Identification and genetic characterization of Jingmen tick virus from ticks sampled in select regions of Kenya; 2022-2024.

Jingmen tick virus (JMTV), an emerging segmented RNA virus classified as an ungrouped flavivirus, poses a growing public health concern globally. Known for its association with febrile illnesses and wide host range, JMTV has been detected in Rhipicephalus, Hyalomma, and Amblyomma ticks collected from cattle, goats, sheep, camels, and chickens in pastoral regions of Kenya, including Baringo, Mandera, Malindi, Lamu, Mombasa, Wajir, Isiolo, and West Pokot. Using viral metagenomics next-generation sequencing, this study analysed adult ticks (n = 1629, 72 pools). A total of 53% (38/72) pools were positive for at least one viral pathogen, with JMTV detected in 87% (33/38) of these pools across all study sites. Phylogenetic analyses revealed evidence of distinct Kenyan JMTV strains, with sequence segments from Malindi and Wajir clustering uniquely in their own clade; suggesting potential localised evolutionary pressures. Time calibrated phylogeny for the segment 1(RdRp) suggested varied ancestral origins and evolutionary relationships for the JMTV strains. MEME, BUSTED and FUBAR methods implemented in the Data-Monkey, unanimously identified codon 290 in segment 1 and 30 in segment 4 to be undergoing episodic positive selection. Recombination analysis performed using the RDP4 recombination detection tool indicated a recombination event in segment 2 of the Lamu JMTV strain that was confirmed by seven detection methods of the RDP4 tool and visualised in BootScan. These findings suggest that Kenyan JMTV strains are undergoing positive selection, potentially driven by unique ecological and host factors. Segmented genome evidence of recombination highlights the increasing virus's potential for antigenic diversity. Host diversity and virus phylogenetic patterns underscore the zoonotic potential and its capacity for regional spread, emphasizing the critical need for enhanced vector surveillance. Temporal and ecological drivers like seasonal tick activity and livestock movement warrant investigation to elucidate JMTV transmission dynamics. Prioritizing tick-borne virus surveillance in Kenya will strengthen public health strategies and mitigates emerging viral risks.