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

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.

The enhanced replication of an S-intact PEDV during coinfection with an S1 NTD-del PEDV in piglets

“…This finding suggests that S1 NTD-del PEDV had no replication advantage and was either outcompeted or coexisted with Sintact PEDV in pigs. This conclusion is in agreement with what were observed in the field (Diep et al, 2017;Su et al, 2018). S1 NTD-del PEDV replicated to a lower peak titer in coinfection than that in single virus infection in both Vero cells and IPEC-DQ cells.…”

“…Previously, our laboratory isolated the first S1 NTD-del PEDV strain, PC177, from Vero cell culture (Oka et al, 2014). Recent studies revealed that S1 NTD-del PEDVs naturally evolved in the field and often coinfected pigs with the S-intact PEDV (Suzuki et al, 2015;Diep et al, 2017;Zhang et al, 2018a;Su et al, 2018). The S1 NTD-del PEDV had no tissue tropism change compared with the S-intact PEDV (Suzuki et al, 2016;Hou et al, 2017).…”

“…PEDV variants with a big deletion in the S1-NTD have been designated as S1 NTD-del PEDVs (Hou et al, 2017). They have been detected in field pig samples, indicating sufficient replication of these S1 NTD-del PEDVs in vivo (Suzuki et al, 2015;Diep et al, 2017;Zhang et al, 2018a;Su et al, 2018). Interestingly, most field S1 NTD-del PEDVs exist as a member of coinfection of pigs with the S-intact PEDV (Diep et al, 2017;Su et al, 2018).…”

Appearance of US-like porcine epidemic diarrhoea virus (PEDV) strains before US outbreaks and genetic heterogeneity of PEDVs collected in Northern Vietnam during 2012-2015

“…The PCR conditions were as follows: denaturation at 94°C for 2 min; 35 cycles of denaturation at 98°C for 10 s, annealing at 55°C for 30 s, and extension at 68°C for 2.5 min; and a final extension step at 68°C for 10 min. Then, the PCR products were used as templates for nested PCR to amplify five DNA fragments spanning the entire S gene using five published primer pairs (CS1–CS5) (Diep, Norimine, Sueyoshi, Lan, & Yamaguchi, ). The amplified PCR products were purified using a FastGene Gel/PCR Extraction Kit (NIPPON Genetics Co., Ltd, Japan) according to the manufacturer's protocol.…”

Impact of porcine epidemic diarrhea on herd and individual Berkshire sow productivity

“…In October 2013, however, a PED outbreak was reported in Japan (Okinawa Prefecture) after an interval of 7 years when there were no infestations reported (Sasaki et al, 2016). The epidemic of PED virus infection spread rapidly throughout Japan (Diep et al, 2017) and was also reported in Kagoshima prefecture, which has the largest number of pig farms in Japan. In Kagoshima, a numbers of farms produce pork from Kagoshima Berkshire pigs ('Kagoshima Kurobuta') which is one of the most sought pork brands in Japan.…”