Characterisation of the virome of Culicoides brevitarsis Kieffer (Diptera: Ceratopogonidae), a vector of bluetongue virus in Australia.

Abstract

Culicoides spp., a common biting midge genus, are haematophagous insects that can transmit pathogens to humans and other animals. Some species transmit arboviruses, including bluetongue virus, epizootic haemorrhagic disease virus, African horse sickness virus and Schmallenberg virus to vertebrates, which can be detrimental to livestock and wild animals. Culicoides spp. can also have a diversity of insect-specific viruses (ISVs) that can only be transmitted between insects and others related to known arboviruses. For Culicoides brevitarsis and other Culicoides spp. in Australia, the virome is largely unexplored. We used high-throughput sequencing to characterise the virome of C. brevitarsis collected from Casino, New South Wales, Australia. For virus detection, the total RNA was extracted from pools of C. brevitarsis followed by rRNA depletion and Illumina short-read-based RNA sequencing. The reads were quality-checked, filtered and assembled into contigs, compared with the non-redundant protein and conserved domain databases for viral detection and genome organisation, respectively. The phylogenetic analysis was used to further characterise the viruses. We detected new virus diversity including ten viruses belonging to eight different families with complete or near-complete coding regions. Seven of these were novel virus species belonging to the families: Chuviridae, Orthomyxoviridae, Peribunyaviridae, Qinviridae, Rhabdoviridae and Solemoviridae. In addition, the novel Peribunyaviridae virus should also be considered part of a new genus. Whilst most of the detected viruses grouped into families with viruses that can infect insects, animals or both, the novel species of Solemoviridae was closely related to an economically important plant pathogen, the sugarcane yellow leaf virus. Our quantitative PCR-based screening confirmed the absence of any Wolbachia endosymbiont within the collected samples. Furthermore, we detected fragments of three more virus families known to infect fungi and plants. The detection of potential arboviruses and ISVs in Culicoides spp. is important in understanding virus epidemiology.