Ssekagiri, A. | bioRxiv Science

bioRxiv2023

Mosquito virus diversity in Western and North-western Uganda

IntroductionSurveillance for mosquito borne arboviruses in Sub Saharan Africa has largely focussed on known viruses including Yellow fever virus (YFV), Rift Valley fever virus (RVFV), Chikungunya virus (CHIKV), West Nile virus (WNV) and Dengue viruses (DENV). Routine surveillance and outbreak investigations traditionally rely on serology, PCR and cell culture. Although such methods are useful, they are do not detect novel or unexpected viruses. MethodsThis study employed unbiased metagenomic next generation sequencing (MNGS) to characterise viruses circulating in mosquitoes of Arua and Kasese districts of Uganda collected systematically as part the ArboViral Infection (AVI) study. Adult mosquito sampling was carried out from multiple sites using light traps baited with solid carbon dioxide (indoors) and pyrethrum spray (outdoors). 10,026 mosquitoes were identified using appropriate morphological identification keys and separated into 96 pools by species and location of collection. Viral RNA extracted from homogenised mosquitoes was reverse transcribed to complimentary DNA and sequenced on the flow cell of an Illumina NextSeq platform. Bioinformatic analysis was performed using a customized in-house metagenomics pipeline. Downstream analyses were carried out in R version 4.2.1. Results97 viruses from 24 families and 31 genera were detected in 96 mosquito pools from Arua and Kasese districts. The abundance of viruses in different families was in the order Rhabdoviridae (33), Flaviviridae (28), Orthomyxoviridae (13), Mesoniviridae (9), Piconarviridae (9), Peribunyaviridae (9), Phasmaviridae (9), Iflaviridae (8), Phenuiviridae (7), Nodaviridae (5), Xinmoviridae (4), Reoviridae (4), Virusidae (2), Nairoviridae (2), Qinviridae (2), Togaviridae (2), Alphatetraviridae (2), Picornaviralesidae (2), Iridoviridae, (1), Nudiviridae (1), Parvoviridae (1), Permutetraviridae (1) and 22 viruses from different families remain unclassified. The Flaviviridae, Togaviridae, Rhabdoviridae, Peribunyaviridae, Phenuiviridae, Nairoviridae, Nodaviridae and Orthomyxoviridae harbor viruses that cause disease in humans and other mammals. Viruses from insect-specific virus families that were detected included the Chuviridae, Iflaviridae, Phasmaviridae and Alphatetraviridae. 92/173 (53%) of the viral genomes had full opening reading frames (ORFs) and diverged by >30% nucleotide pairwise distance from the nearest reference genome. ConclusionThe majority of viruses detected were novel species described for the first time with unknown potential to cause disease. The diversity of virus species in mosquitoes from Uganda, a hotspot for emerging arboviruses has been only partially characterized. This study, carried out in Western and North West Uganda illustrates the scale of richness and virus diversity in the region and the need to further characterise the virome in mosquitoes, especially those with a propensity to feed from human and animal hosts.

genomics↗

bioRxiv2023

Ticks; a reservoir for virus emergence at the human-livestock interface in Uganda

BackgroundUganda is one of the most biodiverse regions on the planet and a hotspot for virus emergence. In particular, the warm-humid lowlands favour tick population growth with the associated risk of tick-borne disease. The prevalent tick species Rhipicephalus appendiculatus, R. evertsi evertsi and Amblyomma variegatum harbour a diverse range of viruses, from harmless to highly pathogenic. Notably, the orthonairoviruses cause human outbreaks of Crimean-Congo haemorrhagic fever (CCHF) regularly within the cattle corridor of Uganda, a region spanning from the south-west to the north-east of the country. MethodsIn the ArboViral Infection (AVI) study, the first to explore the virome of ticks in Uganda using next generation sequencing (NGS), we collected ticks from three geographically diverse areas and subjected these to target-enrichment (TE) NGS. Viral genomes were detected by de novo assembly, mapping and BLASTn. ResultsWe analyzed a total of 2,754 ticks collected from 31 livestock farms in the districts of Arua, Nakaseke and Lyantonde. These were combined into 219 pools by site of collection and tick species, including R. appendiculatus, R. evertsi evertsi, A. variegatum and Hyalomma rufipes. We detected partial or near-complete viral genomes in 163 tick pools; 110 (67%) of which were from Arua, 39 (24%) from Nakaseke and 12 (7%) from Lyantonde districts. 2 pools (2%) were from Arua/Lyantonde. These included 22 species of virus, representing 15 genera and 9 families, including the Nairoviridae, Retroviridae, Orthomyxoviridae, Chuviridae, Rhabdoviridae, Phenuiviridae, Parvoviridae, Poxviridae and Flaviviridae. There were 8 viral species known to be pathogens of humans or animals and 5 highly divergent genomes detected, representing novel virus species. A high abundance of orthonairoviruses was notable, including CCHFV, Dugbe virus and a novel Orthonairovirus species that we have named Macira virus. InterpretationTicks in Uganda are an important reservoir of diverse virus species, many of which remain uncharacterised and of unknown pathogenic potential. Author SummaryTicks are parasitic arachnids that may transmit a spectrum of viral diseases to humans and animals. Uganda is a hotspot for such tick-borne diseases. In this study, we sequenced ticks collected from three geographically diverse regions of Uganda using a semi-agnostic next- generation sequencing method in order to detect viruses from all known virus families. We collected and analyzed 2,754 ticks from 31 farms across the country. Within these ticks, we detected 22 species of virus from 15 genera and 9 viral families, including 8 animal or human pathogens and 5 new novel virus species. Notably, orthonairoviruses, including the highly pathogenic Crimean-Congo haemorrhagic fever virus, were highly prevalent in the ticks. The researchers suggest that ticks in Uganda serve as an important reservoir for diverse viruses, many of which have significant pathogenic potential. This information will inform public health efforts to prevent and control tick-borne diseases in Uganda and other similar regions.

microbiology↗