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

Cover Page

Cite item

Full Text

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

Россия

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

Россия

O. N. Reva

University of Pretoria

Email: fake@neicon.ru
ЮАР

Yu. S. Bukin

Limnological Institute, Siberian Branch, Russian Academy of Sciences

Email: fake@neicon.ru
664082, Irkutsk Россия

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

Россия

T. V. Demina

Irkutsk State Agricultural Academy

Email: fake@neicon.ru
664038,Irkutsk Россия

S. E. Tkachev

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

Email: fake@neicon.ru
630090,Novosibirsk Россия

V. I. Zlobin

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

Email: fake@neicon.ru
664025, Irkutsk Россия

References

  1. Зильбер Л.А. Весенний (весенне-летний) эпидемический клещевой энцефалит. Архив биологических наук. 1939; 2: 9–37.
  2. Thiel H.-J., Collett M. S., Gould E. A., Heinz F. X., Houghton M., Meyers G. et al. Family Flaviviridae. In: Fauquet C.M. et. al., eds. Virus Taxonomy: Classification and Nomenclature. Eighth Report of the International Committee on the Taxonomy of Viruses. Amsterdam: Elsevier; 2005; 981–98.
  3. Демина Т.В., Джиоев Ю.П., Козлова И.В., Верхозина М.М., Ткачев С.Е., Дорощенко Е. К., и др. Генотипы 4 и 5 вируса клещевого энцефалита: особенности структуры геномов и возможный сценарий их формирования. Вопросы вирусологии. 2012; 4: 13–9.
  4. Суходолец В.В. Значение генетических рекомбинаций для сохранения и прогресса видов в эволюции. Журнал общей биологии. 2003; 3: 215–26.
  5. Цилинский Я.Я. Популяционная структура и эволюция вирусов. М.: Медицина; 1988.
  6. Bertrand Y, Tцpel M, Elvдng A, Melik W, Johansson M. First dating of a recombination event in mammalian tick-borne flaviviruses. PLoS One. 2012; (7): 1–12.
  7. Carney J., Daly J.M., Nisalak A., Solomon T. Recombination and positive selection identified in complete genome sequences of Japanese encephalitis virus. Arch. Virol. 2012; 157: 75–3.
  8. Taucher C., Berger A., Mandl C.W. A trans-complementing recombination trap demonstrates a low propensity of flaviviruses for intermolecular recombination. J. Virol. 2010; 84: 599–11.
  9. Twiddy S.S., Holmes E.C. The extent of homologous recombination in members of the genus Flavivirus. J. Gen. Virol. 2003; 84: 429–40.
  10. Джиоев Ю.П., Парамонов А.И., Демина Т.В., Козлова И.В., Верхозина М.М., Ткачев С.Е. и др. Обнаружение рекомбинаций у вируса клещевого энцефалита с помощью компьютерного анализа вирусных геномов. Вопросы вирусологии. 2012; 2: 14–8.
  11. Norberg P., Roth A., Bergström T. Genetic recombination of tickborne flaviviruses among wild-type strains. Virology. 2013; 440: 105–16.
  12. Pletnev A.G., Yamshchikov V.F., Blinov V.M. Nucleotide sequence of the genome and complete amino acid sequence of the polyprotein of tick-borne encephalitis virus. Virology. 1990; 174: 250–63.
  13. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994; 22: 4673–80.
  14. Boni M.F., Posada D., Feldman M.W. An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics. 2007; 176: 1035–47.
  15. Gibbs M.J, Armstrong J.S, Gibbs A.J. Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics. 2000; 16: 573–82.
  16. Martin D.P., Posada D., Crandall K.A., Williamson C. A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res. Hum.Retroviruses. 2005; 21: 98–2.
  17. Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P. Rdp3: A flexible and fast computer program for analyzing recombination. Bioinformatics.2010; 26: 2462–63.
  18. Maynard S.J. Analyzing the mosaic structure of genes. J. Mol. Evol. 1992; 34: 126–9.
  19. Padidam M., Sawyer S., Fauquet C.M. Possible emergence of new Gemini viruses by frequent recombination. Virology.1999; 265: 218– 25.
  20. Posada D., Crandall K.A. Evaluation of methods for detecting recombination from DNA sequences: Computer simulations. Proc. Natl. Acad. Sci. USA. 2001; 98: 13757–62.
  21. Bruen T. C., Philippe H., Bryant D. A quick and robust statistical test to detect the presence of recombination. Genetics.2006; 172: 2665–81.
  22. Huson D.H., Scornavacca C. A survey of combinatorial methods for phylogenetic networks. Genome Biol. Evol. 2011; 3: 23–5.
  23. Bryant D., Moulton V. Neighbor-Net: An agglomerative method for the construction of phylogenetic networks. Mol. Biol. Evol. 2004; 21: 255–65.
  24. Jukes T.H., Cantor C.R. Evolution of Protein Molecules. In: Munvo, ed. Mammalian Protein Metabolism. New York: Academic Press; 1969: 21–132.
  25. Mайр Э. Популяция, виды и эволюция. М.: Мир; 1974.

Supplementary files

Supplementary Files
Action
1. JATS XML
Download

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.

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
СМИ зарегистрировано Федеральной службой по надзору в сфере связи, информационных технологий и массовых коммуникаций (Роскомнадзор).
Регистрационный номер и дата принятия решения о регистрации СМИ: серия ПИ № ФС77-77676 от 29.01.2020.


This website uses cookies

You consent to our cookies if you continue to use our website.

About Cookies