A diverse group of small circular ssDNA viral genomes in human and non-human primate stools

Author(s):Show less -

Ng, Terry Fei Fan ^{[1, 2, 3]} ; Zhang, Wen ^{[2, 4]} ; Sachsenroeder, Jana ^{[2, 5]} ; Kondov, Nikola O. ^[2] ; da Costa, Antonio Charlys ^{[6, 2]} ; Vega, Everardo ^[7] ; Holtz, Lori R. ^[8] ; Wu, Guang ^[9] ; Wang, David ^{[9, 10]} ; Stine, Colin O. ^[11] ; Antonio, Martin ^[12] ; Mulvaney, Usha S. ^[2] ; Muench, Marcus O. ^{[1, 2]} ; Deng, Xutao ^{[1, 2]} ; Ambert-Balay, Katia ^[13] ; Pothier, Pierre ^[13] ; Vinje, Jan ^[14] ; Delwart, Eric ^{[1, 2]}

Affiliation:Show less -

^[1] Univ Calif San Francisco, Dept Lab Med, San Francisco, CA 94143 - USA

^[2] Blood Syst Res Inst, 270 Masonic Ave, San Francisco, CA 94118 - USA

^[3] Ctr Dis Control & Prevent, Natl Ctr Immunizat & Resp Dis, Div Viral Dis, Atlanta, GA - USA

^[4] Jiangsu Univ, Sch Med, Dept Microbiol, Zhenjiang, Jiangsu - Peoples R China

^[5] Fed Inst Risk Assessment, Berlin - Germany

^[6] Univ Sao Paulo, Inst Trop Med, Sao Paulo - Brazil

^[7] Ctr Dis Control & Prevent, NCIRD, Polio & Picornavirus Lab Branch, Atlanta, GA - USA

^[8] Washington Univ, Dept Pediat, St Louis, MO 63130 - USA

^[9] Washington Univ, Dept Mol Microbiol, St Louis, MO 63110 - USA

^[10] Washington Univ, Dept Pathol & Immunol, St Louis, MO 63110 - USA

^[11] Univ Maryland, Sch Med, Baltimore, MD 21201 - USA

^[12] MRC Unit, Banjul - Gambia

^[13] Dijon Univ Hosp, Natl Reference Ctr Enter Viruses, Dijon - France

^[14] Ctr Dis Control & Prevent, NCIRD, Natl Calicivirus Lab, Atlanta, GA - USA

• Document type: Journal article
• Source: VIRUS EVOLUTION; v. 1, n. 1 MAR 2015.
• Web of Science Citations: 25

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 similar to 2.5 kb in length, with bi-directionally oriented Rep and capsid (Cap) encoding genes and a stem loop structure downstreamof 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. (AU)

• FAPESP's process: 14/05211-2 - Viral metagenomics in human plasma of blood donors in two blood centers in Brazil
• Grantee: Antonio Charlys da Costa
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate (Direct)
• FAPESP's process: 12/03417-7 - Complete genomes for dengue virus: viral genetic diversity among seropositive first-time blood donors and recipients in two blood centres in Brazil
• Grantee: Antonio Charlys da Costa
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)