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ARS Home » Midwest Area » Ames, Iowa » National Animal Disease Center » Virus and Prion Research » Research » Publications at this Location » Publication #305783
Title: Identification of eight clades of novel single-stranded circular DNA viruses in pig feces

Author
item Cheung, Andrew
item NG, TERRY FEI FAN - University Of California
item Lager, Kelly
item Alt, David
item DELWART, ERIC - University Of California
item POGRANICHNIY, ROMAN - Purdue University

Submitted to: Proceedings of the International Conference on Emerging Infectious Diseases
Publication Type: Abstract Only
Publication Acceptance Date: 8/15/2014
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Background: Because of the serious shortage of organs from human donors, xenotransplantation has become a valuable alternative. Provided that the genetic incompatibility is overcome, pig organs are considered a good match in size and shape for their human counterparts. However, unknown pathogens, including viruses not harmful in the animal, may pose risks to the organ recipient. Objective: Identification of the circular replication initiator protein (Rep)-encoding single-stranded DNA (CRESS-DNA) viruses in swine feces. Methods: The chimpanzee stool-associated circular viruses (ChiSCV)-related nucleotide sequences identified using viral pyrosequencing were used to design primers for PCR. DNA amplification employing converging primers were used to confirm the presence of contig sequences in the sample and diverging primers to amplify and clone the complete circular viral genomes. The Rep-related sequences were aligned by MAFFT and used to generate a Bayesian interference phylogenetic tree. Results: Metagenomic analysis of fecal samples collected from diarrheal swine was conducted. Complete nucleotide sequences of 18 novel genomes were cloned and determined. Each genome encodes two putative major open reading frames (ORFs): ORF1 encodes a Rep involved in rolling-circle DNA replication and ORF2 encodes a capsid protein. Thus, these new viruses belong to the group of CRESS-DNA genomes, which includes Circoviridae, Gemininviridae, Nanoviridae and other unclassified circular genomes. In this study, phylogenetic analysis revealed that sixteen genomes are in a monophyletic clade with porcine stool-associated virus (PoSCV) previously described, but are divergent enough to be further classified into to six distinct virus clades. One virus shares Rep homology with fur seal stool-associated virus and the other belongs to a unique clade with no known counterparts. Conclusion: The development of metagenomics has revolutionized virus discovery leading to the identification of many new viruses. The impact of this technology is exemplified by the breadth of CRESS-DNA viruses detected in a diverse range of organisms including swine. This work showed that the fecal virome of swine exhibits a very diverse set of viruses.