High-Resolution Metatranscriptomics Reveals the Ecological Dynamics of Mosquito-Associated RNA Viruses in Western Australia

Abstract

Mosquitoes harbor a high diversity of RNA viruses, including many that impact human health. Despite a growing effort to describe the extent and nature of the mosquito virome, little is known about how these viruses persist, spread, and interact with both their hosts and other microbes. To address this issue we performed a metatranscriptomics analysis of 12 Western Australian mosquito populations structured by species and geographic location. Our results identified the complete genomes of 24 species of RNA viruses from a diverse range of viral families and orders, among which 19 are newly described. Comparisons of viromes revealed a striking difference between the two mosquito genera, with viromes of mosquitoes of the Aedes genus exhibiting substantially less diversity and lower abundances than those of mosquitoes of the Culex genus, within which the viral abundance reached 16.87% of the total non-rRNA. In addition, there was little overlap in viral diversity between the two genera, although the viromes were very similar among the three Culex species studied, suggesting that the host taxon plays a major role in structuring virus diversity. In contrast, we found no evidence that geographic location played a major role in shaping RNA virus diversity, and several viruses discovered here exhibited high similarity (95 to 98% nucleotide identity) to those from Indonesia and China. Finally, using abundance-level and phylogenetic relationships, we were able to distinguish potential mosquito viruses from those present in coinfecting bacteria, fungi, and protists. In sum, our metatranscriptomics approach provides important insights into the ecology of mosquito RNA viruses.IMPORTANCE Studies of virus ecology have generally focused on individual viral species. However, recent advances in bulk RNA sequencing make it possible to utilize metatranscriptomic approaches to reveal both complete virus diversity and the relative abundance of these viruses. We used such a metatranscriptomic approach to determine key aspects of the ecology of mosquito viruses in Western Australia. Our results show that RNA viruses are some of the most important components of the mosquito transcriptome, and we identified 19 new virus species from a diverse set of virus families. A key result was that host genetic background plays a more important role in shaping virus diversity than sampling location, with Culex species harboring more viruses at higher abundance than those from Aedes mosquitoes.

Keywords: Australia; ecology; evolution; mosquito; phylogeny; transcriptomics; virome.

FIG 1

Information on the hosts and geographic locations (southwestern Australia) of the mosquito samples collected in this study. (Top) Maximum likelihood phylogeny of the cytochrome c oxidase (cox1) gene from mosquito samples collected in this study. The name of each sequence contains information on the sampling location and host species identification in the field. (Bottom) Locations of four sampling sites, marked by sold black dots.

FIG 2

Overview of the diversity and abundance of the RNA viruses discovered. From top to bottom, we show four column graphs depicting the number of viruses, the composition of viral families, the abundance of the total virome, and the abundance of the host RPL32 gene in each of the 12 pools sequenced here. The mosquito species and location information for each pool are shown at the top.

FIG 3

Similarity of viromes between host species (A) and geographic locations (B). The size of the circle is proportional to the total number of viruses discovered in each mosquito species (A) or geographic location (B). Within the circle, information on the host species or geographic location and the number of viruses (in parentheses) is provided. The thickness of the line connecting the circles reflects the number of viruses shared between species or geographic locations. The number of shared viruses is shown next to the line.

FIG 4

Evolutionary history and genomic features of the negative-sense RNA viruses discovered. The maximum likelihood phylogenetic trees show the positions of newly discovered viruses (solid black circles) in the context of representatives of their closest relatives. The names of mosquito viruses identified in previous studies are marked in red and contain information on the mosquito species from which they were sampled (square brackets). The genome structures of these newly discovered viruses are shown next to their corresponding phylogenies. Predicted ORFs of these genomes are labeled with information on the potential protein or protein domain that they encode.

FIG 5

Evolutionary history and genomic features of the positive-sense RNA viruses discovered. The legend is the same as that for Fig. 4.

FIG 6

Evolutionary history and genomic features of the double-stranded RNA (dsRNA) viruses discovered. The legend is the same as that for Fig. 4.

FIG 7

Matching tree topologies of the Wilkie qin-like viruses and a group of fungi (cox1 gene) discovered in three mosquito pools. Pool information is given in the middle of the two phylogenies, both of which are midpoint rooted for clarity only.