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. 2015 Dec;62(6):575-80.
doi: 10.1111/tbed.12399. Epub 2015 Aug 6.

Newly Emerged Porcine Deltacoronavirus Associated With Diarrhoea in Swine in China: Identification, Prevalence and Full-Length Genome Sequence Analysis

D Song  1 , X Zhou  1 , Q Peng  1 , Y Chen  1 , F Zhang  1 , T Huang  1 , T Zhang  1 , A Li  1 , D Huang  1 , Q Wu  1 , H He  1 , Y Tang  1
Affiliations

Newly Emerged Porcine Deltacoronavirus Associated With Diarrhoea in Swine in China: Identification, Prevalence and Full-Length Genome Sequence Analysis

D Song et al. Transbound Emerg Dis. 2015 Dec.

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.

Keywords: complete genome; diarrhoea; nested RT-PCR; phylogenetic analysis; porcine deltacoronavirus (PDCoV); prevalence.

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Figures

Figure 1
Figure 1
Phylogenetic tree on the basis of the complete genome (panel a) and the deduced aa sequences of the S gene (panel b) of the coronaviruses from four coronavirus genera (Alphacoronavirus, Betacoronavirus, Gammacoronavirus and Deltacoronavirus). The trees were constructed by MEGA 6.05, using the neighbour‐joining method. Bootstrap was set in 1000 replicates. Bars of 2/0.2 indicate nt or aa substitutions per site. Names of each reference strain retrieved from GenBank are followed by corresponding accession numbers of each strain.
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