Abstract
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.
Highlights
Porcine epidemic diarrhea (PED) is a highly contagious enteric disease characterized by vomiting, acute watery diarrhea, and in particular, a high mortality rate in suckling piglets, resulting in substantial economic losses [1]
We report on PED outbreaks with popular prevalence and mixed infection of novel variants characterized by large deletions of the S gene in conjunction with a survey to investigate the origin and identify the heterogeneity among PED virus (PEDV) strains that have been circulating in Japan
PED outbreaks were commonly observed in PED-vaccinated farms, and there was a significant difference in the mortality rate (0–100%) for piglets and durations of diarrhea among PEDV-infected farms
Summary
Porcine epidemic diarrhea (PED) is a highly contagious enteric disease characterized by vomiting, acute watery diarrhea, and in particular, a high mortality rate in suckling piglets, resulting in substantial economic losses [1]. Between 2008 and 2010, new PEDV strains characterized by multiple insertions/deletions or mutations on the spike (S) protein compared with previous endemic strains have been reported in South Korea [5] and China [6, 7]. US-like PEDV strains have been reported in Germany [10], France [11], Belgium [12], South Korea [13], Taiwan [14], and Japan [15]. Three novel PEDV strains with large deletions in the S gene have recently been identified in the US [17], South Korea [18], and Japan [19]
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