title: Small circular single stranded DNA viral genomes in unexplained cases of human encephalitis, diarrhea, and in untreated sewage.
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.
authors.affiliation: Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA.
authors.forename: Tung Gia
authors.initials: TG
authors.lastname: Phan
authors.affiliation: Department of Microbiology, Faculty of Medicine, Oita University, Yufu 879-5593, Japan.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Mori
authors.affiliation: Blood Systems Research Institute, San Francisco, CA 94118, USA.
authors.forename: Xutao
authors.initials: X
authors.lastname: Deng
authors.affiliation: Department of Pediatrics, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka.
authors.forename: Shaman
authors.initials: S
authors.lastname: Rajindrajith
authors.affiliation: Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka.
authors.forename: Udaya
authors.initials: U
authors.lastname: Ranawaka
authors.affiliation: Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA.
authors.forename: Terry Fei
authors.initials: TF
authors.lastname: Fan Ng
authors.affiliation: Department of Microbiology, University of Leon, Nicaragua.
authors.forename: Filemon
authors.initials: F
authors.lastname: Bucardo-Rivera
authors.affiliation: Oswaldo Cruz Foundation, Manaus, Brazil.
authors.forename: Patricia
authors.initials: P
authors.lastname: Orlandi
authors.affiliation: 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.
authors.forename: Kamruddin
authors.initials: K
authors.lastname: Ahmed
authors.affiliation: 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.
authors.forename: Eric
authors.initials: E
authors.lastname: Delwart
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D001938:Brazil; D002555:Cerebrospinal Fluid / Q000821:virology; D002648:Child; D002675:Child, Preschool; D018136:Circoviridae / Q000235:genetics / Q000302:isolation & purification*; D016000:Cluster Analysis; D004270:DNA, Circular / Q000235:genetics* / Q000302:isolation & purification; D004277:DNA, Single-Stranded / Q000235:genetics* / Q000302:isolation & purification; D003967:Diarrhea / Q000821:virology*; D004660:Encephalitis / Q000821:virology*; D005243:Feces / Q000821:virology; D005260:Female; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007223:Infant; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D009527:Nicaragua; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D012722:Sewage / Q000821:virology*; D013188:Sri Lanka; D055815:Young Adult
chemical_list: D004270:DNA, Circular; D004277:DNA, Single-Stranded; D012722:Sewage
keywords: CRESS-DNA; Cyclovirus; Diarrhea; Encephalitis; Gemycircularvirus
references.citation: J Clin Microbiol. 2001 Aug;39(8):2873-9
references.pmid: 11474006
references.citation: J Gen Virol. 2012 Jun;93(Pt 6):1356-61
references.pmid: 22422066
references.citation: J Clin Microbiol. 2009 Nov;47(11):3507-13
references.pmid: 19794058
references.citation: PLoS One. 2015;10(2):e0118070
references.pmid: 25688970
references.citation: J Gen Virol. 2013 Aug;94(Pt 8):1827-40
references.pmid: 23596268
references.citation: Mol Biol Evol. 1987 Jul;4(4):406-25
references.pmid: 3447015
references.citation: Sci Rep. 2014;4:3967
references.pmid: 24495921
references.citation: J Gen Virol. 2014 Apr;95(Pt 4):922-7
references.pmid: 24421114
references.citation: J Virol. 2012 Feb;86(4):2360-5
references.pmid: 22171250
references.citation: Arch Virol. 2014 Dec;159(12):3453-6
references.pmid: 25168044
references.citation: Mol Biol Evol. 2011 Oct;28(10):2731-9
references.pmid: 21546353
references.citation: J Gen Virol. 2012 Dec;93(Pt 12):2668-81
references.pmid: 22915694
references.citation: Cell Host Microbe. 2010 Jun 25;7(6):509-15
references.pmid: 20542254
references.citation: J Gen Virol. 2015 Apr;96(Pt 4):915-20
references.pmid: 25535324
references.citation: PLoS One. 2011;6(6):e20579
references.pmid: 21674005
references.citation: Cold Spring Harb Perspect Med. 2013 Dec;3(12):a015362
references.pmid: 24296350
references.citation: J Clin Virol. 2012 Nov;55(3):209-13
references.pmid: 22824231
references.citation: Emerg Infect Dis. 2013;19(9). doi: 10.3201/eid1909.130404
references.pmid: 23968557
references.citation: J Clin Microbiol. 1990 Aug;28(8):1780-4
references.pmid: 2168438
references.citation: Infect Genet Evol. 2015 Mar;30:278-87
references.pmid: 25577985
references.citation: Virus Res. 2012 Jun;166(1-2):130-5
references.pmid: 22465471
references.citation: Arch Virol. 2010 Jul;155(7):1033-46
references.pmid: 20422235
references.citation: PLoS One. 2012;7(6):e38499
references.pmid: 22723863
references.citation: J Virol. 2012 Aug;86(15):8221-31
references.pmid: 22623790
references.citation: Infect Genet Evol. 2015 Apr;31:73-86
references.pmid: 25583447
references.citation: J Virol. 2011 Aug;85(15):7948-50
references.pmid: 21632766
references.citation: J Gen Virol. 2011 Apr;92(Pt 4):768-72
references.pmid: 21177928
references.citation: Vet Microbiol. 2004 Feb 4;98(2):169-74
references.pmid: 14741130
references.citation: J Med Virol. 2009 Nov;81(11):1895-902
references.pmid: 19774695
references.citation: J Virol. 2010 Jul;84(14):6955-65
references.pmid: 20463061
references.citation: Food Microbiol. 2014 Sep;42:205-11
references.pmid: 24929738
references.citation: Genome Announc. 2014 Aug 28;2(4):null
references.pmid: 25169858
references.citation: Proc Natl Acad Sci U S A. 2010 May 4;107(18):8387-92
references.pmid: 20404139
references.citation: Emerg Infect Dis. 2013 Apr;19(4):534-41
references.pmid: 23628223
references.citation: Emerg Infect Dis. 2013 Nov;19(11):1859-62
references.pmid: 24188380
references.citation: MBio. 2013;4(3):e00231-13
references.pmid: 23781068
references.citation: J Gen Virol. 2011 Nov;92(Pt 11):2646-53
references.pmid: 21795473
references.citation: Arch Virol. 2012 Oct;157(10):1851-71
references.pmid: 22760663
references.citation: Syst Appl Microbiol. 1999 Feb;22(1):97-105
references.pmid: 10188283
references.citation: Med Mycol. 2014 Oct;52(7):667-73
references.pmid: 25082953
references.citation: J Virol. 2010 Feb;84(4):1674-82
references.pmid: 20007276
references.citation: Virus Res. 2012 Mar;164(1-2):114-21
references.pmid: 22155583
references.citation: PLoS One. 2014;9(5):e98201
references.pmid: 24849288
references.citation: J Virol. 2012 Nov;86(22):12161-75
references.pmid: 22933275
references.citation: Adv Virus Res. 2001;57:1-70
references.pmid: 11680382
references.citation: Virus Res. 2013 Nov 6;177(2):209-16
references.pmid: 23994297
references.citation: J Virol. 2012 Apr;86(8):4620-30
references.pmid: 22345464
references.citation: J Clin Microbiol. 2008 Apr;46(4):1349-55
references.pmid: 18287312
references.citation: Virology. 2013 Dec;447(1-2):300-11
references.pmid: 24210127
references.citation: Genome Announc. 2014 Aug 28;2(4):null
references.pmid: 25169859
references.citation: Arch Virol. 2013 Jun;158(6):1389-92
references.pmid: 23358613
references.citation: J Gen Virol. 2011 Jun;92(Pt 6):1302-8
references.pmid: 21367985
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3406-15
references.pmid: 12824337
references.citation: J Virol. 2010 Dec;84(24):13004-18
references.pmid: 20926577