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Prevalence and phylogenetic analysis of porcine diarrhea associated viruses in southern China from 2012 to 2018

机译:2012年至2018年中国南方猪腹泻相关病毒的患病率和系统发育分析

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BACKGROUND:In 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.RESULTS:Porcine 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.CONCLUSIONS:The 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.
机译:背景:在中国,自2010年底以来猪发生了大规模爆发的病毒引起的严重腹泻。为了调查负责爆发的腹泻相关病毒的患病率和遗传演化,共有2987个田间腹泻样品从168次收集2012 - 2018年中国南部五个省份的猪场进行了测试。结果:猪流行性腹泻病毒(PEDV)最常检测到的病毒率在样品中50.21和62.10%之间的患病率和96.43%(162/168)。 , 分别。猪Deltacoronavirus(Pdcov)是第二次普遍存在病毒,其流行率从样品中的19.62%到29.19%,分别在房屋的70.24%(118/168)。传染性胃肠炎病毒(TGEV)和猪轮状病毒(PORV)在样品中的低流行率和10.12%的情况下以低流行率检测到。在这项研究中,我们在中国南方福建省仔猪腹泻样品中鉴定了一种新出现的猪急性腹泻综合征冠状病毒(Sads-Cov),悲伤的患病率为10.29%(7/68)。这些腹泻相关病毒的共同感染是常见的。最常见的共感染PDCOV是Pedv,平均检出率为12.72%(380/2987,范围为8.26-17.3%)。系统发育分析显示,在过去7年期间中国南部循环的Pedvs与基因型IIa的PEDV变异菌株聚集。最常见的突变存在于目前在该领域循环的Pedvs的尖峰基因的胶粘酶当量(CoE)和表位区域中。 Pdcovs的遗传关系与中国,韩国,泰国和老挝公众的那些存在的中国菌株密切相关。结论:本研究的结果表明,变异Pedv,Pdcov和Sads-CoV是领先的病因猪腹泻,以及致病性肠溶COV的单次感染或联合感染在2012 - 2018年中国南部的猪中常见。因此,应对显着的关注有效预防和控制猪病毒腹泻。

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