Dissecting the Species-Specific Virome in Culicoides of Thrace

Abstract

Biting midges (Culicoides) are vectors of arboviruses of both veterinary and medical importance. The surge of emerging and reemerging vector-borne diseases and their expansion in geographical areas affected by climate change has increased the importance of understanding their capacity to contribute to novel and emerging infectious diseases. The study of Culicoides virome is the first step in the assessment of this potential. In this study, we analyzed the RNA virome of 10 Culicoides species within the geographical area of Thrace in the southeastern part of Europe, a crossing point between Asia and Europe and important path of various arboviruses, utilizing the Ion Torrent next-generation sequencing (NGS) platform and a custom bioinformatics pipeline based on TRINITY assembler and alignment algorithms. The analysis of the RNA virome of 10 Culicoides species resulted in the identification of the genomic signatures of 14 novel RNA viruses, including three fully assembled viruses and four segmented viruses with at least one segment fully assembled, most of which were significantly divergent from previously identified related viruses from the Solemoviridae, Phasmaviridae, Phenuiviridae, Reoviridae, Chuviridae, Partitiviridae, Orthomyxoviridae, Rhabdoviridae, and Flaviviridae families. Each Culicoides species carried a species-specific set of viruses, some of which are related to viruses from other insect vectors in the same area, contributing to the idea of a virus-carrier web within the ecosystem. The identified viruses not only expand our current knowledge on the virome of Culicoides but also set the basis of the genetic diversity of such viruses in the area of southeastern Europe. Furthermore, our study highlights that such metagenomic approaches should include as many species as possible of the local virus-carrier web that interact and share the virome of a geographical area.

Meta-Viromic Sequencing Reveals Virome Characteristics of Mosquitoes and Culicoides on Zhoushan Island, China

“…Viruses of the Rhabdoviridae, Polycipiviridae, Phasmaviridae, Phenuiviridae, and other virus families were identified in this study, as in other studies, but in markedly different proportions ( 32 ). In this study, Polycipiviridae viruses (e.g., Hubei picorna-like virus 82, a ssRNA + insect-related virus found in spiders) were very abundant in Culicoides viromes, which has not been reported previously.…”

“…Meta-viromic approaches have enabled the characterization of viromes carried by Culicoides in some regions and promoted the discovery of new viruses. Analysis of the RNA viromes of 10 Culicoides species in Thrace, southeastern Europe, led to the identification of novel RNA viruses with genomic signatures and revealed that each Culicoides species carried a specific virus set ( 32 ). The viromes of Culicoides impunctatus populations in Scotland ( 33 ), Culicoides imicola in Senegal ( 34 ), Culicoides arakawae in Japan ( 35 ), and mixed Culicoides populations ( 6 , 36 ) have been examined.…”

Mitochondrial genome sequencing, mapping, and assembly benchmarking for Culicoides species (Diptera: Ceratopogonidae)

“…Consequently, additional efforts to validate the identity of the generated mitochondrial genomes are needed [ 9 ]. The mitogenome of the host Bos taurus was recovered from C. biguttatus DNA reads, confirming the potential of metagenomics for studying vectors and their hosts simultaneously, as well as potentially vectored pathogens [ 35 – 37 ]. Notably, all C. biguttatus specimens used for mitogenome reconstruction were sampled in a dairy barn.…”

Biting Midges (Diptera: Ceratopogonidae) as Vectors of Viruses

“…Studies on the microbiota of Culicoides biting midges are scarce, mainly restricted to the bacterial midgut fauna, and differentiation, in the best case, to the genus level [183][184][185][186]. A few studies exist on the virome of Culicoides species [187][188][189][190]. Both groups of studies do not consider biotic interactions or correlate the midgut fauna with pathogen infection of the insect host, although an impact of bacteria and viruses must be considered likely based on studies with mosquitoes [191].…”