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

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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.

作者简介

Ekaterina 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

俄罗斯联邦, 123098, Moscow

Tatyana 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

俄罗斯联邦, 123098, Moscow

Alexey 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

俄罗斯联邦, 123098, Moscow

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
俄罗斯联邦, 123098, Moscow

Victor 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

俄罗斯联邦, 123098, Moscow

Mukhammad 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

俄罗斯联邦, 123098, Moscow; 119997, Moscow

Tatyana Grebennikova

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

编辑信件的主要联系方式.
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

俄罗斯联邦, 123098, Moscow

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版权所有 © Ozhmegova E.N., Savochkina T.E., Prilipov A.G., Tikhomirov E..., Larichev V.F., Sayfullin M.A., Grebennikova T.V., 2023

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