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. 2021 Apr 27;13(5):768.
doi: 10.3390/v13050768.

Virome Diversity among Mosquito Populations in a Sub-Urban Region of Marseille, France

Amira Nebbak  1   2   3 , Sonia Monteil-Bouchard  4   5 , Jean-Michel Berenger  1   2 , Lionel Almeras  1   2   6 , Philippe Parola  1   2 , Christelle Desnues  4   5
Affiliations

Virome Diversity among Mosquito Populations in a Sub-Urban Region of Marseille, France

Amira Nebbak et al. Viruses. .

Abstract

Some mosquito species have significant public health importance given their ability to transmit major diseases to humans and animals, making them the deadliest animals in the world. Among these, the Aedes (Ae.) genus is a vector of several viruses such as Dengue, Chikungunya, and Zika viruses that can cause serious pathologies in humans. Since 2004, Ae. albopictus has been encountered in the South of France, and autochthonous cases of Dengue, Chikungunya, and Zika diseases have recently been reported, further highlighting the need for a comprehensive survey of the mosquitoes and their associated viruses in this area. Using high throughput sequencing (HTS) techniques, we report an analysis of the DNA and RNA viral communities of three mosquito species Ae. albopictus, Culex (Cx.) pipiens, and Culiseta (Cs.) longiareolata vectors of human infectious diseases in a small sub-urban city in the South of France. Results revealed the presence of a significant diversity of viruses known to infect bacteria, plants, insects, and mammals. Several novel viruses were detected, including novel members of the Rhabdoviridae, Totiviridae, Iflaviviridae, Circoviridae, and Sobemoviridae families. No sequence related to major zoonotic viruses transmitted by mosquitoes was detected. The use of HTS on arthropod vector populations is a promising strategy for monitoring the emergence and circulation of zoonoses and epizooties. This study is a contribution to the knowledge of the mosquito microbiome.

Keywords: France; diversity; metagenomics; mosquitoes; virome.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1
Mosquito collection sites. Map of Cuges-les-Pins area (France) indicated the location of the six sampling sites and the proportion of each of the three mosquito species collected. Ae. albopictus (blue), Cx. pipiens (red), and Cs. longiareolata (green).
Figure 2
Figure 2
Mosquito species identification by MALDI-TOF MS-based on LSV ranges. (a) Results of MS spectra query for mosquito specimens tested blindly against the MS database were classified according to identification relevance based on LSVs. LSVs > 1.8, reliable identification (green); 1.8 > LSVs > 1.6, identification requiring manual validation (yellow); 1.6 > LSVs; corresponding to unreliable identification and considered as non-identified (red). (b) Representative MS spectra of three mosquito species were collected in this study. Ae. albopictus (A,B), Cx. pipiens (C,D), and Cs. longiareolata (E,F). Spectra analysis was performed using Flex analysis 3.3 software. a.u., arbitrary units; m/z, mass-to-charge ratio.
Figure 3
Figure 3
Taxonomic assignment of reads (a) Taxonomic annotation of the reads by MEGAN after Blast X search against the National Center for Biotechnology Information (NCBI) protein database using DIAMOND. (b) Relative abundance of viral families in mosquito metagenomes according to their target hosts.
Figure 4
Figure 4
Phylogenetic analysis of the mosquito Arboretum virus CLP-1 compared to other Rhabdoviridae viruses.
Figure 5
Figure 5
Phylogenetic analysis of mosquito Cyclovirus CLP-1, mosquito Krikovirus (CLP-1, 2, and 3), and mosquito Smacovirus CLP-1 compared to other Circoviridae viruses.
Figure 6
Figure 6
Phylogenetic analysis of mosquito Totivirus CLP-1 to CLP-8 compared to other Totiviridae viruses.
Figure 7
Figure 7
Phylogenetic analysis of mosquito Somebo-like virus CLP-1 and 2 compared to other Sobemo viruses.
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