De novo profiling of RNA viruses inAnophelesmalaria vector mosquitoes from forest ecological zones in Senegal and Cambodia

Abstract

BackgroundMosquitoes are colonized by a large but mostly uncharacterized natural virome of RNA viruses. Anopheles mosquitoes are efficient vectors of human malaria, and the composition and distribution of the natural RNA virome may influence the biology and immunity of Anopheles malaria vector populations.ResultsAnopheles vectors of human malaria were sampled in forest village sites in Senegal and Cambodia, including Anopheles funestus, Anopheles gambiae group sp., and Anopheles coustani in Senegal, and Anopheles hyrcanus group sp., Anopheles maculatus group sp., and Anopheles dirus in Cambodia. Small and long RNA sequences were depleted of mosquito host and de novo assembled to yield non-redundant contigs longer than 500 nucleotides. Analysis of the assemblies by sequence similarity to known virus families yielded 125 novel virus sequences, 39 from Senegal Anopheles and 86 from Cambodia. Important monophyletic virus clades in the Bunyavirales and Mononegavirales orders are found in these Anopheles from Africa and Asia. Small RNA size and abundance profiles were used to cluster non-host RNA assemblies that were unclassified by sequence similarity. 39 unclassified non-redundant contigs >500 nucleotides strongly matched a pattern of classic RNAi processing of viral replication intermediates, and 1566 unclassified contigs strongly matched a pattern consistent with piRNAs. Analysis of piRNA expression in Anopheles coluzzii after infection with O’nyong nyong virus (family Togaviridae) suggests that virus infection can specifically alter abundance of some piRNAs.ConclusionsRNA viruses ubiquitously colonize Anopheles vectors of human malaria worldwide. At least some members of the mosquito virome are monophyletic with other arthropod viruses. However, high levels of collinearity and similarity of Anopheles viruses at the peptide level is not necessarily matched by similarity at the nucleotide level, indicating that Anopheles from Africa and Asia are colonized by closely related but clearly diverged virome members. The interplay between small RNA pathways and the virome may represent an important part of the homeostatic mechanism maintaining virome members in a commensal or nonpathogenic state, and host-virome interactions could influence variation in malaria vector competence.

The virome of vector mosquitoes

“…Rather, all mosquitoes seem to harbor a diverse and abundant virome, which contrasts with the fact that only a few species are competent vectors for arboviruses. Anopheles mosquitoes, for example, which possess a very rich virome, are only known to transmit a single arbovirus, o'nyong-nyong virus [19,26,27].…”

Differential Small RNA Responses against Co-Infecting Insect-Specific Viruses in Aedes albopictus Mosquitoes

“…Aedes and Culex are two major genera of mosquitoes that transmit medically important arthropod-borne viruses (arboviruses) such as dengue, West Nile and Zika viruses. Recent metagenomics studies have shed light on the virome of these mosquito vectors, revealing diverse virus communities largely composed of insect-specific viruses (ISVs) that specifically infect invertebrates but not vertebrates [1][2][3][4][5][6][7]. ISVs have been shown to negatively regulate some arbovirus infections in mosquito cell cultures and in vivo [8][9][10][11][12][13][14].…”

Decoding rRNA sequences for improved metagenomics of sylvatic mosquito species

“…During library preparations of mosquito samples for RNA-seq, routinely used methods for depleting rRNA are commercial kits optimised for human or mice samples (10)(11)(12)(13)(14)(15) or probe hybridisation followed by ribonuclease digestion where the probes are 80-100 base pair antisense oligos. In cases where the reference rRNA sequence of the target species is not known, oligos would be designed based on the rRNA sequence of the closest related species (25, this study).…”