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

AbstractBackgroundMosquitoes 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.