviridae and order Nidovirales. PDCoV consists of a positive-sense, single-stranded RNA virus, approximately 25.4 kb in length [1]. PDCoV was first detected in rectal swabs in. Specific criteria for the genetic classification of PDCoV strains have been defined to date. Clinical signs of PDCoV include vomiting, anorexia, dehydration, and watery diarrhea in piglets [11,12]. Given that genetic insertions and deletions potentially altering the virulence or infectious pattern of porcine coronavirus have been discovered in Taiwan [13], analysis of the genetic composition of PDCoV might play a pivotal role in the development of preventive strategies to mitigate economic losses caused by outbreaks of this infectious disease

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