title: The fecal virome of South and Central American children with diarrhea includes small circular DNA viral genomes of unknown origin.
abstract: Viral metagenomics of feces collected from 58 Peruvian children with unexplained diarrhea revealed several small circular ssDNA genomes. Two genomes related to sequences previously reported in feces from chimpanzees and other mammals and recently named smacoviruses were characterized and then detected by PCR in 1.7 % (1/58) and 19 % (11/58) of diarrheal samples, respectively. Another three genomes from a distinct small circular ssDNA viral group provisionally called pecoviruses encoded Cap and Rep proteins with <35 % identity to those in related genomes reported in human, seal, porcine and dromedary feces. Pecovirus DNA was detected in 15.5 % (9/58), 5.9 % (3/51) and 3 % (3/100) of fecal samples from unexplained diarrhea in Peru, Nicaragua and Chile, respectively. Feces containing these ssDNA genomes also contained known human enteric viral pathogens. The cellular origins of these circular ssDNA viruses, whether human cells, ingested plants, animals or fungal foods, or residents of the gut microbiome, are currently unknown.
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: Blood Systems Research Institute, San Francisco, CA, 94118, USA.|Institute of Tropical Medicine, School of Medicine, University of São Paulo, São Paulo, Brazil.
authors.forename: Antonio Charlys
authors.initials: AC
authors.lastname: da Costa
authors.affiliation: Faculty of Health Sciences, School of Medicine, Universidad Peruana de Ciencias Aplicadas-UPC, Lima, Peru.|Instituto de Investigación Nutricional, Lima, Peru.
authors.forename: Juana
authors.initials: J
authors.lastname: Del Valle Mendoza
authors.affiliation: Department of Microbiology, University of León, León, Nicaragua.
authors.forename: Filemon
authors.initials: F
authors.lastname: Bucardo-Rivera
authors.affiliation: Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
authors.forename: Johan
authors.initials: J
authors.lastname: Nordgren
authors.affiliation: Microbiology and Mycology Program, Faculty of Medicine, University of Chile, Santiago, Chile.
authors.forename: Miguel
authors.initials: M
authors.lastname: O'Ryan
authors.affiliation: Blood Systems Research Institute, San Francisco, CA, 94118, USA.
authors.forename: Xutao
authors.initials: X
authors.lastname: Deng
authors.affiliation: Blood Systems Research Institute, San Francisco, CA, 94118, USA. delwarte@medicine.ucsf.edu.|Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA, 94118, USA. delwarte@medicine.ucsf.edu.
authors.forename: Eric
authors.initials: E
authors.lastname: Delwart
mesh_terms: D002677:Chile / Q000453:epidemiology; D004270:DNA, Circular / Q000235:genetics*; D004279:DNA, Viral / Q000235:genetics*; D003967:Diarrhea / Q000453:epidemiology / Q000821:virology*; D005243:Feces / Q000821:virology; D016679:Genome, Viral; D006801:Humans; D009527:Nicaragua / Q000453:epidemiology; D010568:Peru / Q000453:epidemiology; D010802:Phylogeny; D014777:Virus Diseases / Q000453:epidemiology / Q000821:virology*
chemical_list: D004270:DNA, Circular; D004279:DNA, Viral