Novel Porcine Epidemic Diarrhea Virus (PEDV) Variants with Large Deletions in the Spike (S) Gene Coexist with PEDV Strains Possessing an Intact S Gene in Domestic Pigs in Japan: A New Disease Situation

• Published in: PloS one Vol. 12; no. 1; p. e0170126
• Main Authors: Diep, Nguyen Van, Norimine, Junzo, Sueyoshi, Masuo, Lan, Nguyen Thi, Yamaguchi, Ryoji
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 2017; Public Library of Science (PLoS)
• Subjects: Agricultural economics; Analysis; Animals; Biology and Life Sciences; Coronavirus Infections - epidemiology; Coronavirus Infections - veterinary; Coronavirus Infections - virology; Diarrhea; Disease; Disease Outbreaks; Economic impact; Epidemics; Epidemiology; Evolution & development; Farms; Genes; Genetic engineering; Genetic Variation; Genomes; Genomics; Genotype; Genotypes; Hogs; Immunoglobulins; Infections; Japan - epidemiology; Laboratories; Medicine and Health Sciences; Mixed infection; Mutation; Outbreaks; Pandemics; Pathogenesis; Pathology; People and Places; Phylogeny; Pigs; Porcine epidemic diarrhea virus; Porcine epidemic diarrhea virus - classification; Porcine epidemic diarrhea virus - genetics; Proteins; Recurrent infection; Research and Analysis Methods; Risk factors; S gene; Sequence Deletion - genetics; Spike Glycoprotein, Coronavirus - genetics; Strains (organisms); Suidae; Sus scrofa; Swine; Swine Diseases - epidemiology; Swine Diseases - virology; Transmissible gastroenteritis; Vaccines; Veterinary medicine; Virology; Viruses
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0170126

Since late 2013, after an absence of seven years, outbreaks of porcine epidemic diarrhea virus (PEDV) infection have reemerged and swept rapidly across Japan, resulting in significant economic losses. In this study, we report the emergence, mixed infection, and genetic characterization of 15 novel field PEDV variants with large genomic deletions. The sizes of deletion varied between 582 nt (194 aa) and 648 nt (216 aa) at positions 28-714 (10-238) on the S gene (protein). Among 17 PEDV samples isolated from individual pigs, all of them contained at least two distinct genotypes with large genomic deletions, and 94.1% of them were found to consist of strains with an intact S gene. These variants were found in eight primary and nine recurrent outbreaks, and they might be associated with persistent PEDV infection in the farms. Full-length S and ORF3 genes of eight variants derived from 2 samples were characterized. This is the first report of mixed infections caused by various genotypes of PEDV and would be important for the studies of viral isolation, pathogenesis, and molecular epidemiology of the disease.