The complex fecal virome of piglets on a high-density farm

Swine are an important source of proteins worldwide but also subject to numerous zoonotic infections capable of infecting humans. Intensive pig farming conditions may also increase viral transmission facilitating the emergence of novel viral recombinants. We describe here the metagenomics-derived fecal virome in healthy and diarrhetic piglets on a high-density US farm. The majority of translated sequence reads showed similarity to eukaryotic viral proteins. An average of 4.2 different mammalian viruses were excreted by 2-4 weeks old piglets. Ninety-nine % of the viral sequences were related to the small RNA Picornaviridae, Astroviridae and Caliciviridae families while 1% were related to the small DNA Circoviridae, and Parvoviridae families. Previously characterized porcine RNA viruses detected here consisted of kobuviruses, teschoviruses, sapeloviruses, porcine enterovirus B, and sapoviruses. The near full genomes of novel species of astrovirus and bocavirus were also acquired and phylogenetically analyzed. The full genomes of small circular DNA genomes containing a Rep gene and highly divergent members of the picornavirales order were also characterized. The possible protozoan and nematode origin of these two groups of new viruses, based on the presence in these pig parasites of closely related sequences, is discussed. Numerous and highly diverse viruses are therefore shed by piglets raised on a high-density farm. Viral metagenomics surveillance of intensely farmed animals can be used to detect viruses to better evaluate their zoonotic potential.