Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis
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...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-11-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/13/12/2365 |
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| author | Endrya do Socorro Fôro Ramos Geovani de Oliveira Ribeiro Fabiola Villanova Flávio Augusto de Padua Milagres Rafael Brustulin Emerson Luiz Lima Araújo Ramendra Pati Pandey V. Samuel Raj Xutao Deng Eric Delwart Adriana Luchs Antonio Charlys da Costa Élcio Leal |
| author_facet | Endrya do Socorro Fôro Ramos Geovani de Oliveira Ribeiro Fabiola Villanova Flávio Augusto de Padua Milagres Rafael Brustulin Emerson Luiz Lima Araújo Ramendra Pati Pandey V. Samuel Raj Xutao Deng Eric Delwart Adriana Luchs Antonio Charlys da Costa Élcio Leal |
| author_sort | Endrya do Socorro Fôro Ramos |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T03:55:24Z |
| format | Article |
| id | doaj.art-aee5e9df68084271bb2e4259294b1c0f |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T03:55:24Z |
| publishDate | 2021-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-aee5e9df68084271bb2e4259294b1c0f2023-11-23T10:56:53ZengMDPI AGViruses1999-49152021-11-011312236510.3390/v13122365Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute GastroenteritisEndrya do Socorro Fôro Ramos0Geovani de Oliveira Ribeiro1Fabiola Villanova2Flávio Augusto de Padua Milagres3Rafael Brustulin4Emerson Luiz Lima Araújo5Ramendra Pati Pandey6V. Samuel Raj7Xutao Deng8Eric Delwart9Adriana Luchs10Antonio Charlys da Costa11Élcio Leal12Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-000, Pará, BrazilLaboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-000, Pará, BrazilLaboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-000, Pará, BrazilSecretary of Health of Tocantins, Palmas 77453-000, Tocantins, BrazilSecretary of Health of Tocantins, Palmas 77453-000, Tocantins, BrazilGeneral Coordination of Public Health, Laboratories of the Strategic Articulation, Department of the Health, Surveillance Secretariat, Ministry of Health (CGLAB/DAEVS/SVS-MS), Brasília 70719-040, Distrito Federal, BrazilCentre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, IndiaCentre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, IndiaVitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94143, USAVitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94143, USAVirology Center, Enteric Disease Laboratory, Adolfo Lutz Institute, São Paulo 01246-000, São Paulo, BrazilFaculdade de Medicina, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, São Paulo, BrazilLaboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-000, Pará, BrazilMetagenomics 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.https://www.mdpi.com/1999-4915/13/12/2365gut viromegastroenteritischildrenvirus-like particlesviral diversity |
| spellingShingle | Endrya do Socorro Fôro Ramos Geovani de Oliveira Ribeiro Fabiola Villanova Flávio Augusto de Padua Milagres Rafael Brustulin Emerson Luiz Lima Araújo Ramendra Pati Pandey V. Samuel Raj Xutao Deng Eric Delwart Adriana Luchs Antonio Charlys da Costa Élcio Leal Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis Viruses gut virome gastroenteritis children virus-like particles viral diversity |
| title | Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis |
| title_full | Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis |
| title_fullStr | Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis |
| title_full_unstemmed | Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis |
| title_short | Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis |
| title_sort | composition of eukaryotic viruses and bacteriophages in individuals with acute gastroenteritis |
| topic | gut virome gastroenteritis children virus-like particles viral diversity |
| url | https://www.mdpi.com/1999-4915/13/12/2365 |
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