Analysis of changes in the genome of the Omsk hemorrhagic fever virus (Flaviviridae: Orthoflavivirus) during laboratory practices for virus preservation

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Abstract

Introduction. Omsk hemorrhagic fever (OHF) is a severe disease identified in the 1940s in Western Siberia, Russia. Disease is caused by the OHF virus, which belongs to the genus Orthoflavivirus.

The purpose of the work. Analysis of changes in the genome associated with the isolation of OHF virus strains in laboratory animals (Mus musculus).

Materials and methods. Whole-genome nucleotide sequences of OHF virus strains from the working collection of the laboratory of arboviral infections of the department of natural focal viral infections of the Omsk Research Institute of Natural Focal Infections of Rospotrebnadzor were used in the study, as well as sequences from GenBank. Assessment of adaptive changes in the genome of the OHF virus was carried out using discriminant analysis methods, analyzing the composition and localization of emerging substitutions in viral RNA sequences obtained during the adaptation of viruses to the mouse organism as a result of passaging. Linked nucleotide substitutions were identified by calculating the mutual information for each pair of columns in the array of aligned nucleotide sequences. In the phylogenetic analysis, the relaxed clock algorithm of the BEAST program was used.

Results. It has been shown that point substitutions during adaptation of OHF viruses to the mouse organism occur in all parts of the genome. Many of these substitutions are included in the pattern of linked substitutions identified in the genome of the OHF virus. Discriminant analysis of differences in nucleotide substitutions for groups combining sequences by the number of passages does not allow reliable discrimination between original sequences obtained from muskrat and sequences from first passages, but it recognizes well sequences from 7 or more passages, which suggests the possibility of adaptive selection of nucleotide substitutions when interacting with the body of a white mouse. Calculation of the average rate of substitutions per site per year without taking into account the occurrence of adaptive and related substitutions gives a value of 10−5, which is almost an order of magnitude different from the result when their presence is taken into account ‒ 10−4.

Conclusion. Changes in the nucleotide sequences of OHF that occur during laboratory virus preservation practices may influence the evolutionary rate values determined when analyzing these sequences and require further study.

About the authors

Zhanna S. Tyulko

Omsk Research Institute of Natural Focal Infections (Federal Service for Supervision of Consumer Rights Protection and Human Welfare); Omsk State Medical University of the Russian Ministry of Health

Author for correspondence.
Email: tjs@omsk-osma.ru
ORCID iD: 0000-0001-8536-0520

senior researcher, Omsk Research Institute of Natural Focal Infections (Federal Service for Supervision of Consumer Rights Protection and Human Welfare); assistant professor, State budget educational institution Omsk State Medical University of the Russian Ministry of Health

Russian Federation, Omsk; Omsk

Artem V. Fadeev

Smorodintsev Research Institute of Influenza, Ministry of Health of Russian Federation

Email: afadeew@gmail.com
ORCID iD: 0000-0003-3558-3261

senior researcher

Russian Federation, St. Petersburg

Aleksei G. Vasilenko

Omsk Research Institute of Natural Focal Infections (Federal Service for Supervision of Consumer Rights Protection and Human Welfare)

Email: Vasilenko_AG@oniipi.org
ORCID iD: 0000-0002-2754-6359

researcher, epidemiologist

Russian Federation, Omsk

Ekaterina A. Gradoboeva

Omsk Research Institute of Natural Focal Infections (Federal Service for Supervision of Consumer Rights Protection and Human Welfare)

Email: Gradoboeva_EA@oniipi.org
ORCID iD: 0000-0002-2046-9872

junior researcher

Russian Federation, Omsk

Valerii V. Yakimenko

Omsk Research Institute of Natural Focal Infections (Federal Service for Supervision of Consumer Rights Protection and Human Welfare)

Email: vyakimenko78@yandex.ru
ORCID iD: 0000-0001-9088-3668

head of laboratory

Russian Federation, Omsk

Andrey B. Komissarov

Smorodintsev Research Institute of Influenza, Ministry of Health of Russian Federation

Email: a.b.komissarov@gmail.com
ORCID iD: 0000-0003-1733-1255

head of laboratory

Russian Federation, St. Petersburg

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Supplementary files

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2. Fig. 1. Phylogenetic tree constructed based on the coding part of the nucleotide sequence of OHF viruses. Bootstrap values are indicated for tree nodes. The sequences belong to the main subtypes of the OHF virus: OHFV-1, OHFV-2, OHFV-3.

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3. Fig. 2. The number of different nucleotides when comparing the coding sequences of OHF viruses. The number of different nucleotides is indicated on the arrows in the diagram.

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4. Fig. 3. Scatterplot for mRNA nucleotide sequences of the OHF viruses in space, where the coordinates along the horizontal axis are the values of the discriminant function f1, and along the vertical axis the values of the discriminant function f2, calculated for each viral nucleotide sequence. 0 ‒ sequences obtained from muskrat and sequences of the 0 passage in the body of a white mouse; 1п ‒sequences of the first passage in the body of a white mouse; 2п ‒sequences of the second passage in the body of a white mouse.

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5. Fig. 4. Scatterplot for mRNA nucleotide sequences of the OHF viruses in space, where the coordinates along the horizontal axis are the values of the discriminant function f1, and along the vertical axis the values of the discriminant function f2, calculated for each viral nucleotide sequence 0 ‒ sequences obtained from muskrat; 0п ‒sequences of the 0 passage in the body of a white mouse; 1п ‒ sequences of the first passage in the body of a white mouse; 2п ‒ sequences of the second passage in the body of a white mouse; 3п ‒ sequences of the third passage in the body of a white mouse; 4+ ‒ sequences of the fourth and higher number of passages in the body of a white mouse; x ‒ sequences with an unknown number of passages.

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6. Supplementary to the article
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Copyright (c) 2024 Tyulko Z.S., Fadeev A.V., Vasilenko A.G., Gradoboeva E.A., Yakimenko V.V., Komissarov A.B.

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