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. 2017 Oct;64(5):1364-1370.
doi: 10.1111/tbed.12690. Epub 2017 Jul 30.

Prevalence, complete genome sequencing and phylogenetic analysis of porcine deltacoronavirus in South Korea, 2014-2016

G Jang  1 , K-K Lee  2 , S-H Kim  2 , C Lee  1
Affiliations

Prevalence, complete genome sequencing and phylogenetic analysis of porcine deltacoronavirus in South Korea, 2014-2016

G Jang et al. Transbound Emerg Dis. 2017 Oct.

Abstract

Porcine deltacoronavirus (PDCoV) is a newly emerged enterotropic swine coronavirus that causes enteritis and diarrhoea in piglets. Here, a nested reverse transcription (RT)-PCR approach for the detection of PDCoV was developed to identify and characterize aetiologic agent(s) associated with diarrhoeal diseases in piglets in South Korea. A PCR-based method was applied to investigate the presence of PDCoV in 683 diarrhoeic samples collected from 449 commercial pig farms in South Korea from January 2014 to December 2016. The molecular-based survey indicated a relatively high prevalence of PDCoV (19.03%) in South Korea. Among those, the monoinfection of PDCoV (9.66%) and co-infection of PDCoV (6.30%) with porcine epidemic diarrhoea (PEDV) were predominant in diarrhoeal samples. The full-length genomes or the complete spike genes of the most recent strains identified in 2016 (KNU16-07, KNU16-08 and KNU16-11) were sequenced and analysed to characterize PDCoV currently prevalent in South Korea. We found a single insertion-deletion signature and dozens of genetic changes in the spike (S) genes of the KNU16 isolates. Phylogenetic analysis based on the entire genome and spike protein sequences of these strains indicated that they are most closely related to other Korean isolates grouped with the US strains. However, Korean PDCoV strains formed different branches within the same cluster, implying continuous evolution in the field. Our data will advance the understanding of the molecular epidemiology and evolutionary characteristics of PDCoV circulating in South Korea.

Keywords: PDCoV; full-length genome; nested RT-PCR; phylogenetic analysis; prevalence.

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Figures

Figure 1
Figure 1
Phylogenetic analysis based on the full‐length genome sequences of four coronavirus genera (Alphacoronavirus, Betacoronavirus, Gammacoronavirus and Deltacoronavirus) (a) and the nucleotide sequences of the complete genomes (b) and the S genes (c) of PDCoV strains. Multiple sequence alignments were performed using the ClustalX program, and the phylogenetic tree was constructed from the aligned nucleotide sequences using the neighbour‐joining method. Numbers at each branch represent bootstrap values greater than 50% of 1000 replicates. Names of the strains, countries, years of isolation, GenBank accession numbers and clades proposed in this study are shown. The porcine deltacoronavirus (PDCoV) isolates identified in this study are indicated by solid circles. Scale bars indicate nucleotide substitutions per site
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