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Identification of several clades of novel single-stranded circular DNA viruses with conserved stem-loop structures in pig feces

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Abstract

Metagenomic analysis of fecal samples collected from diarrheal swine detected sequences encoding a replication initiator protein (Rep). The genomes of ten novel single-stranded DNA viruses were determined, and they exhibited a similar genome organization. The two putative open reading frames (ORFs) encoding Rep and the capsid protein are bidirectionally transcribed and separated by two intergenic regions. Stem-loop structure(s) typical of genomes that undergo the rolling-circle DNA replication mechanism were observed. Phylogenetically, these ten genomes are in a monophyletic clade with the previously described porcine stool-associated virus (PoSCV) but are divergent enough to be further classified into to six distinct virus clades.

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Acknowledgments

The authors thank Mr. Otis for excellent technical support.

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Virus and Prion Diseases Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, PO Box 70, Ames, IA, 50010, USA

    Andrew K. Cheung & Kelly M. Lager

  2. Blood Systems Research Institute and Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA

    Terry Fei Fan Ng & Eric Delwart

  3. Infectious Bacterial Diseases Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, IA, USA

    David P. Alt

  4. Indiana Animal Disease Diagnostic Laboratory and Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, USA

    Roman M. Pogranichniy

Authors
  1. Andrew K. Cheung
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  2. Terry Fei Fan Ng
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  3. Kelly M. Lager
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  4. David P. Alt
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  5. Eric Delwart
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  6. Roman M. Pogranichniy
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Corresponding author

Correspondence to Andrew K. Cheung.

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Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer.

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Cheung, A.K., Ng, T.F.F., Lager, K.M. et al. Identification of several clades of novel single-stranded circular DNA viruses with conserved stem-loop structures in pig feces. Arch Virol 160, 353–358 (2015). https://doi.org/10.1007/s00705-014-2234-9

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  • DOI: https://doi.org/10.1007/s00705-014-2234-9

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