A new genetic variant of the Crimean–Congo hemorrhagic fever virus isolated in Crimea

Abstract

This work represents the results of the genetic identification of the Crimean-Congo hemorrhagic fever virus (CCHF virus) strains isolated in the Crimean Federal District in conducting the epidemiological survey of the imported case of CCHF from Crimea in 2015. One sample of the serum from a patient and 61 pools (506 specimens) of ticks collected during the epizootiological survey of 6 administrative districts of the Crimean Federal District were tested using PCR for the presence of the CCHF virus RNA. RNA of the CCHF virus was detected in serum from a patient and 10 samples of ticks. The genetic identification of the CCHF virus was performed by sequencing the virus genome S-, M-, and L-segments. The result of the molecular-genetic analysis revealed a high degree of identity between the samples of the CCHF virus in human serum and three samples of ticks and their belonging to a new genetic Crimea subclade (Vd) of the genotype Europe 1. Whole genome sequencing of two samples of CCHF virus belonging to the Crimea subgroup (Vd) was performed. CCHF virus variants of the Crimea subclade (Vd) of the Europe- lgenotype were described for the first time. These variants were endemic to the territory of the Crimean peninsula.