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Idiopathic chronic diarrhea (ICD) in rhesus macaques also resembles ulcerative colitis, one form of human inflammatory bowel disease. To test for viral etiologies, we characterized and compared the fecal viromes from 32 healthy animals, 31 animals with acute diarrhea, and 29 animals with ICD. The overall fractions of eukaryotic viral reads were 0.063% for the healthy group, 0.131% for the acute-diarrhea group, and 0.297% for the chronic-diarrhea group. Eukaryotic viruses belonging to 6 viral families, as well as numerous circular Rep-encoding single-stranded DNA (CRESS DNA) viral genomes, were identified. The most commonly detected sequences were from picornaviruses, making up 59 to 88% of all viral reads, followed by 9 to 17% for CRESS DNA virus sequences. The remaining 5 virus families,\n            <jats:named-content content-type=\"genus-species\">Adenoviridae<\/jats:named-content>\n            ,\n            <jats:named-content content-type=\"genus-species\">Astroviridae<\/jats:named-content>\n            ,\n            <jats:named-content content-type=\"genus-species\">Anelloviridae<\/jats:named-content>\n            ,\n            <jats:named-content content-type=\"genus-species\">Picobirnaviridae<\/jats:named-content>\n            , and\n            <jats:named-content content-type=\"genus-species\">Parvoviridae<\/jats:named-content>\n            , collectively made up 1 to 3% of the viral reads, except for parvoviruses, which made up 23% of the viral reads in the healthy group. Detected members of the families\n            <jats:named-content content-type=\"genus-species\">Picornaviridae<\/jats:named-content>\n            and\n            <jats:named-content content-type=\"genus-species\">Parvoviridae<\/jats:named-content>\n            were highly diverse, consisting of multiple genera, species, and genotypes. Coinfections with members of up to six viral families were detected. Complete and partial viral genomes were assembled and used to measure the number of matching short sequence reads in feces from the 92 animals in the two clinical and the healthy control groups. Several enterovirus genotypes and CRESS DNA genomes were associated with ICD relative to healthy animals. Conversely, higher read numbers from different parvoviruses were associated with healthy animals. Our study reveals a high level of enteric coinfections with diverse viruses in a captive rhesus macaque colony and identifies several viruses positively or negatively associated with ICD.\n          <\/jats:p>","DOI":"10.1128\/jvi.00952-17","type":"journal-article","created":{"date-parts":[[2017,6,29]],"date-time":"2017-06-29T00:30:22Z","timestamp":1498696222000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":52,"title":["Case-Control Comparison of Enteric Viromes in Captive Rhesus Macaques with Acute or Idiopathic Chronic Diarrhea"],"prefix":"10.1128","volume":"91","author":[{"given":"Beatrix","family":"Kapusinszky","sequence":"first","affiliation":[{"name":"Blood Systems Research Institute, San Francisco, California, USA"},{"name":"Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amir","family":"Ardeshir","sequence":"additional","affiliation":[{"name":"California National Primate Research Center, School of Veterinary Medicine, University of California at Davis, Davis, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Usha","family":"Mulvaney","sequence":"additional","affiliation":[{"name":"Blood Systems Research Institute, San Francisco, California, USA"},{"name":"University of San Francisco, Department of Biology, San Francisco, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xutao","family":"Deng","sequence":"additional","affiliation":[{"name":"Blood Systems Research Institute, San Francisco, California, USA"},{"name":"Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6296-4484","authenticated-orcid":false,"given":"Eric","family":"Delwart","sequence":"additional","affiliation":[{"name":"Blood Systems Research Institute, San Francisco, California, USA"},{"name":"Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1002\/ajp.22150"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.71.7.4079-4086.2003"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.4291\/wjgp.v5.i1.48"},{"key":"e_1_3_3_5_2","first-page":"356","article-title":"Diarrhea rates and risk factors for developing chronic diarrhea in infant and juvenile rhesus monkeys","volume":"42","author":"Elmore DB","year":"1992","unstructured":"Elmore DB Anderson JH Hird DW Sanders KD Lerche NW . 1992. 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