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. 2021 Aug;21(6):1788-1807.
doi: 10.1111/1755-0998.13378. Epub 2021 Apr 2.

A library preparation optimized for metagenomics of RNA viruses

Patricia Gil  1   2 , Virginie Dupuy  1   2 , Rachid Koual  1   2 , Antoni Exbrayat  1   2 , Etienne Loire  1   2 , Assane G Fall  3 , Geoffrey Gimonneau  1   2   3 , Biram Biteye  3 , Momar Talla Seck  3 , Ignace Rakotoarivony  1   2 , Albane Marie  4 , Benoît Frances  4 , Gregory Lambert  4 , Julie Reveillaud  1 , Thomas Balenghien  1   2 , Claire Garros  1   2 , Emmanuel Albina  1   2 , Marc Eloit  5   6   7 , Serafin Gutierrez  1   2
Affiliations

A library preparation optimized for metagenomics of RNA viruses

Patricia Gil et al. Mol Ecol Resour. 2021 Aug.

Abstract

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.

Keywords: insects; library preparation; metagenomics; shotgun sequencing; virome; virus.

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