Evidence map›Paper›PMID 25839169›Full record

ArticleVirology2015

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

Abstract read
In one paragraph

Article in Virology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.

0numbers the graph read from it
0cells of the map it votes in
64citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

64 citing papers in PubMed.

  1. Article
  2. Article
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  5. Viral Metagenomics of the Bharal (Polish journal of microbiology · 2025
    Article
  6. Article
  7. Article
  8. Review
  9. Article
  10. The Blood Virome: A new frontier in biomedical science.Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · 2024
    Review
  11. Gemykibivirus detection in acute encephalitis patients from Nepal.medRxiv : the preprint server for health sciences · 2024
    Article
  12. Article
  13. Article
  14. Article
  15. Article
  16. Article
  17. Article
  18. Article
  19. Article
  20. Article

4 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Tung Gia PhanBlood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA.
Daisuke MoriDepartment of Microbiology, Faculty of Medicine, Oita University, Yufu 879-5593, Japan.
Xutao DengBlood Systems Research Institute, San Francisco, CA 94118, USA.
Shaman RajindrajithDepartment of Pediatrics, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka.
Udaya RanawakaDepartment of Medicine, Faculty of Medicine, University of Kelaniya, Ragama, Sri Lanka.
Terry Fei Fan NgBlood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA.
Filemon Bucardo-RiveraDepartment of Microbiology, University of Leon, Nicaragua.
Patricia OrlandiOswaldo Cruz Foundation, Manaus, Brazil.
Kamruddin AhmedDepartment 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.
Eric DelwartBlood 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.

Funding

Metagenomic detection of emerging viruses in the blood supplyR01HL105770 · NHLBI · VITALANT · PI DELWART, ERIC L · 2011 to 2015
$2.4M
NHLBI NIH HHS R01 HL105770NHLBI NIH HHS R01HL105770
6 · The paper itself

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.

Indexed as

Genome, ViralAdolescentAdultAgedBrazilCerebrospinal FluidChildChild, PreschoolCircoviridaeCluster AnalysisDiarrheaDNA, CircularDNA, Single-StrandedEncephalitisFecesFemaleDNA, CircularDNA, Single-StrandedSewageCRESS-DNACyclovirusDiarrheaEncephalitisGemycircularvirus

Identifiers

PMID25839169
PMCPMC4461510

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.