Abstract
Hyalomma rufipes is a widely distributed tick species and a competent vector of Crimean-Congo Hemorrhagic Fever Virus (CCHFV), a serious zoonotic pathogen endemic to over 30 countries. Despite the epidemiological importance of CCHFV and H. rufipes in East Africa, little is known about the genetic structure and movement of H. rufipes populations, limiting the understanding of CCHFV transmission dynamics in this region. This study developed and characterized 14 polymorphic microsatellite markers to support population genetic studies of H. rufipes. H. rufipes ticks were collected from livestock in Garissa and Isiolo counties in northern Kenya. Morphological identification was confirmed using 16S rRNA Sanger sequencing and phylogenetic analysis. Low-pass whole genome sequencing was performed on representative samples, and the Quality and Diversity of DNA (QDD) pipeline was used to identify and design microsatellite primers. Of 59,201 candidate loci, 30 were selected for initial screening; 14 loci consistently amplified and were polymorphic. These included mostly tetranucleotide repeats and showed high allelic richness and gene diversity. Several loci showed signs of null alleles, but no evidence of stuttering or allelic dropout was found. These newly developed microsatellite markers provide a valuable tool for investigating H. rufipes population dynamics and dispersal, with the ultimate goal of understanding CCHFV transmission dynamics in East Africa.