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The fecal virome of South and Central American children with diarrhea includes small circular DNA viral genomes of unknown origin

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Abstract

Viral metagenomics of feces collected from 58 Peruvian children with unexplained diarrhea revealed several small circular ssDNA genomes. Two genomes related to sequences previously reported in feces from chimpanzees and other mammals and recently named smacoviruses were characterized and then detected by PCR in 1.7 % (1/58) and 19 % (11/58) of diarrheal samples, respectively. Another three genomes from a distinct small circular ssDNA viral group provisionally called pecoviruses encoded Cap and Rep proteins with <35 % identity to those in related genomes reported in human, seal, porcine and dromedary feces. Pecovirus DNA was detected in 15.5 % (9/58), 5.9 % (3/51) and 3 % (3/100) of fecal samples from unexplained diarrhea in Peru, Nicaragua and Chile, respectively. Feces containing these ssDNA genomes also contained known human enteric viral pathogens. The cellular origins of these circular ssDNA viruses, whether human cells, ingested plants, animals or fungal foods, or residents of the gut microbiome, are currently unknown.

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Acknowledgements

We acknowledge NHLBI Grant R01 HL105770 to E.L.D and the Blood Systems Research Institute for support. A.C.C. was supported by Sao Paulo Research Foundation (FAPESP), Grant numbers 2014/05211-2 and 2012/03417-7.

Author information

Authors and Affiliations

  1. Blood Systems Research Institute, San Francisco, CA, 94118, USA

    Tung Gia Phan, Antonio Charlys da Costa, Xutao Deng & Eric Delwart

  2. Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA

    Tung Gia Phan & Eric Delwart

  3. Institute of Tropical Medicine, School of Medicine, University of São Paulo, São Paulo, Brazil

    Antonio Charlys da Costa

  4. Faculty of Health Sciences, School of Medicine, Universidad Peruana de Ciencias Aplicadas-UPC, Lima, Peru

    Juana del Valle Mendoza

  5. Instituto de Investigación Nutricional, Lima, Peru

    Juana del Valle Mendoza

  6. Department of Microbiology, University of León, León, Nicaragua

    Filemon Bucardo-Rivera

  7. Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden

    Johan Nordgren

  8. Microbiology and Mycology Program, Faculty of Medicine, University of Chile, Santiago, Chile

    Miguel O’Ryan

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  1. Tung Gia Phan
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Corresponding author

Correspondence to Eric Delwart.

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Funding

This study was funded by NHLBI Grant R01 HL105770 to E.L.D and by Sao Paulo Research Foundation (FAPESP) Grant numbers 2014/05211-2 and 2012/03417-7 to A.C.C.

Conflict of interest

All authors declare that there is no conflict of interest.

Ethical approval

All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

Informed consent

Pre-existing and anonymized clinical samples were used.

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Phan, T.G., da Costa, A.C., del Valle Mendoza, J. et al. The fecal virome of South and Central American children with diarrhea includes small circular DNA viral genomes of unknown origin. Arch Virol 161, 959–966 (2016). https://doi.org/10.1007/s00705-016-2756-4

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  • DOI: https://doi.org/10.1007/s00705-016-2756-4

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