Detection and characterisation of novel vector-borne viruses in Mozambique

Abstract: Arthropod vectors carry a wide variety of viruses that can cause vector-borne infectious diseases that affect the health of both humans and animals. The vector-borne viruses present in nature show high diversity and can infect a broad range of hosts. Moreover, some of these viruses may be transmitted to new hosts in the future and possibly become pathogenic and/or zoonotic. This thesis describes the detection and characterisation of novel vector-borne viruses circulating in arthropod vectors from an understudied area, the Zambezi Valley of Mozambique, using a viral metagenomic approach. A combination of sequence-independent amplification, high-throughput sequencing and different bioinformatic tools were used to investigate the viromes of mosquitos and ticks in this area. The results of this study resulted in the identification of a broad range of viruses belonging to several viral families, including Flaviviridae, Rhabdoviridae, Iflaviridae, Picornaviridae, and Dicistroviridae, as well as a number of unclassified RNA viruses that were present in Culex and Mansonia spp. mosquitoes. The full-length genome of a novel flavivirus from Mansonia was characterised, and an analysis of conserved domains showed that it belongs to the insect-specific flaviviruses and is closely related to Nakiwogo virus. Further, a near full-length genome of a highly divergent picorna-like virus from Culex mosquitoes was characterised, and the phylogenetic analysis showed that the novel picorna-like virus clustered with members of iflaviruses, confirming that it belongs to the Iflaviridae viral family in the order Picornavirales. Analysis of the Rhipicephalus tick virome identified a number of reads classified as being in the Orthomyxoviridae family. The assembled contigs showed an amino acid identity (32-52%) towards known viruses in the genus Quaranjavirus. Overall, viral metagenomics was successfully used to detect and characterise the viromes of important vectors (mosquitoes and ticks) from Mozambique. All the viral sequences identified from this study were divergent from previously known viruses and potentially represent novel viruses that are circulating in the Zambezi Valley of Mozambique. These results constitute the basis for further studies on viruses that are circulating in vectors and on the evolution, viral maintenance and transmission of pathogenic arboviruses.

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