贵州省健康仔猪病毒宏基因组学研究

Viral Metagenomic Analysis of Piglets in Guizhou Province

为了初步了解贵州省规模化猪场健康仔猪携带病毒的病原本底,在贵州4个猪场采集了151头健康仔猪的咽拭子和肛拭子。病毒宏基因组学分析显示这些仔猪共携带25个科的病毒,包括噬菌体、昆虫病毒、脊椎动物病毒等。在脊椎动物相关的病毒科中,其中4个猪场共同存在星状病毒、冠状病毒、微小核糖核酸病毒等11个病毒科。此外,在每个猪场中,疱疹病毒、黄病毒在咽拭子中的reads数均大于肛拭子中的reads数;数圆环病毒、呼肠弧病毒、微小核糖核酸病毒、星状病毒、冠状病毒在肛拭子中的reads数均大于咽拭子中的reads数,提示这些病毒的组织嗜性。对猪瘟病毒、类圆环病毒、博卡细小病毒、星状病毒、萨佩罗病毒的contigs进行进化分析,结果发现星状病毒具有丰富的遗传多样性,而其他病毒与各自参考毒株进化关系较近;猪类圆环病毒与牛类圆环病毒核苷酸同源性很高,提示存在跨种传播或基因重组。对突隆病毒进行了检测,发现其广泛分布于4个猪场健康仔猪的咽拭子和肛拭子,阳性率为75%-100%。研究为健康仔猪携带病毒的多样性和本底情况提供了重要的基础数据。

In order to preliminarily understand the background of viral pathogens in large-scale pig farms in China,we collected pharynx and anal swabs from 151 healthy piglets at four sites in Guizhou province.Viral metagenomic analysis revealed 25 viral families,including those infecting vertebrate,plants,insects and bacteria.Of the vertebrate related virus families,eleven virus families are common to four pig farms,including Astroviridae,Coronaviridae,Picornaviridae,Picobirnaviridae,Retroviridae,Reoviridae,Anelloviridae,Circoviridae,Parvoviridae and Herpesviridae.In addition,the number of reads from Herpesviridae and Flaviviridae in pharynx swabs were higher than that from anal swabs in each pig farm,while the number of reads of Circoviridae,Reoviridae,Picornaviridae,Astroviridae and Coronaviridae from anal swabs were higher than that from pharynx swabs,suggesting different organ tropisom of these viruses.Contigs of CSFV,Po-Circo-like virus,porcine bocavirus,astrovirus and sapelovirus were phylogenetically analyzed.Results showed that the astrovirus was widely distributed and had rich genetic diversity.The other viruses were closely related to their reference strains.PoCirco-like virus has high homology with Bo-Circo-like virus,suggesting that cross-host transmission or recombination.PCR was performed to detect torovirus,which was found to be widely distributed in pharynx and anal swabs of healthy piglets in four pig farms,with positive rate range of 75%-100%.This study provides important basic data for the diversity and background of virus in healthy piglets.