Genomic characterisation of Crimean-Congo haemorrhagic fever virus (CCHFV) in Tajikistan identifies a novel reassortant virus

Abstract

Crimean-Congo haemorrhagic fever virus (CCHFV) is an important human tick-borne pathogen, able to cause severe haemorrhagic fever. CCHFV is endemic in Tajikistan, which records between 5–38 cases of CCHF a year from southern regions. Molecular surveillance of CCHFV is crucial to implement effective prevention and control strategies, understand viral evolution, study transmission dynamics, and develop effective diagnostics, therapeutics, and vaccines. While the presence of Asia-1 and Asia-2 genotypes has been previously reported, only two historical samples from Tajikistan have been fully sequenced. In this study we developed and applied a genotype IV-specific tiling PCR enrichment approach recovering 52 CCHFV genome segment sequences from clinical and Hyalomma tick samples collected between 2017–2023. Most sequences belonged to the Asia-2 genotype, but one virus exhibited an Asia-1 S segment combined with Asia-2 M and L segments, representing the first evidence of such viral reassortment event in Tajikistan. Author summary: Crimean-Congo haemorrhagic fever (CCHF) is a severe haemorrhagic disease caused by CCHF virus. The virus is found in Europe, Africa and Asia, and is predominantly transmitted by Hyalomma ticks. The negative-sense RNA genome is highly diverse and consists of the small (S), medium (M) and large (L) segments. Traditionally, different CCHFV genotypes have been named after their main geographic location, with Central Asian countries mostly reporting the presence of Asia-1 and Asia-2 viruses (genotypes IVa and IVb). In this study, we have developed a novel PCR-based enrichment methodology designed to amplify genotype IV CCHFV genome segments and characterised viruses from clinical as well as tick samples collected from Tajikistan, an endemic region for the virus with limited genomic output. Furthermore, we described for the first time in the region a novel clinical reassortant CCHFV containing an Asia-1 S segment and Asia-2 M and L segments, further elucidating previously unknown genetic diversity within Tajikistan. The genetic characterisation of circulating viruses from endemic regions is crucial to develop and implement local public health strategies aimed at preventing and controlling virus transmission, as well as develop effective diagnostics, therapeutics and vaccines.

Original publication: PLOS Neglected Tropical Diseases (2026-04-07). Source. Source DOI: 10.1371/journal.pntd.0014204.