{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T16:55:40Z","timestamp":1791824140337,"version":"4.3.4"},"reference-count":69,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2021,11,25]],"date-time":"2021-11-25T00:00:00Z","timestamp":1637798400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Metagenomics based on the next-generation sequencing (NGS) technique is a target-independent assay that enables the simultaneous detection and genomic characterization of all viruses present in a sample. There is a limited amount of data about the virome of individuals with gastroenteritis (GI). In this study, the enteric virome of 250 individuals (92% were children under 5 years old) with GI living in the northeastern and northern regions of Brazil was characterized. Fecal samples were subjected to NGS, and the metagenomic analysis of virus-like particles (VLPs) identified 11 viral DNA families and 12 viral RNA families. As expected, the highest percentage of viral sequences detected were those commonly associated with GI, including rotavirus, adenovirus, norovirus (94.8%, 82% and 71.2%, respectively). The most common co-occurrences, in a single individual, were the combinations of rotavirus-adenovirus, rotavirus-norovirus, and norovirus-adenovirus (78%, 69%, and 62%, respectively). In the same way, common fecal-emerging human viruses were also detected, such as parechovirus, bocaporvirus, cosavirus, picobirnavirus, cardiovirus, salivirus, and Aichivirus. In addition, viruses that infect plants, nematodes, fungi, protists, animals, and arthropods could be identified. A large number of unclassified viral contigs were also identified. We show that the metagenomics approach is a powerful and promising tool for the detection and characterization of different viruses in clinical GI samples.<\/jats:p>","DOI":"10.3390\/v13122365","type":"journal-article","created":{"date-parts":[[2021,12,1]],"date-time":"2021-12-01T03:12:56Z","timestamp":1638328376000},"page":"2365","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis"],"prefix":"10.3390","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5229-896X","authenticated-orcid":false,"given":"Endrya","family":"do Socorro F\u00f4ro Ramos","sequence":"first","affiliation":[{"name":"Laborat\u00f3rio de Diversidade Viral, Instituto de Ci\u00eancias Biol\u00f3gicas, Universidade Federal do Par\u00e1, Bel\u00e9m 66075-000, Par\u00e1, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8832-7803","authenticated-orcid":false,"given":"Geovani","family":"de Oliveira Ribeiro","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Diversidade Viral, Instituto de Ci\u00eancias Biol\u00f3gicas, Universidade Federal do Par\u00e1, Bel\u00e9m 66075-000, Par\u00e1, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4442-5855","authenticated-orcid":false,"given":"Fabiola","family":"Villanova","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Diversidade Viral, Instituto de Ci\u00eancias Biol\u00f3gicas, Universidade Federal do Par\u00e1, Bel\u00e9m 66075-000, Par\u00e1, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fl\u00e1vio Augusto","family":"de Padua Milagres","sequence":"additional","affiliation":[{"name":"Secretary of Health of Tocantins, Palmas 77453-000, Tocantins, Brazil"},{"name":"Public Health Laboratory of Tocantins State (LACEN\/TO), Palmas 77016-330, Tocantins, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rafael","family":"Brustulin","sequence":"additional","affiliation":[{"name":"Secretary of Health of Tocantins, Palmas 77453-000, Tocantins, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emerson Luiz Lima","family":"Ara\u00fajo","sequence":"additional","affiliation":[{"name":"General Coordination of Public Health, Laboratories of the Strategic Articulation, Department of the Health, Surveillance Secretariat, Ministry of Health (CGLAB\/DAEVS\/SVS-MS), Bras\u00edlia 70719-040, Distrito Federal, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5196-6468","authenticated-orcid":false,"given":"Ramendra Pati","family":"Pandey","sequence":"additional","affiliation":[{"name":"Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"V. Samuel","family":"Raj","sequence":"additional","affiliation":[{"name":"Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xutao","family":"Deng","sequence":"additional","affiliation":[{"name":"Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94143, USA"},{"name":"Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, 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":"Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94143, USA"},{"name":"Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adriana","family":"Luchs","sequence":"additional","affiliation":[{"name":"Virology Center, Enteric Disease Laboratory, Adolfo Lutz Institute, S\u00e3o Paulo 01246-000, S\u00e3o Paulo, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5516-5177","authenticated-orcid":false,"given":"Antonio Charlys","family":"da Costa","sequence":"additional","affiliation":[{"name":"Faculdade de Medicina, Instituto de Medicina Tropical, Universidade de S\u00e3o Paulo, S\u00e3o Paulo 05403-000, S\u00e3o Paulo, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3463-0492","authenticated-orcid":false,"given":"\u00c9lcio","family":"Leal","sequence":"additional","affiliation":[{"name":"Laborat\u00f3rio de Diversidade Viral, Instituto de Ci\u00eancias Biol\u00f3gicas, Universidade Federal do Par\u00e1, Bel\u00e9m 66075-000, Par\u00e1, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,11,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1038\/nature09199","article-title":"Viruses in the Faecal Microbiota of Monozygotic Twins and Their Mothers","volume":"466","author":"Reyes","year":"2010","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1616","DOI":"10.1101\/gr.122705.111","article-title":"The Human Gut Virome: Inter-Individual Variation and Dynamic Response to Diet","volume":"21","author":"Minot","year":"2011","journal-title":"Genome Res."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Fernandez-Cassi, X., Mart\u00ednez-Puchol, S., Silva-Sales, M., Cornejo, T., Bartolome, R., Bofill-Mas, S., and Girones, R. 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