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

Abstract

Background Mosquitoes are colonized by a large but mostly uncharacterized natural virome of RNA viruses, and the composition and distribution of the natural RNA virome may influence the biology and immunity of Anopheles malaria vector populations. Results Anopheles mosquitoes were sampled in malaria endemic 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. The most frequent mosquito species sampled at both study sites are human malaria vectors. Small and long RNA sequences were depleted of mosquito host sequences, de novo assembled and clustered to yield non-redundant contigs longer than 500 nucleotides. Analysis of the assemblies by sequence similarity to known virus families yielded 115 novel virus sequences, and evidence supports a functional status for at least 86 of the novel viral contigs. Important monophyletic virus clades in the Bunyavirales and Mononegavirales orders were found in these Anopheles from Africa and Asia. The remaining non-host RNA assemblies that were unclassified by sequence similarity to known viruses were clustered by small RNA profiles, and 39 high-quality independent contigs strongly matched a pattern of classic RNAi processing of viral replication intermediates, suggesting they are entirely undescribed viruses. One thousand five hundred sixty-six additional high-quality unclassified contigs matched a pattern consistent with Piwi-interacting RNAs (piRNAs), suggesting that strand-biased piRNAs are generated from the natural virome in Anopheles . To functionally query piRNA effect, we analyzed piRNA expression in Anopheles coluzzii after infection with O’nyong nyong virus (family Togaviridae ), and identified two piRNAs that appear to display specifically altered abundance upon arbovirus infection. Conclusions Anopheles vectors of human malaria in Africa and Asia are ubiquitously colonized by RNA viruses, some of which are monophyletic but clearly diverged from other arthropod viruses. The interplay between small RNA pathways, immunity, and the virome may represent part of the homeostatic mechanism maintaining virome members in a commensal or nonpathogenic state, and could potentially influence vector competence. Electronic supplementary material The online version of this article (10.1186/s12864-019-6034-1) contains supplementary material, which is available to authorized users.

Viromics on Honey-Baited FTA Cards as a New Tool for the Detection of Circulating Viruses in Mosquitoes

“…In agreement with previous virome studies, most of the taxa derived from honey-baited FTA cards have been identified in various invertebrates [39] and associated to mosquitoes [40]. Additionally, mosquito-specific viruses detected in FTA cards (Table 2) have been described as part of the viral communities harbored by several mosquito species in different geographic regions [41][42][43][44][45][46][47][48]. Bold type corresponds to the selected viruses for primers design.…”

Identification of diverse viruses associated with grasshoppers unveils phylogenetic congruence between hosts and viruses

“…Similar viRNAs distributions were observed in other insects, such as in whiteflies [24], thrips [29] and bumblebees [27]. It is possible that the 21nt peak we seen in brachycera species such as flies and mosquitoes is unusual for insects [51][52].…”

Leaning Into the Bite: The piRNA Pathway as an Exemplar for the Genetic Engineering Need in Mosquitoes

“…2) Cluster content, number and genomic distribution is diverged in both genera [( George et al, 2015 ; Crava et al, 2020 ; Palatini et al, 2020 ). 3) A strong activity of PIWIs and piRNAs in the soma and 4] multiple distinct roles in gene expression are evident in both genera ( Belda et al, 2019 ; Halbach et al, 2020 ). As such, the piRNA pathway represents an enigmatic biological system in mosquitoes, warranting a more aggressive study of the system in mosquito species.…”