Comparative Analysis of the Diversity of SARS-CoV-2 Lines Circulating in Omsk Region in 2020–2022

E. A. Gradoboeva, Zh.S. Tyulko, A. Fadeev, A. Yakimenko, V. Yakimenko
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引用次数: 1

Abstract

Relevance. To date, no detailed analysis of the variants of the pathogen circulating at different times on the territory of the Omsk region has been carried out.Aim. Comparative analysis of the diversity of circulating variants of SARS­CoV­-2 based on molecular genetic data, determine the lines and time of their appearance, compare the data obtained with data from the GISAID database.Materials and methods. Genome­wide sequencing of 222 primary and 5 culture (passages on Vero E6 and SPEV cell cultures) samples of SARS­-CoV­-2 from the Omsk region, collected from April 2020 to February 2022, on Oxford Nanopore Technologies and Illumina platforms, was carried out. Genetic lines were determined in Pangolin. The analysis was performed in MEGA7 and BioEdit.Results. 227 genome­wide SARS­-CoV­-2 sequences were obtained. 222 genomes have been uploaded to the GISAID database. The lines to which the samples belong were determined, phylogenetic trees were constructed for various regions of the SARS-CoV­-2 genome, the levels of virus homology were assessed and mutations in the S­protein region were analyzed.Conclusions. According to the data obtained, it is possible to roughly judge the time of the appearance of a particular variant, its consolidation and distribution in the population, and observe the rare mutations and the circulation of some rare lines. To assess the possibility of significant geographically linked changes in the SARS­-CoV­-2 in the Omsk region, the data obtained are insufficient. Virus variants circulating in the region are grouped into one cluster with identical variants from other regions or countries. A more pronounced intracluster differentiation of the lines can be observed when analyzing the RBD region. The situation with COVID­-19 in the Omsk region generally coincides with that in the whole country and the world. However, this does not exclude the parallel occurrence of certain mutations in remote territories from each other.
鄂木斯克地区2020-2022年SARS-CoV-2病毒株多样性比较分析
的相关性。迄今为止,尚未对鄂木斯克州境内不同时间流行的病原体变体进行详细分析。基于分子遗传数据对SARS-CoV -2流行变体多样性进行比较分析,确定其出现的线和时间,并将数据与GISAID数据库数据进行比较。材料和方法。在Oxford Nanopore Technologies和Illumina平台上,对2020年4月至2022年2月从Omsk地区收集的222个SARS -CoV -2原代和5个培养(在Vero E6和SPEV细胞培养上的传代)样本进行了全基因组测序。测定了穿山甲的遗传系。分析在MEGA7和BioEdit.Results中进行。获得227个全基因组SARS -CoV -2序列。222个基因组已经上传到GISAID数据库。鉴定样品所属系,构建SARS-CoV -2基因组各区域的系统发育树,评估病毒同源性水平,分析s蛋白区突变。根据所获得的资料,可以大致判断某一特定变异出现的时间、它在种群中的巩固和分布,并观察罕见突变和一些罕见系的循环。为了评估鄂木斯克地区SARS -冠状病毒-2发生重大地理相关变化的可能性,所获得的数据不足。在该区域传播的病毒变体与来自其他区域或国家的相同变体归为一类。在分析RBD区域时,可以观察到更明显的线簇内分化。鄂木斯克地区的COVID -19情况与全国和世界的情况基本一致。然而,这并不排除某些突变在遥远地区的平行发生。
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