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

Q3 Medicine

Voprosy virusologii Pub Date : 2023-02-07 DOI:10.36233/0507-4088-146

E N Ozhmegova, T E Savochkina, A G Prilipov, E Tikhomirov, V F Larichev, M A Sayfullin, T V Grebennikova

{"title":"[Molecular epidemiological analysis of SARS-CoV-2 genovariants in Moscow and Moscow region].","authors":"E N Ozhmegova, T E Savochkina, A G Prilipov, E Tikhomirov, V F Larichev, M A Sayfullin, T V Grebennikova","doi":"10.36233/0507-4088-146","DOIUrl":null,"url":null,"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.","PeriodicalId":23669,"journal":{"name":"Voprosy virusologii","volume":"67 6","pages":"496-505"},"PeriodicalIF":0.0000,"publicationDate":"2023-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"1","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Voprosy virusologii","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.36233/0507-4088-146","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"Medicine","Score":null,"Total":0}

引用次数: 1

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.

查看原文本刊更多论文

[莫斯科及莫斯科地区SARS-CoV-2基因变异的分子流行病学分析]。

SARS-CoV-2是2019年底在中国出现的一种严重急性呼吸道疾病病毒，目前仍在全球迅速传播，并积累了突变，引起了严重关注。目前已知的病毒变体有五种:Alpha (B.1.1.7)、Beta (B.1.351)、Gamma (P.1)、Delta (B.1.617.2)和Omicron (B.1.1.529)。在这项研究中，我们对莫斯科和该地区最流行的基因变异进行了分子流行病学分析。该研究的目的是估计各种变体SARS-CoV-2在莫斯科市和莫斯科州的分布。材料和方法:使用227个SARS-CoV-2序列进行分析。在Vero E6细胞培养上分离SARS-CoV-2病毒。测序采用Sanger法。采用MAFFT、IQ-TREE v1.6.12、jModelTest 2.1.7、Nextstrain、吉瑞斯v2.34等软件包进行生物信息学分析。结果:通过系统发育分析，我们确定了大流行期间在俄罗斯流行的主要病毒变体，即:变体B.1.1.7占30% (9/30)，AY.122占16.7% (5/30)，BA.1.1占20%(6/30)和B.1.1占33.3%(10/30)。当检测莫斯科样本中不同基因变异的SARS-CoV-2结构蛋白是否存在突变时，记录到的最常见替换比例显著:S蛋白D614G(86.7%)、P681H/R(63.3%)、E蛋白T9I (20.0%);M蛋白I82T (30.0%)， D3G (20.0%)， Q19E(20.0%)，最后N蛋白R203K/M (90.0%)， G204R/P(73.3%)。结论:研究病毒的突变频率和影响，分析病毒的优势变异体，对开发和改进预防COVID-19的疫苗具有重要意义。因此，需要进行持续的分子流行病学研究，因为这些数据提供了有关流行的SARS-CoV-2变体基因组变化的重要信息。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Voprosy virusologii Medicine-Infectious Diseases

CiteScore

2.00

自引率

0.00%

发文量

期刊介绍： The journal deals with advances in virology in Russia and abroad. It publishes papers dealing with investigations of viral diseases of man, animals and plants, the results of experimental research on different problems of general and special virology. The journal publishes materials are which promote introduction into practice of the achievements of the virological science in the eradication and incidence reduction of infectious diseases, as well as their diagnosis, treatment and prevention. The reader will find a description of new methods of investigation, new apparatus and devices.