Molecular epidemiological analysis of SARS-CoV-2 genovariants in Moscow and Moscow region

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Abstract

Introduction. SARS-CoV-2, a severe acute respiratory illness virus that emerged in China in late 2019, continues to spread rapidly around the world, accumulating mutations and thus causing serious concern. Five virus variants of concern are currently known: Alpha (lineage B.1.1.7), Beta (lineage B.1.351), Gamma (lineage P.1), Delta (lineage B.1.617.2), and Omicron (lineage B.1.1.529). In this study, we conducted a molecular epidemiological analysis of the most prevalent genovariants in Moscow and the region.

The aim of the study is to estimate the distribution of various variants of SARS-CoV-2 in Moscow city and the Moscow Region.

Materials and methods. 227 SARS-CoV-2 sequences were used for analysis. Isolation of the SARS-CoV-2 virus was performed on Vero E6 cell culture. Sequencing was performed by the Sanger method. Bioinformatic analysis was carried out using software packages: MAFFT, IQ-TREE v1.6.12, jModelTest 2.1.7, Nextstrain, Auspice v2.34.

Results. As a result of phylogenetic analysis, we have identified the main variants of the virus circulating in Russia that have been of concern throughout the existence of the pandemic, namely: variant B.1.1.7, which accounted for 30% (9/30), AY.122, which accounted for 16.7% (5/30), BA.1.1 with 20% (6/30) and B.1.1 with 33.3% (10/30). When examining Moscow samples for the presence of mutations in SARS-CoV-2 structural proteins of different genovariants, a significant percentage of the most common substitutions was recorded: S protein – D614G (86.7%), P681H/R (63.3%), E protein – T9I (20.0%); M protein – I82T (30.0%), D3G (20.0%), Q19E (20.0%) and finally N protein – R203K/M (90.0%), G204R/P (73.3 %).

Conclusion. The study of the frequency and impact of mutations, as well as the analysis of the predominant variants of the virus are important for the development and improvement of vaccines for the prevention of COVID-19. Therefore, ongoing molecular epidemiological studies are needed, as these data provide important information about changes in the genome of circulating SARS-CoV-2 variants.

About the authors

Ekaterina N. Ozhmegova

National Research Center for Epidemiology and Microbiology named after honorary academician N.F. Gamaleya, Ministry of Health of the Russian Federation

Email: ozhmegova.eka@gmail.com
ORCID iD: 0000-0002-3110-0843

Researcher, Laboratory of leukemia viruses

Russian Federation, 123098, Moscow

Tatyana E. Savochkina

National Research Center for Epidemiology and Microbiology named after honorary academician N.F. Gamaleya, Ministry of Health of the Russian Federation

Email: tasavochkina@yandex.ru
ORCID iD: 0000-0003-4366-8476

Junior Researcher, Laboratory of Molecular Diagnostics

Russian Federation, 123098, Moscow

Alexey G. Prilipov

National Research Center for Epidemiology and Microbiology named after honorary academician N.F. Gamaleya, Ministry of Health of the Russian Federation

Email: a_prilipov@mail.ru
ORCID iD: 0000-0001-8755-1419

Doctor of Biological Sciences, Head Laboratory of Molecular Genetics Center

Russian Federation, 123098, Moscow

E. .E. Tikhomirov

National Research Center for Epidemiology and Microbiology named after honorary academician N.F. Gamaleya, Ministry of Health of the Russian Federation

Email: ozhmegova.eka@gmail.com
Russian Federation, 123098, Moscow

Victor F. Larichev

National Research Center for Epidemiology and Microbiology named after honorary academician N.F. Gamaleya, Ministry of Health of the Russian Federation

Email: vlaritchev@mail.ru
ORCID iD: 0000-0001-8262-5650

doctor of med. sci, Leading Researcher of laboratory of biology and indication of arbovirus infections

Russian Federation, 123098, Moscow

Mukhammad A. Sayfullin

National Research Center for Epidemiology and Microbiology named after honorary academician N.F. Gamaleya, Ministry of Health of the Russian Federation; Pirogov Russian National Research Medical University

Email: dr_saifullin@mail.ru
ORCID iD: 0000-0003-1058-3193

PhD, Associate Professor, Department of Infectious Diseases in Children, Faculty of Pediatrics, Sen. оf laboratory of biology and indication of arbovirus infections

Russian Federation, 123098, Moscow; 119997, Moscow

Tatyana V. Grebennikova

National Research Center for Epidemiology and Microbiology named after honorary academician N.F. Gamaleya, Ministry of Health of the Russian Federation

Author for correspondence.
Email: t_grebennikova@mail.ru
ORCID iD: 0000-0002-6141-9361

Doctor of Biological Sciences, Professor, Corresponding Member RAS, Head Laboratory of Molecular Diagnostics, Head of department

Russian Federation, 123098, Moscow

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2. Fig. 1. Maximum likelihood dendrogram for 30 Moscow sequences obtained from Infectious Clinical Hospital No. 1 together with 196 available sequences from the GISAID database (Nextstrain reference variants were used). The tree is rooted using a reference sample from Wuhan (hCoV-19/Wuhan/WIV04/2019 (WIV04)). Variants of concern and interest (VOC and VOI) are marked with color and captions.

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3. Fig. 2. Maximum likelihood dendrograms of Moscow samples. Illuminated dots indicate Moscow samples from IKH№1. The numbers at the tree nodes indicate highly supported branches (bootstrap support > 0.9). The names of the specimens are given according to the names from the GISAID database: a – line B.1.1 together with reference strains from Japan, USA and Russia, b – line B.1.1.7 (Alpha) with reference strains from Germany, USA and Sweden, c – line BA.1.1 (B.1.1.529; Omicron) together with reference strains from Luxembourg, USA and Italy, d – line AY.122 (B.1.617 .2; Delta) with reference strains from England, Scotland, USA, Switzerland, Germany and Singapore.

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4. Fig. 3. Frequency of mutations in SARS-CoV-2 structural proteins (S, E, M, N) in Moscow samples from Infectious Clinical Hospital No. 1.

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Copyright (c) 2023 Ozhmegova E.N., Savochkina T.E., Prilipov A.G., Tikhomirov E..., Larichev V.F., Sayfullin M.A., Grebennikova T.V.

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This work is licensed under a Creative Commons Attribution 4.0 International License.

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