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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. [ABSTRACT FROM AUTHOR]

To estimate the vector competence of Aedes aegypti populations sampled from distinct anthropogenic environments in French Guiana, Guadeloupe and Martinique for the strain CHIKV 06.21. F/F females were orally infected at titres of 10 and 10 pfu/ml in blood-meals. Disseminated infection rates (DIR) of mosquitoes were estimated using indirect fluorescent antibody assay on heads' squashes, 7 or 14 days post-infection (pi). At a titre of 10 pfu/ml, DIR ranged from 88.9% to 100.0% and were not significantly different whether assessed at day 7 or 14 pi. At a titre of 10 pfu/ml, DIR observed 7 days pi ranged from 37.6 to 62.0%. Ae. aegypti from French Guiana and French West Indies are highly competent to transmit CHIKV. An evaluation of DIR 7 days rather than 14 days pi is adequate to estimate vector competence. The titre of 10 pfu/ml allows us to distinguish Ae. aegypti populations originating from distinct environments (dense or diffuse housing) by their vector competence. This assessment is a prerequisite to better evaluate the potential risk of Chikungunya outbreaks once the virus is introduced from endemic regions. [ABSTRACT FROM AUTHOR]