title: Newly Emerged Porcine Deltacoronavirus Associated With Diarrhoea in Swine in China: Identification, Prevalence and Full-Length Genome Sequence Analysis.
abstract: To identify and characterize aetiologic agent(s) associated with an outbreak of a severe diarrhoea in piglets in Jiangxi, China, in March 2015, a nested reverse transcription-polymerase chain reaction (RT-PCR) for the detection of porcine deltacoronavirus (PDCoV) was developed. A survey based on the nested RT-PCR established indicated that the monoinfection of PDCoV (33.71%) and coinfection of PDCoV (19.66%) with porcine epidemic diarrhoea virus (PEDV) were common in diarrhoeal pigs in Jiangxi, China. A high prevalence of PDCoV (58.33%) in diarrhoeal samples which were PEDV negative was observed. The complete genome sequence of a representative PDCoV strain, PDCoV/CHJXNI2/2015, was determined. Phylogenetic analysis of complete genome and S protein sequences of PDCoV/CHJXNI2/2015 demonstrated that it was most closely related to Hong Kong and US PDCoVs. To our knowledge, this is the first report on the identification, prevalence, complete genome sequencing and molecular characterizations of PDCoV in diarrhoeal samples in pigs in China.
authors.affiliation: Jiangxi Agricultural University, Nanchang, Jiangxi, China.
authors.forename: D
authors.initials: D
authors.lastname: Song
authors.affiliation: Jiangxi Agricultural University, Nanchang, Jiangxi, China.
authors.forename: X
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Jiangxi Agricultural University, Nanchang, Jiangxi, China.
authors.forename: Q
authors.initials: Q
authors.lastname: Peng
authors.affiliation: Jiangxi Agricultural University, Nanchang, Jiangxi, China.
authors.forename: Y
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Jiangxi Agricultural University, Nanchang, Jiangxi, China.
authors.forename: F
authors.initials: F
authors.lastname: Zhang
authors.affiliation: Jiangxi Agricultural University, Nanchang, Jiangxi, China.
authors.forename: T
authors.initials: T
authors.lastname: Huang
authors.affiliation: Jiangxi Agricultural University, Nanchang, Jiangxi, China.
authors.forename: T
authors.initials: T
authors.lastname: Zhang
authors.affiliation: Jiangxi Agricultural University, Nanchang, Jiangxi, China.
authors.forename: A
authors.initials: A
authors.lastname: Li
authors.affiliation: Jiangxi Agricultural University, Nanchang, Jiangxi, China.
authors.forename: D
authors.initials: D
authors.lastname: Huang
authors.affiliation: Jiangxi Agricultural University, Nanchang, Jiangxi, China.
authors.forename: Q
authors.initials: Q
authors.lastname: Wu
authors.affiliation: Jiangxi Agricultural University, Nanchang, Jiangxi, China.
authors.forename: H
authors.initials: H
authors.lastname: He
authors.affiliation: Jiangxi Agricultural University, Nanchang, Jiangxi, China.
authors.forename: Y
authors.initials: Y
authors.lastname: Tang
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002681:China / Q000453:epidemiology; D018352:Coronavirus Infections / Q000453:epidemiology / Q000235:genetics / Q000662:veterinary*; D003967:Diarrhea / Q000662:veterinary* / Q000821:virology; D004196:Disease Outbreaks / Q000662:veterinary*; D016679:Genome, Viral; D006723:Hong Kong / Q000453:epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D053485:Porcine epidemic diarrhea virus / Q000235:genetics / Q000302:isolation & purification*; D015995:Prevalence; D017422:Sequence Analysis, DNA; D013552:Swine; D013553:Swine Diseases / Q000453:epidemiology / Q000821:virology*
keywords: complete genome; diarrhoea; nested RT-PCR; phylogenetic analysis; porcine deltacoronavirus (PDCoV); prevalence