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 SARS-CoV-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. Genome-wide 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 genome-wide 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 S-protein 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 genome 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. © 2022, Numikom. All rights reserved.
ABSTRACT
Spectral-statistical approach was applied to comparative analysis of coronavirus genomes from the four genus Alphacoronavirus, Betacoronavirus (including new SARS-CoV-2 virus), Gammacoronavirus and Deltacoronavirus. This analysis was done from the point of view of 3-regularity and latent triplet profile periodicity existence in the coding sequences of four structural genes: ORF1ab encoding transcriptase;S-gene of glycoprotein forming spikes;M-gene of membrane protein;N-gene of nucleoprotein. A whole number of the genomes analyzed was equal to 3410. Gene numbers in each of the four groups in the study respectively were the same. In the result, practically, in the CDSs of all analyzed genes of ORF1ab, S and N the latent profile triplet periodicity was revealed and high value of 3-regularity index, being a quality estimate of coding triplet structure conservation, was determined. On the contrary, for coding structure of M-genes a tendency was revealed to diffuse up to homogeneity for 60% of the genes in the genomes of alphacoronaviruses analyzed and for 67% of the genes of the gammacoronaviruses. Tendency of the such structure diffusion, being accompanied by decrease of 3-regularity index average value in comparison with other genes, while the triplet profile periodicity remains saved, was also noted for M-genes of SARS-CoV-2 viruses. Probably, this tendency reflects a significance of M-genes variability in coronavirus adaptation to the novel hosts of genus. Analysis of 3- profile periodicity matrices of the four groups of SARS-CoV-2 genes considered in the work, for the viruses isolated in Europe, Asia and USA, did not revealed their significant difference, that is allowing to propose a single source of this virus propagation. © 2020. All Rights Reserved.