title: A diverse group of small circular ssDNA viral genomes in human and non-human primate stools.
abstract: Viral metagenomics sequencing of fecal samples from outbreaks of acute gastroenteritis from the US revealed the presence of small circular ssDNA viral genomes encoding a replication initiator protein (Rep). Viral genomes were ∼2.5 kb in length, with bi-directionally oriented Rep and capsid (Cap) encoding genes and a stem loop structure downstream of Rep. Several genomes showed evidence of recombination. By digital screening of an in-house virome database (1.04 billion reads) using BLAST, we identified closely related sequences from cases of unexplained diarrhea in France. Deep sequencing and PCR detected such genomes in 7 of 25 US (28 percent) and 14 of 21 French outbreaks (67 percent). One of eighty-five sporadic diarrhea cases in the Gambia was positive by PCR. Twenty-two complete genomes were characterized showing that viruses from patients in the same outbreaks were closely related suggesting common origins. Similar genomes were also characterized from the stools of captive chimpanzees, a gorilla, a black howler monkey, and a lemur that were more diverse than the human stool-associated genomes. The name smacovirus is proposed for this monophyletic viral clade. Possible tropism include mammalian enteric cells or ingested food components such as infected plants. No evidence of viral amplification was found in immunodeficient mice orally inoculated with smacovirus-positive stool supernatants. A role for smacoviruses in diarrhea, if any, remains to be demonstrated.
authors: Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Department of laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA.
authors: Terry Fei Fan
authors: TF
authors: Ng
authors: Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Department of Microbiology, School of Medicine, Jiangsu University, Jiangsu, Zhenjiang, China.
authors: Wen
authors: W
authors: Zhang
authors: Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Federal Institute for Risk Assessment, Berlin, Germany.
authors: Jana
authors: J
authors: Sachsenröder
authors: Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA.
authors: Nikola O
authors: NO
authors: Kondov
authors: Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Institute of Tropical Medicine, University of Sao Paulo, São Paulo, Brazil.
authors: Antonio Charlys
authors: AC
authors: da Costa
authors: NCIRD, Polio and Picornavirus Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors: Everardo
authors: E
authors: Vega
authors: Department of Pediatrics.
authors: Lori R
authors: LR
authors: Holtz
authors: Department of Molecular Microbiology, and.
authors: Guang
authors: G
authors: Wu
authors: Departments of Molecular Microbiology and Pathology & Immunology, Washington University in St. Louis, St. Louis, MO, USA.
authors: David
authors: D
authors: Wang
authors: University of Maryland School of Medicine, Baltimore, MD, USA.
authors: Colin O
authors: CO
authors: Stine
authors: Medical Research Council Unit, Banjul, The Gambia.
authors: Martin
authors: M
authors: Antonio
authors: Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA.
authors: Usha S
authors: US
authors: Mulvaney
authors: Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Department of laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA.
authors: Marcus O
authors: MO
authors: Muench
authors: Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Department of laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA.
authors: Xutao
authors: X
authors: Deng
authors: National Reference Centre for enteric viruses, Dijon University Hospital, Dijon, France and.
authors: Katia
authors: K
authors: Ambert-Balay
authors: National Reference Centre for enteric viruses, Dijon University Hospital, Dijon, France and.
authors: Pierre
authors: P
authors: Pothier
authors: NCIRD, National Calicivirus Laboratory, Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors: Jan
authors: J
authors: Vinjé
authors: Blood Systems Research Institute, San Francisco, 270 Masonic Ave, San Francisco, CA 94118, USA, ; Department of laboratory Medicine, University of California at San Francisco, San Francisco, CA, USA.
authors: Eric
authors: E
authors: Delwart
keywords: acute gastroenteritis; deep sequencing; digital screening; metagenomics; smacovirus; ssDNA virus