Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis

do Socorro Fôro Ramos, Endrya; de Oliveira Ribeiro, Geovani; Villanova, Fabiola; de Padua Milagres, Flávio Augusto; Brustulin, Rafael; Araújo, Emerson Luiz Lima; Pandey, Ramendra Pati; Raj, V. Samuel; Deng, Xutao; Delwart, Eric; Luchs, Adriana; da Costa, Antonio Charlys; Leal, Élcio

doi:10.3390/v13122365

Open AccessArticle

Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis

by

Endrya do Socorro Fôro Ramos

¹

,

Geovani de Oliveira Ribeiro

¹

,

Fabiola Villanova

¹

,

Flávio Augusto de Padua Milagres

^2,3,

Rafael Brustulin

²,

Emerson Luiz Lima Araújo

⁴,

Ramendra Pati Pandey

⁵

,

V. Samuel Raj

⁵,

Xutao Deng

^6,7,

Eric Delwart

^6,7

,

Adriana Luchs

⁸,

Antonio Charlys da Costa

^9,†

and

Élcio Leal

^1,*,†

¹

Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66075-000, Pará, Brazil

²

Secretary of Health of Tocantins, Palmas 77453-000, Tocantins, Brazil

³

Public Health Laboratory of Tocantins State (LACEN/TO), Palmas 77016-330, Tocantins, Brazil

⁴

General 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, Brazil

⁵

Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, Haryana, India

⁶

Vitalant Research Institute, 270 Masonic Avenue, San Francisco, CA 94143, USA

⁷

Department Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA

⁸

Virology Center, Enteric Disease Laboratory, Adolfo Lutz Institute, São Paulo 01246-000, São Paulo, Brazil

⁹

Faculdade de Medicina, Instituto de Medicina Tropical, Universidade de São Paulo, São Paulo 05403-000, São Paulo, Brazil

^*

Author to whom correspondence should be addressed.

^†

These authors jointly supervised this work.

Viruses 2021, 13(12), 2365; https://doi.org/10.3390/v13122365

Submission received: 19 October 2021 / Revised: 20 November 2021 / Accepted: 23 November 2021 / Published: 25 November 2021

(This article belongs to the Special Issue Applications of Next-Generation Sequencing in Virus Discovery)

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Abstract

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.

Keywords: gut virome; gastroenteritis; children; virus-like particles; viral diversity

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MDPI and ACS Style

do Socorro Fôro Ramos, E.; de Oliveira Ribeiro, G.; Villanova, F.; de Padua Milagres, F.A.; Brustulin, R.; Araújo, E.L.L.; Pandey, R.P.; Raj, V.S.; Deng, X.; Delwart, E.; et al. Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis. Viruses 2021, 13, 2365. https://doi.org/10.3390/v13122365

AMA Style

do Socorro Fôro Ramos E, de Oliveira Ribeiro G, Villanova F, de Padua Milagres FA, Brustulin R, Araújo ELL, Pandey RP, Raj VS, Deng X, Delwart E, et al. Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis. Viruses. 2021; 13(12):2365. https://doi.org/10.3390/v13122365

Chicago/Turabian Style

do Socorro Fôro Ramos, Endrya, 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, and et al. 2021. "Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis" Viruses 13, no. 12: 2365. https://doi.org/10.3390/v13122365

APA Style

do Socorro Fôro Ramos, E., de Oliveira Ribeiro, G., Villanova, F., de Padua Milagres, F. A., Brustulin, R., Araújo, E. L. L., Pandey, R. P., Raj, V. S., Deng, X., Delwart, E., Luchs, A., da Costa, A. C., & Leal, É. (2021). Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis. Viruses, 13(12), 2365. https://doi.org/10.3390/v13122365

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Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis

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