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

Tung Gia Phan; Daisuke Mori; Xutao Deng; Shaman Rajindrajith; Udaya Ranawaka; Terry Fei Fan Ng; Filemon Bucardo-Rivera; Patricia Orlandi; Kamruddin Ahmed; Eric Delwart

doi:10.1016/j.virol.2015.03.011

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

Virology. 2015 Aug:482:98-104. doi: 10.1016/j.virol.2015.03.011. Epub 2015 Apr 1.

Authors

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.

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.

Keywords: CRESS-DNA; Cyclovirus; Diarrhea; Encephalitis; Gemycircularvirus.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Adolescent
Adult
Aged
Brazil
Cerebrospinal Fluid / virology
Child
Child, Preschool
Circoviridae / genetics
Circoviridae / isolation & purification*
Cluster Analysis
DNA, Circular / genetics*
DNA, Circular / isolation & purification
DNA, Single-Stranded / genetics*
DNA, Single-Stranded / isolation & purification
Diarrhea / virology*
Encephalitis / virology*
Feces / virology
Female
Genome, Viral*
High-Throughput Nucleotide Sequencing
Humans
Infant
Male
Middle Aged
Molecular Sequence Data
Nicaragua
Phylogeny
Polymerase Chain Reaction
Sequence Analysis, DNA
Sequence Homology
Sewage / virology*
Sri Lanka
Young Adult

Substances

DNA, Circular
DNA, Single-Stranded
Sewage

Associated data

GENBANK/KP133075
GENBANK/KP133076
GENBANK/KP133077
GENBANK/KP133078
GENBANK/KP133079
GENBANK/KP133080
GENBANK/KP151567

Abstract

Publication types

MeSH terms

Substances

Associated data

Grants and funding