A library preparation optimized for metagenomics of RNA viruses

Gil Patricia, Dupuy Virginie, Koual Rachid, Exbrayat Antoni, Loire Etienne, Fall Assane Gueye, Gimonneau Geoffrey, Biteye Biram, Talla Seck Monar, Rakotoarivony Ignace, Marie Albane, Francés Benoit, Lambert Grégory, Reveillaud Julie, Balenghien Thomas, Garros Claire, Albina Emmanuel, Eloit Marc, Gutierrez Serafin. 2021. A library preparation optimized for metagenomics of RNA viruses. Molecular Ecology Resources, 21 (6) : 1788-1807.

Url - jeu de données - Entrepôt autre : https://www.ncbi.nlm.nih.gov/nuccore/MN567480 / Url - autres données associées : https://github.com/Aexbrayat/snakevir

Quartile : Q1, Sujet : BIOCHEMISTRY & MOLECULAR BIOLOGY / Quartile : Q1, Sujet : ECOLOGY / Quartile : Q1, Sujet : EVOLUTIONARY BIOLOGY

Résumé : Our understanding of the viral communities associated to animals has not yet reached the level attained on the bacteriome. This situation is due to, among others, technical challenges in adapting metagenomics using high‐throughput sequencing to the study of RNA viromes in animals. Although important developments have been achieved in most steps of viral metagenomics, there is yet a key step that has received little attention: the library preparation. This situation differs from bacteriome studies in which developments in library preparation have largely contributed to the democratisation of metagenomics. Here, we present a library preparation optimized for metagenomics of RNA viruses from insect vectors of viral diseases. The library design allows a simple PCR‐based preparation, such as those routinely used in bacterial metabarcoding, that is adapted to shotgun sequencing as required in viral metagenomics. We first optimized our library preparation using mock viral communities and then validated a full metagenomic approach incorporating our preparation in two pilot studies with field‐caught insect vectors; one including a comparison with a published metagenomic protocol. Our approach provided a fold increase in virus‐like sequences compared to other studies, and nearly‐full genomes from new virus species. Moreover, our results suggested conserved trends in virome composition within a population of a mosquito species. Finally, the sensitivity of our approach was compared to a commercial diagnostic PCR for the detection of an arbovirus in field‐caught insect vectors. Our approach could facilitate studies on viral communities from animals and the democratization of metagenomics in community ecology of viruses.

Mots-clés Agrovoc : virus à ARN, génomique, banque de gènes, PCR, vecteur de maladie, Culex pipiens, Aedes vexans, Culicoides, virus bluetongue, virus maladie de newcastle, caulimovirus mosaïque du chou fleur

Mots-clés géographiques Agrovoc : France, Sénégal

Mots-clés libres : Insects, Library preparation, Metagenomics, Shotgun sequencing, Virome, Virus

Classification Agris : S50 - Santé humaine
L73 - Maladies des animaux
L72 - Organismes nuisibles des animaux

Champ stratégique Cirad : CTS 4 (2019-) - Santé des plantes, des animaux et des écosystèmes

Agences de financement européennes : European Commission

Programme de financement européen : FP7

Projets sur financement : (EU) Emerging viral vector borne diseases, (EU) Animal Health and Welfare

Auteurs et affiliations

• Gil Patricia, CIRAD-BIOS-UMR ASTRE (FRA) ORCID: 0000-0001-7984-7340
• Dupuy Virginie, CIRAD-BIOS-UMR ASTRE (FRA)
• Koual Rachid, CIRAD-BIOS-UMR ASTRE (FRA)
• Exbrayat Antoni, CIRAD-BIOS-UMR ASTRE (FRA)
• Loire Etienne, CIRAD-BIOS-UMR ASTRE (FRA)
• Fall Assane Gueye, ISRA (SEN)
• Gimonneau Geoffrey, CIRAD-BIOS-UMR INTERTRYP (SEN) ORCID: 0000-0002-0613-841X
• Biteye Biram, ISRA (SEN)
• Talla Seck Monar, ISRA (SEN)
• Rakotoarivony Ignace, CIRAD-BIOS-UMR ASTRE (FRA) ORCID: 0009-0002-3480-6734
• Marie Albane, EID (FRA)
• Francés Benoit, EID (FRA)
• Lambert Grégory, EID (FRA)
• Reveillaud Julie, INRAE (FRA)
• Balenghien Thomas, CIRAD-BIOS-UMR ASTRE (MAR) ORCID: 0009-0008-4495-4814
• Garros Claire, CIRAD-BIOS-UMR ASTRE (FRA) ORCID: 0000-0003-4378-5031
• Albina Emmanuel, CIRAD-BIOS-UMR ASTRE (GLP)
• Eloit Marc, Institut Pasteur (FRA)
• Gutierrez Serafin, CIRAD-BIOS-UMR ASTRE (FRA) ORCID: 0000-0002-5277-7239 - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/598082/)

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