Genetic variability of Crimean-Congo haemorrhagic fever virus in Russia and Central Asia.

Hyalomma marginatum ticks (449 pools, 4787 ticks in total) collected in European Russia and Dermacentor niveus ticks (100 pools, 1100 ticks in total) collected in Kazakhstan were screened by ELISA for the presence of Crimean-Congo haemorrhagic fever virus (CCHFV). Virus antigen was found in 10.2 and 3.0 % of the pools, respectively. RT-PCR was used to recover partial sequences of the CCHFV small (S) genome segment from seven pools of antigen-positive H. marginatum ticks, one pool of D. niveus ticks, four CCFH cases and four laboratory virus strains. Additionally, the entire S genome segments of the CCHFV strains STV/HU29223 (isolated from a patient in European Russia) and TI10145 (isolated from H. asiaticum in Uzbekistan) were amplified, cloned and sequenced. Phylogenetic analysis placed all CCHFV sequences from Russia in a single, well-supported clade (nucleotide sequence diversity up to 3.2 %). Virus sequences from H. marginatum were closely related or identical to those recovered from patients in the same regions of southern Russia. Newly described CCHFV strains from Central Asian countries fell into two genetic lineages. The first lineage was novel and included closely related virus sequences from Kazakhstan and Tajikistan (nucleotide sequence diversity up to 3.2 %). In contrast, a newly described CCHFV strain from Uzbekistan, strain TI10145, clustered on the phylogenetic trees with strains from China.