Genetic characterization of arboviruses and associated biting midges and related vectors in selected counties in Kenya

Abstract

Biting midges are small insects (1-3mm long) in the order diptera. Medical and veterinary importance of biting midges lies in the ability of certain members of these insects to transmit protozoa and filariae as well as act as vectors of viral diseases in humans and domestic animals. These vectors have been implicated in the transmission of African horse sickness virus, Bluetongue virus, Oropouche virus, Shmallenberg, Epizootic Haemorrhagic Disease and Akabane virus among other pathogenic viruses, which have been associated with diseases in human and livestock animals. The aim of the study was to identify and genetically characterize arboviruses among biting midges and related vectors collected from various sites in Kenya including; Turkana, Baringo, Kacheliba, Budalangi and Isiolo. Further, the study sought to characterize the biting midge vectors so as to determine the species of vectors associated with the identified viruses. Insect specimens from the field were first sorted and pooled according to the collection site. The pooled specimens were homogenized and clarified by centrifugation. The supernatant was used to extract the viral RNA while the pellet was used to extract the vector DNA. The extracted RNA was subjected to sequencing using the metagenomics approach while extracted DNA was used to carry out amplicon-based high-throughput sequencing. The sequence data were initially cleaned and assembled for subsequent analysis. The sequences obtained were taxonomically classified through BLAST analysis. Subsequently, phylogenetic analysis was conducted to show the relationship of the identified viruses to existing ones in public databases. The study identified 15 viruses that were phylogenetically distinct. These viruses are classified into seven families, with one virus belonging to the newly proposed negevirus taxon. Partitiviridae, Iflaviridae, Picornaviridae, Tombusviridae, Solemoviridae, Totiviridae, and Chuviridae are among the seven virus families. In addition, a wide variety of midge species was discovered that could be linked to the viruses discovered. Midges within the Ceratopogonidae family were the most common insects identified. Others included those in the Chironomidae and Cecidomydiae families. The findings show a wide range of RNA viruses in Kenyan midges, including previously unknown viruses. Furthermore, metabarcoding analysis using COI barcodes reveals a high species richness among the insects characterized. The findings in this study highlights the presence of a number of viruses in midges from different sites across Kenya, some of which can be considered as novel viruses. Further, different species of biting midges were identified in this study that are possibly associated with these viruses identified. These findings are therefore important in mapping the potential areas with significant risk for disease occurrence based on the knowledge of species of insect vectors associated with particular viral pathogens. Nonetheless, the study recommends further studies to identify any viral pathogens among the insect vectors that have been associated with disease in this region.