A library preparation optimized for metagenomics of RNA viruses

Autor: Biram Biteye, Marc Eloit, Ignace Rakotoarivony, Thomas Balenghien, Claire Garros, Rachid Koual, Patricia Gil, Virginie Dupuy, Serafin Gutierrez, Antoni Exbrayat, Assane Gueye Fall, Grégory L'Ambert, Emmanuel Albina, Etienne Loire, Geoffrey Gimonneau, Albane Marie, Benoit Francés, Julie Reveillaud, Momar Talla Seck
Přispěvatelé: Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Laboratoire National d'Elevage et de Recherches Vétérinaires [Dakar] (LNERV), Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides (UMR INTERTRYP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université de Bordeaux (UB), Entente Interdépartementale pour la démoustication du littoral méditerranéen (EID), École nationale vétérinaire - Alfort (ENVA), Découverte de pathogènes – Pathogen discovery, Institut Pasteur [Paris] (IP), Centre Collaborateur de l'OIE de Détection et identification chez l’homme des pathogènes animaux émergents et développement d’outils pour leur diagnostic / Collaborating Center for the Detection and identification in humans of emerging animal pathogens and development of tools for their diagnoses (CCOIE-OIECC), Institut Pasteur [Paris] (IP)-Organisation Mondiale de la Santé Animale / World Organisation Animal Health [Paris] (OIE), This work was funded by the Direction Générale de l’Alimentation from the French Ministry in charge of agriculture. This work was also funded by the European Union’s Seventh Framework Programme through grants Vmerge (FP7‐613996) and CuliOme (FP7‐291815)., European Project: 291815,EC:FP7:KBBE,FP7-ERANET-2011-RTD,ANIHWA(2012), European Project: 613996,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,VMERGE(2013), European Project: 7247564(1972), Université de Bordeaux (UB)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), École nationale vétérinaire d'Alfort (ENVA), Institut Pasteur [Paris], Institut Pasteur [Paris]-Organisation Mondiale de la Santé Animale / World Animal Health Information System (OIE-WAHIS)
Jazyk: angličtina
Rok vydání: 2021
Předmět:
0106 biological sciences
0301 basic medicine
Viral metagenomics
[SDV]Life Sciences [q-bio]
Banque de gènes
Caulimovirus mosaïque du chou fleur
L73 - Maladies des animaux
01 natural sciences
Genome
shotgun sequencing
Aedes vexans
Culex pipiens
insects
viromevirus
education.field_of_study
Shotgun sequencing
Virome
[SDV.BA]Life Sciences [q-bio]/Animal biology
Culicoides
PCR
Vecteur de maladie
S50 - Santé humaine
L72 - Organismes nuisibles des animaux
Biotechnology
Population
Computational biology
Genome
Viral
Biology
010603 evolutionary biology
génomique
03 medical and health sciences
Virus bluetongue
Genetics
Animals
RNA Viruses
Human virome
education
Ecology
Evolution
Behavior and Systematics
Virus classification
Gene Library
metagenomics
Virus maladie de newcastle
Bacteriome
030104 developmental biology
Metagenomics
Metagenome
library preparation
Zdroj: Molecular Ecology Resources
Molecular Ecology Resources, 2021, ⟨10.1111/1755-0998.13378⟩
Molecular Ecology Resources, Wiley/Blackwell, 2021, ⟨10.1111/1755-0998.13378⟩
ISSN: 1755-098X
1755-0998
Popis: International audience; 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.
Databáze: OpenAIRE
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