Stable distinct core eukaryotic viromes in different mosquito species from Guadeloupe, using single mosquito viral metagenomics

Abstract

Background Mosquitoes are the most important invertebrate viral vectors in humans and harbor a high diversity of understudied viruses, which has been shown in many mosquito virome studies in recent years. These studies generally performed metagenomics sequencing on pools of mosquitoes, without assessment of the viral diversity in individual mosquitoes. To address this issue, we applied our optimized viral metagenomics protocol (NetoVIR) to compare the virome of single and pooled Aedes aegypti and Culex quinquefasciatus mosquitoes collected from different locations in Guadeloupe, in 2016 and 2017. Results The total read number and viral reads proportion of samples containing a single mosquito have no significant difference compared with those of pools containing five mosquitoes, which proved the feasibility of using single mosquito for viral metagenomics. A comparative analysis of the virome revealed a higher abundance and more diverse eukaryotic virome in Aedes aegypti , whereas Culex quinquefasciatus harbors a richer and more diverse phageome. The majority of the identified eukaryotic viruses were mosquito-species specific. We further characterized the genomes of 11 novel eukaryotic viruses. Furthermore, qRT-PCR analyses of the six most abundant eukaryotic viruses indicated that the majority of individual mosquitoes were infected by several of the selected viruses with viral genome copies per mosquito ranging from 267 to 1.01 × 10 8 (median 7.5 × 10 6 ) for Ae . aegypti and 192 to 8.69 × 10 6 (median 4.87 × 10 4 ) for Cx . quinquefasciatus . Additionally, in Cx . quinquefasciatus , a number of phage contigs co-occurred with several marker genes of Wolbachia sp. strain wPip. Conclusions We firstly demonstrate the feasibility to use single mosquito for viral metagenomics, which can provide much more precise virome profiles of mosquito populations. Interspecific comparisons show striking differences in abundance and diversity between the viromes of Ae . aegypti and Cx . quinquefasciatus . Those two mosquito species seem to have their own relatively stable "core eukaryotic virome", which might have important implications for the competence to transmit important medically relevant arboviruses. The presence of Wolbachia in Cx . quinquefasciatus might explain (1) the lower overall viral load compared to Ae . aegypti ...

The conservation of a core virome inAedesmosquitoes across different developmental stages and continents

“…It has been suggested that is maintained in nature through vertical transmission [55]. A recent study has reported that GMV is closely related to Wenzhou sobemo-like virus 4 and Hubei mosquito virus 2 [56]. GMV related virus has been detected only in mosquito sample collected from the field, indicating it is likely acquired horizontally from the environment.…”

“…The viral genomes contain two segments, encoding an RdRp and one hypothetical protein on segment 1 (1500 - 1600 nt), and a capsid and one hypothetical protein encoded by segment 2 (3000 - 3200 nt). GMV, Wenzhou sobemo-like virus 4 and Hubei mosquito virus 2 are all newly described and currently unclassified viruses with distant relationship to the family Luteoviridae and Sobemoviridae [56].…”

“…albopictus contains a “vertically transmitted core virome” as was described before for Ae. aegypti and Culex quinquefasciatus from Guadeloupe [56]. In addition, another set of viruses was identified to be shared by the field collected Ae.…”

“…To investigate the level of conservation of the eukaryotic core viruses identified in Chinese samples from this study with those of other Aedes mosquitoes worldwide, we retrieved 46 published SRA datasets (including 25 datasets of Aedes sp. from Guadeloupe [33], eight from Puerto Rico [24], four from USA [24], seven from Australia [43, 44], one from Thailand [44] and one from China [45]) (Additional file 1 and Fig. 1).…”

“…In a recent study we showed the presence of a relatively stable “core eukaryotic virome” in field Ae. aegypti and Culex quinquefasciatus mosquitoes from Guadeloupe [33]. However, the presence of insect specific viruses (ISVs) in mosquito lab colonies is barely known, which limit our understanding in their role in the development and physiology of mosquitoes.…”