Genetic characteristics of porcine epidemic diarrhea virus in Chinese mainland, revealing genetic markers of classical and variant virulent parental/attenuated strains

Gene ◽  
2016 ◽  
Vol 588 (1) ◽  
pp. 95-102 ◽  
Author(s):  
Fangzhou Chen ◽  
Xugang Ku ◽  
Zhonghua Li ◽  
Atta Muhammad Memon ◽  
Shiyi Ye ◽  
...  
Keyword(s):  
Genetic Markers ◽  
Porcine Epidemic Diarrhea Virus ◽  
Chinese Mainland ◽  
Genetic Characteristics ◽  
Diarrhea Virus ◽  
Porcine Epidemic Diarrhea

scholarly journals Molecular Characteristics and Pathogenicity of Porcine Epidemic Diarrhea Virus Isolated in Some Areas of China in 2015–2018

2020 ◽  
Vol 7 ◽  
Author(s):  
Linyang Yu ◽  
Yanling Liu ◽  
Shuangyun Wang ◽  
Leyi Zhang ◽  
Pengshuai Liang ◽  
...  
Keyword(s):  
Porcine Epidemic Diarrhea Virus ◽  
Vero Cells ◽  
Economic Losses ◽  
Molecular Characteristics ◽  
Phylogenetic Tree Analysis ◽  
Genetic Characteristics ◽  
Diarrhea Virus ◽  
Severe Diarrhea ◽  
Positive Rate ◽  
Porcine Epidemic Diarrhea

Since 2010, Porcine epidemic diarrhea virus (PEDV) has caused severe diarrhea disease in piglets in China, resulting in large economic losses. To understand the genetic characteristics of the PEDV strains that circulated in some provinces of China between 2015 and 2018, 375 samples of feces and small intestine were collected from pigs and tested. One hundred seventy-seven samples tested positive and the PEDV-positive rate was 47.20%. A phylogenetic tree analysis based on the entire S gene showed that these strains clustered into four subgroups, GI-a, GI-b, GII-a, and GII-b, and that the GII-b strains have become dominant in recent years. Compared with previous strains, these strains have multiple variations in the SP and S1-NTD domains and in the neutralizing epitopes of the S protein. We also successfully isolated and identified a new virulent GII-b strain, GDgh16, which is well-adapted to Vero cells and caused a high mortality rate in piglets in challenge experiments. Our study clarifies the genetic characteristics of the prevalent PEDV strains in parts of China, and suggests that the development of effective novel vaccines is both necessary and urgent.

Porcine epidemic diarrhea virus recombinant and its genetic characteristics

2019 ◽  
Vol 22 (07) ◽  
pp. 21-27
Author(s):  
M.V. Nefedeva ◽  
◽  
I.A. Titov ◽  
A.S. Malogolovkin ◽  
◽  
...  
Keyword(s):  
Porcine Epidemic Diarrhea Virus ◽  
Genetic Characteristics ◽  
Diarrhea Virus ◽  
Virus Recombinant ◽  
Porcine Epidemic Diarrhea

scholarly journals Molecular characteristics and pathogenicity of porcine epidemic diarrhea virus in some areas of China from 2015 to 2018

2020 ◽  
Author(s):  
Linyang Yu ◽  
Jianguo Dong ◽  
Shuangyun Wang ◽  
Yanling Liu ◽  
Leyi Zhang ◽  
...  
Keyword(s):  
Small Intestine ◽  
Phylogenetic Tree ◽  
Porcine Epidemic Diarrhea Virus ◽  
Evolutionary Relationship ◽  
Vero Cells ◽  
Economic Losses ◽  
Molecular Characteristics ◽  
Genetic Characteristics ◽  
Diarrhea Virus ◽  
Porcine Epidemic Diarrhea

Abstract Background Since 2010, porcine epidemic diarrhea virus (PEDV) has caused severe diarrhea disease in piglets, which has led to large economic losses in China. To understand the genetic characteristics of PEDV strains that have been circulating in some provinces of China from 2015 to 2018, 362 feces and small intestine samples in pigs were collected and tested. Methods The S gene of PEDV in collected samples were amplified by RT-PCR. A phylogenetic tree was constructed using MEGA6.0 software with the neighbor-joining method to analyze the evolutionary relationship. Nucleotide and deduced amino acid (AA) sequences of S were aligned using the MegAlign program of DNASTAR7.1 software to determine sequence homology. PEDV GDgh16 strain isolation, IFA identification and titer detection were performed in Vero cells. Six 4-day-old healthy colostrum deprived suckling piglets were used for challenging experiment of PEDV GDgh16 strain. Virus copies from the small intestine were detected by RT-qPCR. The other section was stained with the anti-N protein McAb at 1:1000 dilution for immunohistochemical (IHC) examinations. Results The results showed that 160 samples tested positive and the PEDV-positive prevalence was 44.20%. Phylogenetic tree analysis of entire S genes showed that these strains were clustered into four subgroups, G1-b, G1-c, G2-a and G2-b, and that the G2-b strains had become dominant in recent years. Compared with previous strains, these strains had multiple variations in the SP and S1-NTD domains and in the neutralizing epitope of the S protein. Furthermore, we successfully isolated and identified a new virulent G2-b strain, GDgh16, which was well adapted to Vero cells and had a high mortality rate in piglets through challenge experiments. Conclusions Our study provides full insights into the genetic characteristics of prevalent PEDV strains in parts of China, suggesting that the development of novel effective vaccines is necessary and urgent.

scholarly journals Isolation and evolutionary analyses of porcine epidemic diarrhea virus in Asia

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10114
Author(s):  
Wan Liang ◽  
Danna Zhou ◽  
Chao Geng ◽  
Keli Yang ◽  
Zhengying Duan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Porcine Epidemic Diarrhea Virus ◽  
Virus Isolation ◽  
Vaccine Development ◽  
Evolutionary Analysis ◽  
Genetic Characteristics ◽  
S Protein ◽  
Diarrhea Virus ◽  
Comparative Genomics Analysis ◽  
Porcine Epidemic Diarrhea

Porcine epidemic diarrhea virus (PEDV) is a leading cause of diarrhea in pigs worldwide. Virus isolation and genetic evolutionary analysis allow investigations into the prevalence of epidemic strains and provide data for the clinical diagnosis and vaccine development. In this study, we investigated the genetic characteristics of PEDV circulation in Asia through virus isolation and comparative genomics analysis. APEDV strain designated HB2018 was isolated from a pig in a farm experiencing a diarrhea outbreak. The complete genome sequence of HB2018 was 28,138 bp in length. Phylogenetic analysis of HB2018 and 207 PEDVs in Asia showed that most PEDV strains circulating in Asia after 2010 belong to genotype GII, particularly GII-a. The PEDV vaccine strain CV777 belonged to GI, and thus, unmatched genotypes between CV777 and GII-a variants might partially explain incomplete protection by the CV777-derived vaccine against PEDV variants in China. In addition, we found the S protein of variant strains contained numerous mutations compared to the S protein of CV777, and these mutations occurred in the N-terminal domain of the S protein. These mutations may influence the antigenicity, pathogenicity, and neutralization properties of the variant strains.

scholarly journals Genetic characterization and phylogenetic analysis of porcine epidemic diarrhea virus in Guangdong, China, between 2018 and 2019

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0253622
Author(s):  
Feng Wen ◽  
Jing Yang ◽  
Anqi Li ◽  
Zhonggui Gong ◽  
Lulu Yang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Porcine Epidemic Diarrhea Virus ◽  
Southern China ◽  
Guangdong Province ◽  
Clinical Samples ◽  
Transmissible Gastroenteritis Virus ◽  
Genetic Characteristics ◽  
Common Amino Acid ◽  
Diarrhea Virus ◽  
Porcine Epidemic Diarrhea

Porcine epidemic diarrhea virus (PEDV), a leading cause of piglet diarrhea outbreaks, poses a significant danger to the swine industry. The aim of this study was to investigate the epidemic characteristics of PEDV that was circulating in Guangdong province, one of China’s major pig producing provinces. Clinical samples were collected from eight pig farms in Guangdong province between 2018 and 2019 and tested for the major porcine enteric pathogens, including PEDV, transmissible gastroenteritis virus (TGEV), Swine enteric coronavirus (SeCoV), Swine acute diarrhea syndrome coronavirus (SADS-CoV), porcine deltacoronavirus (PDCoV), and porcine rotavirus (RV). As a result, only PEDV and RV were detected at a rate of 47.0% (16/34) and 18.6% (8/34), respectively. Coinfectoin with PEDV and RV occurred at a rate of PEDV 12.5% (2/16). Subsequently, the full-length S gene sequences of 13 PEDV strains were obtained, and phylogenetic analysis suggested the presence of GII-c group PEDV strains in this region (non-S-INDEL). Two novel common amino acid insertions (55T/IG56 and 551L) and one novel glycosylation site (1199G+) were detected when the CV777 and ZJ08 vaccine strains were compared. Furthermore, intragroup recombination events in the S gene regions 51–548 and 2478–4208 were observed in the PEDV strains studied. In summary, the observations provide current information on the incidence of viral agents causing swine diarrhea in southern China and detailed the genetic characteristics and evolutionary history of the dominant PEDV field strains. Our findings will aid in the development of an updated vaccine for the prevention and control of PEDV variant strains.

scholarly journals Origin, Evolution, and Virulence of Porcine Deltacoronaviruses in the United States

mBio ◽  
2015 ◽  
Vol 6 (2) ◽  
Author(s):  
Yuanmei Ma ◽  
Yu Zhang ◽  
Xueya Liang ◽  
Fangfei Lou ◽  
Michael Oglesbee ◽  
...  
Keyword(s):  
United States ◽  
Porcine Epidemic Diarrhea Virus ◽  
Clinical Signs ◽  
The United States ◽  
Immune Serum ◽  
Watery Diarrhea ◽  
Economic Losses ◽  
Genetic Characteristics ◽  
Diarrhea Virus ◽  
Porcine Epidemic Diarrhea

ABSTRACTA novel porcine deltacoronavirus (PdCV) was first discovered in Ohio and Indiana in February 2014, rapidly spread to other states in the United States and Canada, and caused significant economic loss in the swine industry. The origin and virulence of this novel porcine coronavirus are not known. Here, we characterized U.S. PdCV isolates and determined their virulence in gnotobiotic and conventional piglets. Genome analyses revealed that U.S. PdCV isolates possess unique genetic characteristics and share a close relationship with Hong Kong and South Korean PdCV strains and coronaviruses (CoVs) of Asian leopard cats and Chinese ferret-badgers. The PdCV-positive intestinal content (Ohio CVM1) and the cell culture-adapted PdCV Michigan (MI) strain were orally inoculated into gnotobiotic and/or conventional piglets. Within 1 to 3 days postinfection, profuse watery diarrhea, vomiting, and dehydration were observed. Clinical signs were associated with epithelial necrosis in the gastric pits and small intestine, the latter resulting in severe villous atrophy. Mild interstitial pneumonia was identified in the lungs of PdCV-infected piglets. High levels of viral RNA (8 to 11 log RNA copies/g) were detected in intestinal tissues/luminal contents and feces of infected piglets, whereas moderate RNA levels (2 to 5 log RNA copies/g) were detected in blood, lung, liver, and kidney, indicating multisystemic dissemination of the virus. Polyclonal immune serum against PdCV but not immune serum against porcine epidemic diarrhea virus (PEDV) reacted with PdCV-infected small-intestinal epithelial cells, indicating that PdCV is antigenically distinct from PEDV. Collectively, we demonstrate for the first time that PdCV caused severe gastrointestinal diseases in swine.IMPORTANCEPorcine coronaviruses (CoVs) are major viral infectious diseases of swine. Examples of porcine CoVs include porcine transmissible gastroenteritis coronavirus (TGEV), porcine epidemic diarrhea virus (PEDV), and porcine respiratory coronavirus (PRCV). In February 2014, another porcine CoV, porcine deltacoronavirus (PdCV), emerged in Ohio and Indiana and subsequently spread rapidly across the United States and Canada,causing significant economic losses. Here, we report the detailed genetic characterization, phylogeny, and virulence of emergent PdCV strains in the United States. We found that PdCV caused severe diarrhea, vomiting, and dehydration in gnotobiotic and conventional piglets, signs that were clinically indistinguishable from those caused by PEDV and TGEV. In addition to extensive intestinal lesions, PdCV caused significant lesions in the stomach and mild pulmonary lesions that have not been reported for TGEV and PEDV. The finding that PdCV is a significant enteric disease of swine highlights the need to develop effective measures to control this disease.

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