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Changes in the Genome of the Tick-Borne Encephalitis Virus during Cultivation

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Abstract

The tick-borne encephalitis virus (TBEV) strain C11-13 (GenBank acc. no. OQ565596) of the Siberian genotype was previously isolated from the brain of a deceased person. TBEV C11-13 variants obtained at passages 3 and 8 in SPEV cells were inoculated into the brains of white mice for subsequent passages. Full genome sequences of all virus variants were analyzed by high-throughput sequencing. A total of 41 single nucleotide substitutions were found to occur mainly in the genes for the nonstructural proteins NS3 and NS5 (GenBank MF043953, OP902894, and OP902895), and 12 amino acid substitutions were identified in the deduced protein sequences. Reverse nucleotide and amino acid substitutions were detected after three passages through mouse brains. The substitutions restored the primary structures that were characteristic of the isolate C11-13 from a human patient and changed during the eight subsequent passages in SPEV cells. In addition, the 3′-untranslated region (3′-UTR) of the viral genome increased by 306 nt. The Y3 and Y2 3'-UTR elements were found to contain imperfect L and R repeats, which were probably associated with inhibition of cellular XRN1 RNase and thus involved in the formation of subgenomic flaviviral RNAs (sfRNAs). All TBEV variants showed high-level reproduction in both cell cultures and mouse brains. The genomic changes that occurred during successive passages of TBEV are most likely due to its significant genetic variability, which ensures its efficient reproduction in various hosts and its broad distribution in various climatic zones.

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ACKNOWLEDGMENTS

We are grateful to Cand. Sci. (Phys.-Math.) A.N. Shvalov for discussion and help in processing the metagenomic sequencing data.

Funding

This work was supported by state contracts no. 9/21 and 7/21 with the State Research Center of Virology and Biotechnology “Vector” (Russian Service for Surveillance on Consumer Rights Protection and Human Wellbeing).

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  1. State Research Center of Virology and Biotechnology “Vector”, 630559, Koltsovo, Novosibirsk Oblast, Russia

    V. A. Ternovoi, E. P. Ponomareva, E. V. Protopopova, N. L. Tupota, T. P. Mikryukova & V. B. Loktev

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  1. V. A. Ternovoi
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  2. E. P. Ponomareva
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Correspondence to E. P. Ponomareva.

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All procedures with animals were carried out in compliance with the effective documents “Rules for Working with Experimental Animals” (https://docs.cntd.ru/document/456016716) and “Guidelines on Rearing and Use of Laboratory Animals” (Washington, 1996). The study was approved by Ethics Committee no. 1 at State Research Center of Virology and Biotechnology “Vector” (protocol no. 1-04.2021 dated April 30, 2021).

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Ternovoi, V.A., Ponomareva, E.P., Protopopova, E.V. et al. Changes in the Genome of the Tick-Borne Encephalitis Virus during Cultivation. Mol Biol 58, 266–278 (2024). https://doi.org/10.1134/S0026893324020146

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