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Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams

Many recent pandemics have been recognized as zoonotic viral diseases. While their origins remain frequently unknown, environmental contamination may play an important role in emergence. Thus, being able to describe the viral diversity in environmental samples contributes to understand the key issue...

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Autores principales: Bonny, Patrice, Schaeffer, Julien, Besnard, Alban, Desdouits, Marion, Ngang, Jean Justin Essia, Le Guyader, Françoise S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8669915/
https://www.ncbi.nlm.nih.gov/pubmed/34917052
http://dx.doi.org/10.3389/fmicb.2021.770385
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author Bonny, Patrice
Schaeffer, Julien
Besnard, Alban
Desdouits, Marion
Ngang, Jean Justin Essia
Le Guyader, Françoise S.
author_facet Bonny, Patrice
Schaeffer, Julien
Besnard, Alban
Desdouits, Marion
Ngang, Jean Justin Essia
Le Guyader, Françoise S.
author_sort Bonny, Patrice
collection PubMed
description Many recent pandemics have been recognized as zoonotic viral diseases. While their origins remain frequently unknown, environmental contamination may play an important role in emergence. Thus, being able to describe the viral diversity in environmental samples contributes to understand the key issues in zoonotic transmission. This work describes the use of a metagenomic approach to assess the diversity of eukaryotic RNA viruses in river clams and identify sequences from human or potentially zoonotic viruses. Clam samples collected over 2years were first screened for the presence of norovirus to verify human contamination. Selected samples were analyzed using metagenomics, including a capture of sequences from viral families infecting vertebrates (VirCapSeq-VERT) before Illumina NovaSeq sequencing. The bioinformatics analysis included pooling of data from triplicates, quality filtering, elimination of bacterial and host sequences, and a deduplication step before de novo assembly. After taxonomic assignment, the viral fraction represented 0.8–15% of reads with most sequences (68–87%) remaining un-assigned. Yet, several mammalian RNA viruses were identified. Contigs identified as belonging to the Astroviridae were the most abundant, with some nearly complete genomes of bastrovirus identified. Picobirnaviridae sequences were related to strains infecting bats, and few others to strains infecting humans or other hosts. Hepeviridae sequences were mostly related to strains detected in sponge samples but also strains from swine samples. For Caliciviridae and Picornaviridae, most of identified sequences were related to strains infecting bats, with few sequences close to human norovirus, picornavirus, and genogroup V hepatitis A virus. Despite a need to improve the sensitivity of our method, this study describes a large diversity of RNA virus sequences from clam samples. To describe all viral contaminants in this type of food, and being able to identify the host infected by viral sequences detected, may help to understand some zoonotic transmission events and alert health authorities of possible emergence.
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spelling pubmed-86699152021-12-15 Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams Bonny, Patrice Schaeffer, Julien Besnard, Alban Desdouits, Marion Ngang, Jean Justin Essia Le Guyader, Françoise S. Front Microbiol Microbiology Many recent pandemics have been recognized as zoonotic viral diseases. While their origins remain frequently unknown, environmental contamination may play an important role in emergence. Thus, being able to describe the viral diversity in environmental samples contributes to understand the key issues in zoonotic transmission. This work describes the use of a metagenomic approach to assess the diversity of eukaryotic RNA viruses in river clams and identify sequences from human or potentially zoonotic viruses. Clam samples collected over 2years were first screened for the presence of norovirus to verify human contamination. Selected samples were analyzed using metagenomics, including a capture of sequences from viral families infecting vertebrates (VirCapSeq-VERT) before Illumina NovaSeq sequencing. The bioinformatics analysis included pooling of data from triplicates, quality filtering, elimination of bacterial and host sequences, and a deduplication step before de novo assembly. After taxonomic assignment, the viral fraction represented 0.8–15% of reads with most sequences (68–87%) remaining un-assigned. Yet, several mammalian RNA viruses were identified. Contigs identified as belonging to the Astroviridae were the most abundant, with some nearly complete genomes of bastrovirus identified. Picobirnaviridae sequences were related to strains infecting bats, and few others to strains infecting humans or other hosts. Hepeviridae sequences were mostly related to strains detected in sponge samples but also strains from swine samples. For Caliciviridae and Picornaviridae, most of identified sequences were related to strains infecting bats, with few sequences close to human norovirus, picornavirus, and genogroup V hepatitis A virus. Despite a need to improve the sensitivity of our method, this study describes a large diversity of RNA virus sequences from clam samples. To describe all viral contaminants in this type of food, and being able to identify the host infected by viral sequences detected, may help to understand some zoonotic transmission events and alert health authorities of possible emergence. Frontiers Media S.A. 2021-11-30 /pmc/articles/PMC8669915/ /pubmed/34917052 http://dx.doi.org/10.3389/fmicb.2021.770385 Text en Copyright © 2021 Bonny, Schaeffer, Besnard, Desdouits, Essia Ngang and Le Guyader. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Bonny, Patrice
Schaeffer, Julien
Besnard, Alban
Desdouits, Marion
Ngang, Jean Justin Essia
Le Guyader, Françoise S.
Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams
title Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams
title_full Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams
title_fullStr Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams
title_full_unstemmed Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams
title_short Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams
title_sort human and animal rna virus diversity detected by metagenomics in cameroonian clams
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8669915/
https://www.ncbi.nlm.nih.gov/pubmed/34917052
http://dx.doi.org/10.3389/fmicb.2021.770385
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