Genotyping of tick-borne encephalitis and Kemerovo viruses in taiga ticks collected in the Komi Republic

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Abstract

Over the last years, an increasing rate of ixodes tick bites has been registered in the northern regions of the European Russia. In addition, the number of subjects request medical assistance due to tick bites has been dramatically increased in the Komi Republic. In addition, incidence of tick-borne encephalitis was also increased particularly starting since 2009. However, highly limited data on pathogen genetic diversity related to viral tick-borne infections in this region are currently available. Taiga ticks (Ixodespersulcatus) collected from the Komi Republic southern and central part vegetation were examined to identify and genotype tick-borne viruses. Individual ticks were used to identify by RT-PCR viral RNA coupled to tick-borne encephalitis and Kemerovo viruses. Viral genome fragment sequencing allowed to unambiguously identify these viruses. It was found that viral RNA tick-borne encephalitis was detected in 6.8±1.2% individual ticks. Moreover, tick-linked isolate genotyping based on analyzing E protein gene fragment nucleotide sequence derived from tick-borne encephalitis discovered that 35% and 65% isolates belonged to the Far Eastern and Siberian subtype, respectively. In addition, subsequent phylogenetic analysis demonstrated that at least four variants of the Siberian and Far Eastern subtypes of tick-borne encephalitis virus were detected, which were close to the viruses circulating in the Urals and Siberia. In contrast, prevalence of Kemerovo virus in taiga ticks was 0.8±0.2%. Sequencing of Kemerovo virus RNA-dependent RNA polymerase gene fragment showed around 94% homology with the remainder of the Kemerovo virus strains. Phylogenetic analysis of the Kemerovo virus genome fragments demonstrated at least two subtypes circulating in the Komi Republic. Thus, it was suggested that tick-borne encephalitis virus was introduced relatively recently from the Urals and Siberian region into the natural foci of the Komi Republic. Moreover, genetic differences found in Kemerovo virus strains presume for them a longer lasting evolution throughout the natural foci of this region. In addition, a potential role for birds and their ticks in rapid spreading of viral tick-borne infections in the Komi Republic is also discussed. Thus, the data on genetic diversity of the viral agents related to tick-born encephalitis and Kemerovo fever may be useful for improving their diagnostics, prevention and treatment in the Komi Republic.

About the authors

M. Yu Kartashov

State Research Center for Virology and Biotechnology “Vector”; Novosibirsk State University

Email: mikkartash@yandex.ru
ORCID iD: 0000-0002-7857-6822

Mikhail Yu. Kartashov - PhD (Biology), Senior Researcher, Department of Molecular Virology for Flaviviruses and Viral Hepatitis, SRC for Virology and Biotechnology “Vector”, Koltsovo; Researcher, Biotechnology and Virology Laboratory, NSU.

630559, Novosibirsk Region, Koltsovo, Phone: +7 923 419-31-92 (mobile), Fax: +7 (383) 336-74-09

Russian Federation

T. P. Mikryukova

State Research Center for Virology and Biotechnology “Vector”

Email: mikryukova_tp@vector.nsc.ru
ORCID iD: 0000-0003-4350-4260

PhD (Biology), Senior Researcher, Department Molecular Virology for Flaviviruses and Viral Hepatitis, SRC for Virology and Biotechnology “Vector”.

Koltsovo, Novosibirsk Region Russian Federation

E. I. Krivosheina

State Research Center for Virology and Biotechnology “Vector”; Novosibirsk State University

Email: krivosheina_ei@vector.nsc.ru

Research Assistant, Department of Molecular Virology for Flaviviruses and Viral Hepatitis, SRC for Virology and Biotechnology “Vector”; Master, Chair of Biotechnology, NSU.

Koltsovo, Novosibirsk Region

Russian Federation

A. I. Kuznetsov

State Research Center for Virology and Biotechnology “Vector”; Novosibirsk State University

Email: kuznetsov_ai@vector.nsc.ru

Research Assistant, Department of Molecular Virology for Flaviviruses and Viral Hepatitis, SRC for Virology and Biotechnology “Vector”; Master, Chair of Information Biology, NSU.

Novosibirsk Russian Federation

L. I. Glushkova

Federal Service for Surveillance in Consumer Rights Protections and Human Well-Being, Department of the Komi Republic

Email: gigprof@list.ru

PhD, MD (Medicine), Professor, Head of the Komi Republic Department of FS for Surveillance in Consumer Rights Protections and Human Well-Being.

Syktyvkar

Russian Federation

I. V. Korabel`nikov

“Disinfection ”, Federal Service for Surveillance in Consumer Rights Protections and Human Well-Being

Email: gigprof@list.ru

PhD, MD (Medicine), Professor, Head of the “Disinfection”, FS for Surveillance in Consumer Rights Protections and Human Well-Being.

Syktyvkar

Russian Federation

Yu. I. Egorova

“Disinfection ”, Federal Service for Surveillance in Consumer Rights Protections and Human Well-Being

Email: gigprof@list.ru

Entomologist, “Disinfection”, FS for Surveillance in Consumer Rights Protections and Human Well- Being.

Syktyvkar

Russian Federation

V. A. Ternovoi

State Research Center for Virology and Biotechnology “Vector”

Email: tern@vector.nsc.ru
ORCID iD: 0000-0003-1275-171X

PhD (Biology), Head of the Laboratory of Molecular Epidemiology of Highly Dangerous Infections, Department of Molecular Virology for Flaviviruses and Viral Hepatitis SRC for Virology and Biotechnology “Vector”.

Koltsovo, Novosibirsk Region

Russian Federation

V. B. Loktev

State Research Center for Virology and Biotechnology “Vector”; Novosibirsk State University; Institute of Cytology and Genetics the Siberian Branch of the RAS

Author for correspondence.
Email: valeryloktev@gmail.com
ORCID iD: 0000-0002-0229-321X

PhD, MD (Biology), Professor, Head of the Department of Molecular Virology for Flaviviruses and Viral Hepatitis, SRC for Virology and Biotechnology “Vector”.

Koltsovo, Novosibirsk Region

Russian Federation

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Copyright (c) 2020 Kartashov M.Y., Mikryukova T.P., Krivosheina E.I., Kuznetsov A.I., Glushkova L.I., Korabel`nikov I.V., Egorova Y.I., Ternovoi V.A., Loktev V.B.

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