Prototype strains of SARS-CoV-2 genetic lineages identified in the Primorsky Krai during the COVID-19 pandemic (2020–2023)

Introduction. The evolutionary changes in the genome of the original SARS-CoV-2 virus clones associated with various combinations of mutations may be determined by geographical features. Monitoring of the molecular genetics and biological properties of regional strains is important for early detection of threats, forecasting the epidemic situation, assessing the risks of drug resistance and developing strategies to combat the virus. The formation of a collection of regional prototype strains reflecting the key characteristics of the Wuhan, Delta, and Omicron gene variants that circulated in Primorsky Krai during the pandemic will provide the basis for a subsequent comparative analysis of the genetic polymorphism and biological characteristics of the evolving variants of the virus. Furthermore, prototype strains can be used as test objects in evaluating the antiviral activity of known and newly developed compounds. The aim of the study: formation of a collection of characterized prototype regional SARS-CoV-2 strains representing the genetic lineages of the main genetic variants: Wuhan, Delta, Omicron isolated in Primorsky Krai during the COVID-19 pandemic. Materials and methods. SARS-CoV-2 strains were cultured in Vero E6 cells. The quantitative determination of the virus was carried out by titration in Vero E6 cells and by RT-qPCR. The genomic sequences of the virus were determined by nanopore sequencing. To assess the adequacy of the strains, remdesivir, an inhibitor of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), was used as reference drug in determining sensitivity to therapeutic agents. Results. A panel of prototype SARS-CoV-2 strains representing the dominant sublineages of the Wuhan, Delta, and Omicron genetic variants circulating in the Primorsky Krai during the pandemic (2020–2023) has been formed. Their molecular, genetic, and biological properties have been characterized. Multiple mutations have been identified in the ORF1ab, ORF3a, ORF6, ORF7, ORF8, S, M, E, and N genes characteristic of the corresponding genetic lineages in combinations forming the regional portrait of the virus. A regular decrease in the replicative activity of the virus in Vero E6 cell culture from Wuhan-like genetic variants to Omicron SARS-CoV-2 genetic variants has been established. The adequacy of using regional strains of SARS-CoV-2 as test objects for evaluating the effectiveness of the reference drug, the SARS-CoV-2 RNA-dependent RNA polymerase inhibitor has been proven. Conclusion. Prototype strains of SARS-CoV-2 for genetic lineages isolated during the COVID-19 pandemic, having different virulence and containing a large set of mutations, can be used in virological, molecular biological and pharmaceutical methods for comparative study of the genetic relationship and biological properties of SARS-CoV-2 genetic variants, as well as for the development of treatments and COVID-19 prevention.