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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.

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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.

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All authors declare that there is no conflict of interest.

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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.

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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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