Abstract
BackgroundIn China, large-scale outbreaks of severe diarrhea caused by viruses have occurred in pigs since late 2010. To investigate the prevalence and genetic evolution of diarrhea-associated viruses responsible for the outbreaks, a total of 2987 field diarrheal samples collected from 168 pig farms in five provinces in Southern China during 2012–2018 were tested.ResultsPorcine epidemic diarrhea virus (PEDV) was most frequently detected virus with prevalence rates between 50.21 and 62.10% in samples, and 96.43% (162/168) in premises, respectively. Porcine deltacoronavirus (PDCoV) was the second prevalent virus with prevalence rates ranging from 19.62 to 29.19% in samples, and 70.24% (118/168) in premises, respectively. Both transmissible gastroenteritis virus (TGEV) and porcine rotavirus (PoRV) were detected at low prevalence rates of < 3% in samples and 10.12% in premises. In this study, we identified a newly emerged swine acute diarrhea syndrome coronavirus (SADS-CoV) in diarrheal samples of piglets from Fujian province in Southern China, and the prevalence rate of SADS-CoV was 10.29% (7/68). Co-infections of these diarrhea-associated viruses were common. The most frequent co-infection was PEDV with PDCoV, with an average detection rate of 12.72% (380/2987, ranging from 8.26–17.33%). Phylogenetic analysis revealed that PEDVs circulating in Southern China during the last 7 years were clustered with the variant strains of PEDV in genotype IIa. The most frequent mutations were present in the collagenase equivalent (COE) and epitope regions of the spike gene of the PEDVs currently circulating in the field. Genetic relationships of PDCoVs were closely related with Chinese strains, other than those present in the USA, South Korea, Thailand and Lao’s public.ConclusionsThe findings of this study indicated that variant PEDV, PDCoV, and SADS-CoV were leading etiologic agents of porcine diarrhea, and either mono-infections or co-infections of pathogenic enteric CoVs were common in pigs in Southern China during 2012–2018. Thus, significant attention should be paid in order to effectively prevent and control porcine viral diarrhea.
Highlights
In China, large-scale outbreaks of severe diarrhea caused by viruses have occurred in pigs since late 2010
We investigated the prevalence of five major porcine diarrhea-associated viruses, including porcine epidemic diarrhea virus (PEDV), porcine deltacoronavirus (PDCoV), transmissible gastroenteritis virus (TGEV), porcine rotavirus (PoRV) and SADS-CoV from diarrheal samples of pigs collected from 2012 to 2018 from five provinces (Jiangxi, Zhejiang, Fujian, Guangdong, and Hunan) in Southern China
Prevalence of PEDV, PDCoV, TGEV, PoRV and SADS-CoV A total of 2987 specimens sampled in 168 pig farms from five provinces in Southern China from 2012 to 2018 were tested in this study
Summary
In China, large-scale outbreaks of severe diarrhea caused by viruses have occurred in pigs since late 2010. Enteropathogenic viruses, including porcine epidemic diarrhea virus (PEDV), porcine deltacoronavirus (PDCoV), transmissible gastroenteritis virus (TGEV), and porcine rotavirus (PoRV) are causative agents for viral diarrhea in pigs [2]. Data from previous studies demonstrate that in recent years, highly virulent variant PEDV is the most common etiological pathogen responsible for porcine diarrhea in China. Porcine epidemic diarrhea (PED), caused by PEDV, was first recognized as transmissible gastroenteritis (TGE)-like diarrhea in pigs in Shanghai, China, in 1973. Since late 2010, variant strains of PEDV have emerged in China, and rapidly spread throughout the country [4, 5]. Thereafter, diarrhea outbreaks caused by variant PEDVs appeared in other Asian countries (Thailand, South Korea, Vietnam, and Philippines) [11,12,13,14], America (Canada, Mexico, etc) [15, 16], and European countries (Austria, Ukraine, Belgium, Germany, etc) [17, 18]
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