Abstract
<jats:p>In this study, a molecular genetic characterization of a strain of Crimean-Congo hemorrhagic fever virus (CCHFV) isolated in the Karazhal village area of the Ulytau region, Republic of Kazakhstan, was conducted. The relevance of this work is due to the persistent epidemiological significance of the pathogen, the high case fatality rate, and the need for continuous monitoring of its genetic diversity and circulation patterns. The study also addresses the limited availability of whole-genome data on circulating CCHFV strains in Kazakhstan, which complicates comprehensive comparative analyses and evaluation of the virus’s evolutionary dynamics. The obtained results contribute to clarifying molecular-epidemiological relationships between local and foreign isolates and to improving the effectiveness of early outbreak response systems. Nucleic acid extraction was performed using the QIAamp Viral RNA Mini Kit. The presence of viral RNA was confirmed by real-time polymerase chain reaction (RT-PCR) using the RealStar CCHFV RT-PCR Kit 1.0, as well as according to the protocol of the UK Health Security Agency (UKHSA). For analysis, an aliquot with a threshold cycle (Ct) value of 24.25 was selected, indicating a sufficient viral load for high-accuracy sequencing. Whole-genome sequencing was carried out on the MinION platform (Oxford Nanopore Technologies) with prior PCR enrichment, which improved genome coverage. The data were processed offline on a Linux-based system using MRIGlobal algorithms, including quality control, consensus sequence assembly, and alignment with reference genomes. Phylogenetic analysis demonstrated that the isolated strain belongs to the Asia 1 lineage, which is widely distributed in southern regions of Kazakhstan and across Central Asia. The sample clustered with isolates from India, Iran, and Uganda, indicating the broad geographic distribution of this lineage and potential transboundary transmission routes. These findings expand current knowledge of CCHFV genetic diversity and have practical significance for improving molecular epidemiology, diagnostics, and infection prevention.</jats:p>