Epidemiological survey of porcine epidemic diarrhea virus in swine farms in Shanghai, China

Ge, Fei-Fei; Yang, De-Quan; Ju, Huiming; Wang, Jian; Liu, Jian; Liu, Peihong; Zhou, Jinlin

doi:10.1007/s00705-013-1722-7

Cited by 29 publications

(20 citation statements)

References 10 publications

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“…Based on the rates of infection documented in our work, it revealed that PEDV (78.25%) was still the primary cause of the porcine diarrhoea, which is consistent with previous studies that PEDV has been considered to be the major pathogen responsible for the porcine diarrhoea epidemic in China since 2010 (Ge et al., ; Sun et al., ; Zhao et al., ). Except PEDV, SADS‐CoV had the second high infection rate (43.53%), which exhibits an evidently prevailing tendency in pigs.…”

Section: Discussionsupporting

confidence: 91%

Retrospective detection and phylogenetic analysis of swine acute diarrhoea syndrome coronavirus in pigs in southern China

Zhou

Sun

Lan

et al. 2019

Transbound Emerg Dis

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Swine acute diarrhea syndrome coronavirus (SADS-CoV), a novel coronavirus, was first discovered in southern China in January 2017 and caused a large scale outbreak of fatal diarrheal disease in piglets. Here, we conducted a retrospective investigation of 236 samples from 45 swine farms with a clinical history of diarrheal disease to evaluate the emergence and the distribution of SADS-CoV in pigs in China. Our results suggest that SADS-CoV has emerged in China at least since August 2016. Meanwhile, we detected a prevalence of SADS-CoV (43.53%), porcine deltacoronavirus (8.83%), porcine epidemic diarrhea virus (PEDV) (78.25%), rotavirus (21.77%) and transmissible gastroenteritis virus (0%), and we also found the co-infection of SADS-CoV and PEDV occurred most frequently with the rate of 17.65%. We screened and obtained two new complete genomes, five N and five S genes of SADS-CoV. Phylogenetic analysis based on these sequences revealed that all SADS-CoV sequences in this study clustered with previously reported SADS-CoV strains to formed a well defined branch that grouped with the bat coronavirus HKU2 strains. This study is the first retrospective investigation for SADS-CoV and provides the epidemiological information of this new virus in China, which highlights the urgency to develop effective measures to control SADS-CoV. This article is protected by copyright. All rights reserved.

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Section: Discussionsupporting

confidence: 91%

Retrospective detection and phylogenetic analysis of swine acute diarrhoea syndrome coronavirus in pigs in southern China

Zhou

Sun

Lan

et al. 2019

Transbound Emerg Dis

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“…Porcine diarrhea can be caused by PEDV, TGEV, and PRoV, but PEDV was the pathogen responsible for a porcine diarrhea epidemic in China in 2010 (Chen et al, , 2013bGao et al, 2013;Ge et al, 2013;Li et al, 2012;Sun et al, 2012), that resulted in major economic losses in the swine industry. Th e prevalence of PKV ranges from 19.3-99.0% in diff erent countries (Wang et al, 2011), and it can infect pigs of all ages and varieties.…”

Section: Discussionmentioning

confidence: 99%

The rate of co-infection for piglet diarrhea viruses in China and the genetic characterization of porcine epidemic diarrhea virus and porcine kobuvirus

Zp¹,

Yang²,

Wd³

et al. 2016

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Summary. -Piglet diarrhea epidemics result in major economic losses for the swine industry. Four viruses are closely linked to porcine diarrhea: porcine kobuvirus (PKV), porcine epidemic diarrhea virus (PEDV), porcine transmissible gastroenteritis virus (TGEV), and porcine rotavirus (PRoV). We have conducted an epidemiology study to determine the frequency of infection and co-infection with these viruses in China, and characterized the genetic variation of the isolated PEDV and PKV strains. Stool and intestinal samples (n = 314) were collected from piglets with diarrhea in China from years 2012 to 2014. RT-PCR was used to detect PKV, PEDV, TGEV, and PRoV. Phylogenetic relationships between reference strains and the isolated PEDV and PKV strains were determined based on the M and 3D gene sequence. Th e rates of infection with PKV, PEDV, TGEV and PRoV were 29.9%, 24.2%, 1.91%, and 0.31%, respectively. Co-infections with PKV and the other three viruses were very common. Co-infection of PKV and PEDV was detected in 15.0% (47/314) of the samples. Phylogenetic analysis of the PKV 3D gene indicated that there were some phylogenetic diff erences in the PKV strains across regions within China. However, according to the PEDV M gene, strains clustered into three groups and the primary group was distinct from the vaccine strain CV777. Th is study provides insights in to the prevalence of diarrhea viruses and their prevention and control in China.Keywords: porcine diarrhea viruses; co-infection; porcine kobuvirus; porcine epidemic diarrhea virus; porcine gastroenteritis; porcine rotavirus * Corresponding authors: E-mail: wenjiejin1@163.com, aijian@ yzu.edu.cn; phone: +8613815809571.# Th ese authors contributed equally to this work. Abbreviations: PKV = porcine kobuvirus; PEDV = porcine epidemic diarrhea virus; TGEV = porcine transmissible gastroenteritis virus; ProV = porcine rotavirus

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“…Thus, the S glycoprotein is often used as an important viral component to understand the genetic relationships of different PEDV strains and the epidemiological status of PEDV in the field . Nevertheless, the high variability of other genes including ORF3, E, M or N protein has been previously utilized for phylogenetic inference (Chen et al, 2013a;Ge et al, 2013;Kubota et al, 1999;Pan et al, 2012;Temeeyasen et al, 2014;Yang et al, 2013). In order to get better phylogenetic resolution, several studies used PEDV full genome sequences for analysis Pan et al, 2012;Sun et al, 2015;; however, sequencing the full genome is expensive from a laboratory perspective and also limits the rapid characterization of novel PEDV strains.…”

Section: Introductionmentioning

confidence: 99%

Evolutionary characterization of the emerging porcine epidemic diarrhea virus worldwide and 2014 epidemic in Taiwan

Sung

Deng

Chung

et al. 2015

Infection, Genetics and Evolution

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Since 2010, a new variant of PEDV belonging to Genogroup 2 has been transmitting in China and further spreading to the Unites States and other Asian countries including Taiwan. In order to characterize in detail the temporal and geographic relationships among PEDV strains, the present study systematically evaluated the evolutionary patterns and phylogenetic resolution in each gene of the whole PEDV genome in order to determine which regions provided the maximal interpretative power. The result was further applied to identify the origin of PEDV that caused the 2014 epidemic in Taiwan. Thirty-four full genome sequences were downloaded from GenBank and divided into three non-mutually exclusive groups, namely, worldwide, Genogroup 2 and China, to cover different ranges of secular and spatial trends. Each dataset was then divided into different alignments by different genes for likelihood mapping and phylogenetic analysis. Our study suggested that both nsp3 and S genes contained the highest phylogenetic signal with substitution rate and phylogenetic topology similar to those obtained from the complete genome. Furthermore, the proportion of nodes with high posterior support (posterior probability >0.8) was similar between nsp3 and S genes. The nsp3 gene sequences from three clinical samples of swine with PEDV infections were aligned with other strains available from GenBank and the results suggested that the virus responsible for the 2014 PEDV outbreak in Taiwan clustered together with Clade I from the US within Genogroup 2. In conclusion, the current study identified the nsp3 gene as an alternative marker for a rapid and unequivocal classification of the circulating PEDV strains which provides complementary information to the S gene in identifying the emergence of epidemic strain resulting from recombination.

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Epidemiological survey of porcine epidemic diarrhea virus in swine farms in Shanghai, China

Cited by 29 publications

References 10 publications

Retrospective detection and phylogenetic analysis of swine acute diarrhoea syndrome coronavirus in pigs in southern China

Retrospective detection and phylogenetic analysis of swine acute diarrhoea syndrome coronavirus in pigs in southern China

The rate of co-infection for piglet diarrhea viruses in China and the genetic characterization of porcine epidemic diarrhea virus and porcine kobuvirus

Evolutionary characterization of the emerging porcine epidemic diarrhea virus worldwide and 2014 epidemic in Taiwan

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