Small circular single stranded DNA viral genomes in unexplained cases of human encephalitis, diarrhea, and in untreated sewage

Phan TG 1 , Mori D 2 , Deng X 3 , Rajindrajith S 4 , Ranawaka U 5 , Fan Ng TF 1 Show all authors , Bucardo-Rivera F 6 , Orlandi P 7 , Ahmed K 8 , Delwart E 9

Affiliations 

  • 1 Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA
  • 2 Department of Microbiology, Faculty of Medicine, Oita University, Yufu 879-5593, Japan
  • 3 Blood Systems Research Institute, San Francisco, CA 94118, USA
  • 4 Department of Pediatrics, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
  • 5 Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka
  • 6 Department of Microbiology, University of Leon, Nicaragua
  • 7 Oswaldo Cruz Foundation, Manaus, Brazil
  • 8 Department of Microbiology, Faculty of Medicine, Oita University, Yufu 879-5593, Japan; Research Promotion Institute, Oita University, Yufu 879-5593, Oita, Japan; Department of Pathobiology and Medical Diagnostics, Faculty of Medicine, Universiti Malaysia Sabah, 88400 Kota Kinabalu, Sabah, Malaysia
  • 9 Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA. Electronic address: delwarte@medicine.ucsf.edu
Virology, 2015 Aug;482:98-104.
PMID: 25839169 DOI: 10.1016/j.virol.2015.03.011

Abstract

Viruses with small circular ssDNA genomes encoding a replication initiator protein can infect a wide range of eukaryotic organisms ranging from mammals to fungi. The genomes of two such viruses, a cyclovirus (CyCV-SL) and gemycircularvirus (GemyCV-SL) were detected by deep sequencing of the cerebrospinal fluids of Sri Lankan patients with unexplained encephalitis. One and three out of 201 CSF samples (1.5%) from unexplained encephalitis patients tested by PCR were CyCV-SL and GemyCV-SL DNA positive respectively. Nucleotide similarity searches of pre-existing metagenomics datasets revealed closely related genomes in feces from unexplained cases of diarrhea from Nicaragua and Brazil and in untreated sewage from Nepal. Whether the tropism of the cyclovirus and gemycircularvirus reported here include humans or other cellular sources in or on the human body remains to be determined.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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