Molecular-genetic characteristics of variants of the Crimean-Congo hemorrhagic fever virus, isolated in the territory of the Republic of Crimea in 2015-2017

• A.S. Volynkina
• Кotenev Е.S.
• Lisitskaya Ya.V.
• Tikhonov S.N.
• Kulichenko A.N.

Abstract

In June 2017, the first case since 1967 of CCHF in the Republic of Crimea was registered. 183 pools of ixodid ticks collected during the epizootic survey of the 5 administrative regions of the Republic of Crimea were tested by PCR, CCHF virus RNA was detected in 29 pools (15.9%).

The aim of the work was molecular genetic characteristics of the RNA isolates of the CCHF virus detected in samples of clinical and field samples collected in the Crimea in 2017, a comparative analysis of the genetic variants of the CCHF virus circulating in the Republic of Crimea in 2015-2017.

Material and methods. 1 sample of blood of CCHF patient, registered in 2017 in the Republic of Crimea and 29 pools of ixodid ticks positive for the presence of RNA of CCHF virus, collected in 2017 in Chernomorsky and Leninsky administrative districts of the Republic of Crimea. The genetic identification of the CCHF virus was carried out by sequencing the fragments of the S-, M- and L-segments of the virus genome. Phylogenetic analysis was carried out in the Mega 5.05 program using the Neighboor joining method, according to the Kimura-2 algorithm.

Results. The nucleotide sequence of fragments of the S-, M- and L-segments of the genome of RNA isolates of CCHF virus detected in a sample of plasma of the patient with CHF and 6 samples of suspensions of ticks with sufficient viral load was determined. As a result of sequencing of fragments of the genome of RNA isolates of CCHF virus, it was established that in 2017 in the Republic of Crimea the isolates of the CCHF virus of the genotype "Europe-1", belonging to the subtypes Va "Stavropol-Rostov-Astrakhan" and Vd "Crimea", were circulating simultaneously. In 2015, only strains of the subtype Vd were found in the Crimea. The Vd subtype "Crimea" is an endemic genetic variant of the CCHF virus for the Crimean peninsula. RNA isolates of the CCHF virus of the subtype Va "Stavropol-Rostov-Astrakhan" were not detected in the territory of the Republic of Crimea before. The emergence in 2017 in the Crimean region of strains of the CCHF virus subtype Va is possibly associated with the importation of CCHF virus infected ticks, during the transportation of cattle to the Crimea from the territory of subjects of the south of Russia, enzootic according to CCHF. To assess the genetic diversity of the CCHF virus population in the Republic of Crimea and to reveal the regularities in the distribution of genetic variants, it is necessary to conduct further molecular genetic studies of the strains and RNA isolates of the CCLF virus detected in the territory of the Republic of Crimea.

Keywords:Crimean-Congo haemorrhagic fever, molecular epidemiology, phylogenetic analysis, Republic of Crimea

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