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

Abstract

Background: Uganda 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. Methods: In 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. Results: We 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.

Widespread human exposure to ledanteviruses in Uganda: A population study

“…It remains unclear as to whether the rodent was incidentally infected or is part of a more established host-vector-virus relationship. Metagenomic NGS of mosquito and livestock–associated tick pools collected in Arua concurrent to the rodent collections described in this paper revealed no evidence of ledanteviruses [ 29 , 46 ], suggesting that further studies should focus on close ectoparasites of rodents such as ticks and fleas.…”

“…Several years later FUKV was again isolated in Japan, this time from cattle serum drawn from febrile sentinel surveillance animals [ 27 ]. Barur virus (BARV) has been isolated from both rodents and ticks in India, and on several occasions from Rhipicephalus ticks in Africa where it has recently been detected by mNGS of ticks parasitising Ugandan cattle [ 28 , 29 ]. A virus serologically indistinguishable from BARV has also been isolated from Rhipicephalus pulchellus ticks in Kenya, however molecular identification was not performed in this case [ 30 ].…”