title: ORF3a deletion in field strains of porcine-transmissible gastroenteritis virus in China: A hint of association with porcine respiratory coronavirus.
abstract: Porcine-transmissible gastroenteritis virus (TGEV) is a pathogenic coronavirus responsible for high diarrhoea-associated morbidity and mortality in suckling piglets. We analysed the TGEV ORF3 gene using nested polymerase chain reaction and identified an ORF3a deletion in three field strains of TGEV collected from piglets in China in 2015. Eight TGEV ORF3 sequences were obtained in this study. Phylogenetic tree analysis of ORF3 showed that the eight TGEV ORF3 genes all belonged to the Miller cluster. CH-LNCT and CH-MZL were closely correlated with Miller M6, while CH-SH was correlated with Miller M60. These results thus indicate that the existence of Miller, as well as the Purdue cluster, in Chinese field strains of TGEV. Furthermore, we found the first evidence for a large deletion in ORF3 resulting in the loss of ORF3a, previously reported in porcine respiratory coronavirus, in three field strains (CH-LNCT, CH-MZL, and CH-SH) of TGEV. The results of the present study thus provide important information regarding the underlying evolution mechanisms of coronaviruses.
authors.affiliation: State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of the Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China.
authors.forename: X
authors.initials: X
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of the Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China.
authors.forename: Y
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of the Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China.
authors.forename: X
authors.initials: X
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of the Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China.
authors.forename: J
authors.initials: J
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of the Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China.
authors.forename: H
authors.initials: H
authors.lastname: Shi
authors.affiliation: State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of the Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China.
authors.forename: D
authors.initials: D
authors.lastname: Shi
authors.affiliation: State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of the Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China.|Molecular Biology, Gembloux Agro-Bio Tech, University of Liège, Liège, Belgium.
authors.forename: H
authors.initials: H
authors.lastname: Dong
authors.affiliation: State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of the Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang, China.
authors.forename: L
authors.identifier: http://orcid.org/0000-0003-4731-5627
authors.initials: L
authors.lastname: Feng
mesh_terms: D000818:Animals; D002681:China / Q000453:epidemiology; D018352:Coronavirus Infections / Q000150:complications / Q000662:veterinary* / Q000821:virology; D005761:Gastroenteritis, Transmissible, of Swine / Q000150:complications / Q000453:epidemiology / Q000821:virology*; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D045722:Porcine Respiratory Coronavirus / Q000302:isolation & purification*; D013552:Swine; D005760:Transmissible gastroenteritis virus / Q000302:isolation & purification*
keywords: 
  ORF3a
  ; deletion; transmissible gastroenteritis virus