Detection of potential sites of recombination in the Tick-borne encephalitis virus by the methods of comparative genomics

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Abstract

The results of the bioinformatic search for the potential sites of the recombination in the genome-wide structures of the tick-borne encephalitis virus (TBEV) through a series of software techniques were presented in this work. The genomes of the 55 TBEV strains were assayed, 21 of them showed the presence of the recombination sites. Recombinant strains belonged to the Far Eastern (19 strains) and European (2 strains) genotypes. 22 sites of the recombination attributed were identified to five types based on position, strain, and regional characteristics. The parental strains were identified based on the genotypic and geographical parameters, which do not contradict the possibility of the formation of the recombinants. Nearly two-thirds of the sites are located in the regions of NS4a and Ns4b genes, which are the "hot spots" of the recombination, most of them being concentrated in the gene NS4. it was shown that the recombination processes did not occur at the level of the genotypes (European genotype) or certain groups within the genotype (Far East) and were typical of the peripheral populations.

About the authors

Yu. P. Dzhioev

Irkutsk State Medical University, Ministry of Health of the Russian Federation; Scientific Center of Family Health Problems and Human Reproduction, Siberian Branch, Russian Academy of Medical Sciences

Author for correspondence.
Email: alanir07@mail.ru

Yuriy Dzhioev, MD, PhD

664025, Irkutsk

664003, Irkutsk

Russian Federation

A. Paramonov

Irkutsk State Medical University, Ministry of Health of the Russian Federation; Scientific Center of Family Health Problems and Human Reproduction, Siberian Branch, Russian Academy of Medical Sciences

Email: fake@neicon.ru

664025, Irkutsk

664003, Irkutsk

Russian Federation

O. N. Reva

University of Pretoria

Email: fake@neicon.ru
South Africa

Yu. S. Bukin

Limnological Institute, Siberian Branch, Russian Academy of Sciences

Email: fake@neicon.ru
664082, Irkutsk Russian Federation

I. V. Kozlova

Irkutsk State Medical University, Ministry of Health of the Russian Federation; Scientific Center of Family Health Problems and Human Reproduction, Siberian Branch, Russian Academy of Medical Sciences

Email: fake@neicon.ru

664025, Irkutsk

664003, Irkutsk

Russian Federation

T. V. Demina

Irkutsk State Agricultural Academy

Email: fake@neicon.ru
664038,Irkutsk Russian Federation

S. E. Tkachev

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences

Email: fake@neicon.ru
630090,Novosibirsk Russian Federation

V. I. Zlobin

Irkutsk State Medical University, Ministry of Health of the Russian Federation

Email: fake@neicon.ru
664025, Irkutsk Russian Federation

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Copyright (c) 2015 Dzhioev Y.P., Paramonov A., Reva O.N., Bukin Y.S., Kozlova I.V., Demina T.V., Tkachev S.E., Zlobin V.I.

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