Ahead of Print -Novel Porcine Epidemic Diarrhea Virus Variant with Large Genomic Deletion, South Korea - Volume 20, Number 12—December 2014 - Emerging Infectious Disease journal - CDC
Volume 20, Number 12—December 2014
Novel Porcine Epidemic Diarrhea Virus Variant with Large Genomic Deletion, South Korea
Porcine epidemic diarrhea virus (PEDV) (family Coronaviridae, subfamily Coronavirinae, genusAlphacoronavirus) is an enveloped, positive-sense, single-stranded RNA virus. PEDV causes an acute and highly contagious enteric disease characterized by severe diarrhea, dehydration, and a high death rate in pigs that results in substantial economic losses in the swine industry (1). PEDV was first reported in Belgium and the United Kingdom in 1978; since then, it has been identified in many swine-raising countries in Europe and Asia, notably Belgium, Hungary, Italy, South Korea, Thailand, Japan, and China (1,2). PEDV was not reported in North and South America until 2013, when it was officially confirmed in the United States; it is spreading rapidly across the country (3). We report the emergence and genetic characterization of a novel PEDV variant with a large genomic deletion, which was serendipitously recognized in fecal and intestinal samples of suckling pigs with diarrhea in South Korea as a result of a systematic surveillance program to monitor activity for porcine diarrhea–associated viruses.
A total of 2,634 fecal and intestinal samples were collected from pigs exhibiting diarrhea from 569 swine farms in all 9 provinces of South Korea, during January 1–December 31, 2008; age groups of the pigs are defined in the Table. All samples were processed as 10% (v/v) suspensions with phosphate-buffered saline (PBS; 0.1 M, pH 7.2), and viral RNA was extracted from them. Subsequently, reverse transcription PCR (RT-PCR) was performed by using 3 primer pairs as described previously (4). To determine complete spike (S) gene sequence, we purified, cloned, and sequenced PCR products on an automated DNA sequencer by using T7, SP6 primers, and newly designed S gene–specific primers (primer sequences available on request). Sequences were analyzed by ClustalX version 1.83 program (http://www.clustal.org) and MegAlign software (DNAStar Inc., Madison, WI, USA), and compared with those of reference strains in GenBank. Phylogenetic analysis was conducted with MEGA version 5.22 (5). The complete S gene sequence of the PEDV variant with a large genomic deletion (strain MF3809/2008/South Korea) described here has been deposited in GenBank under accession no. KF779469.
Dr Seongjun Park is a virologist at the Viral Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology and the Forensic Medicine Division, Daegu Institute, National Forensic Service. His research interests include diagnosis, molecular virology, and epidemiology of emerging viral pathogens of public health significance.
This study was supported by a grant (PJ009015) from BioGreen 21 Program, South Korea. This work was supported by a National Agenda Project grant from the Korea Research Council of Fundamental Science and Technology and the KRIBB Initiative program (KGM3121322).
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Suggested citation for this article: Park S, Kim S, Song D, Park B. Novel porcine epidemic diarrhea virus variant with large genomic deletion, South Korea. Emerg Infect Dis [Internet]. 2014 Dec [date cited]. http://dx.doi.org/10.3201/eid2012.131642
1These authors were co-principal investigators for this study.