The Fecal Virome of Pigs on a High-Density Farm
The Fecal Virome of Pigs on a High-Density Farm
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DOI：
10.1128/jvi.05217-11
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发表时间：
2011-11-01
影响因子：
5.4
通讯作者：
Delwart, Eric
中科院分区：
文献类型：
--
作者：
Shan, Tongling;Li, Linlin;Delwart, Eric
猪是世界范围内蛋白质的重要来源，但经常发生病毒爆发和许多能够感染人类的感染。现代农业条件也可能增加病毒传播和潜在的人畜共患病传播。我们在这里描述的宏基因组学衍生的病毒组在24个健康和12个高密度的猪场仔猪粪便中。健康仔猪平均散发4.2种不同的哺乳动物病毒，反映了高水平的无症状感染。腹泻的猪平均排出5.4种不同的哺乳动物病毒。99%的病毒序列与RNA病毒科小核糖核酸病毒科、星状病毒科、冠状病毒科和杯状病毒科相关，而1%与小DNA病毒科圆环病毒科和细小病毒科相关。鉴定的猪RNA病毒，按照序列读数数量递减的顺序，包括kobuvirus、星状病毒、肠道病毒、sapoviruses、sapeloviruses、冠状病毒、博卡病毒和捷申病毒。产生了猪星状病毒和博卡病毒的多个新物种的近全基因组，并对其进行了遗传学分析。多个小的环状DNA基因组编码复制酶蛋白加上两个高度不同的成员的小核糖核酸病毒目也进行了表征。根据最接近的序列相似性，这些病毒基因组可能来自猪感染的原生动物和线虫，进行了讨论。总之，对密集养殖动物粪便中病毒的无偏倚调查显示，与高度多样化的病毒组频繁合并感染，为病毒重组提供了有利条件。动物病毒调查可以很容易地记录已知病毒和新病毒的传播，便于检测新出现的病毒，并对其致病性和人畜共患病潜力进行前瞻性评估。
Swine are an important source of proteins worldwide but are subject to frequent viral outbreaks and numerous infections capable of infecting humans. Modern farming conditions may also increase viral transmission and potential zoonotic spread. We describe here the metagenomics-derived virome in the feces of 24 healthy and 12 diarrheic piglets on a high-density farm. An average of 4.2 different mammalian viruses were shed by healthy piglets, reflecting a high level of asymptomatic infections. Diarrheic pigs shed an average of 5.4 different mammalian viruses. Ninety-nine percent of the viral sequences were related to the RNA virus families Picornaviridae, Astroviridae, Coronaviridae, and Caliciviridae, while 1% were related to the small DNA virus families Circoviridae, and Parvoviridae. Porcine RNA viruses identified, in order of decreasing number of sequence reads, consisted of kobuviruses, astroviruses, enteroviruses, sapoviruses, sapeloviruses, coronaviruses, bocaviruses, and teschoviruses. The near-full genomes of multiple novel species of porcine astroviruses and bocaviruses were generated and phylogenetically analyzed. Multiple small circular DNA genomes encoding replicase proteins plus two highly divergent members of the Picornavirales order were also characterized. The possible origin of these viral genomes from pig-infecting protozoans and nematodes, based on closest sequence similarities, is discussed. In summary, an unbiased survey of viruses in the feces of intensely farmed animals revealed frequent coinfections with a highly diverse set of viruses providing favorable conditions for viral recombination. Viral surveys of animals can readily document the circulation of known and new viruses, facilitating the detection of emerging viruses and prospective evaluation of their pathogenic and zoonotic potentials.