The Fecal Virome of Pigs on a High-Density Farm

摘要: Swine are an important source of proteins worldwide but subject to frequent viral outbreaks and numerous infections capable infecting humans. Modern farming conditions may also increase transmission potential zoonotic spread. We describe here the metagenomics-derived virome in feces 24 healthy 12 diarrheic piglets on a high-density farm. An average 4.2 different mammalian viruses were shed by piglets, reflecting high level asymptomatic infections. Diarrheic pigs 5.4 viruses. Ninety-nine percent sequences related RNA virus families Picornaviridae, Astroviridae, Coronaviridae, Caliciviridae, while 1% small DNA Circoviridae, Parvoviridae. Porcine identified, order decreasing number sequence reads, consisted kobuviruses, astroviruses, enteroviruses, sapoviruses, sapeloviruses, coronaviruses, bocaviruses, teschoviruses. The near-full genomes multiple novel species porcine astroviruses bocaviruses generated phylogenetically analyzed. Multiple circular encoding replicase plus two highly divergent members Picornavirales characterized. possible origin these from pig-infecting protozoans nematodes, based closest similarities, is discussed. In summary, unbiased survey intensely farmed animals revealed coinfections with diverse set providing favorable for recombination. Viral surveys can readily document circulation known new viruses, facilitating detection emerging prospective evaluation their pathogenic potentials.