Premium
Prevalence, complete genome sequencing and phylogenetic analysis of porcine deltacoronavirus in South Korea, 2014–2016
Author(s) -
Jang G.,
Lee K.K.,
Kim S.H.,
Lee C.
Publication year - 2017
Publication title -
transboundary and emerging diseases
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.392
H-Index - 63
eISSN - 1865-1682
pISSN - 1865-1674
DOI - 10.1111/tbed.12690
Subject(s) - phylogenetic tree , biology , genome , virology , coronavirus , porcine epidemic diarrhea virus , diarrhoeal disease , phylogenetics , gene , molecular epidemiology , genetics , covid-19 , diarrhea , genotype , infectious disease (medical specialty) , medicine , disease , pathology
Summary Porcine deltacoronavirus ( PDC oV) 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 PDC oV 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 PDC oV 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 PDC oV (19.03%) in South Korea. Among those, the monoinfection of PDC oV (9.66%) and co‐infection of PDC oV (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 ( KNU 16‐07, KNU 16‐08 and KNU 16‐11) were sequenced and analysed to characterize PDC oV currently prevalent in South Korea. We found a single insertion‐deletion signature and dozens of genetic changes in the spike (S) genes of the KNU 16 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 PDC oV 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 PDC oV circulating in South Korea.