Monitoring the Spread of SARS-CoV-2 Gene Variants in Sverdlovsk and Chelyabinsk Oblasts and Perm Krai

Abstract

A genomic diversity study of SARS-CoV-2 was conducted in the context of lifting the coronavirus restrictions and reopening Russia’s national borders. SARS-CoV-2 genovariants in Sverdlovsk and Chelyabinsk oblasts and Perm krai were identified. A total of 1127 nasopharyngeal smears from patients with a new coronavirus infection treated in Sverdlovsk and Chelyabinsk oblasts and Perm krai were studied by Sanger sequencing. The paper presents the dynamics of new coronavirus strains and its several mutations for the period from May to December 2022 using descriptive statistics. The study period was notable for Omicron predominance (~97%) with a greater number of amino acid mutations compared with that for the Delta and Alpha variants. The Omicron BA.2 subvariant prevailed during the study period from May to September and from October to December 2022, then BA.2 was displaced by BA.4/BA.5 subvariants. Molecular similarity analysis for assessment of SARS-CoV-2 showed the presence of atypical mutations at positions E484K, G485R, and R408I in some samples, as well as an increase in the number of mutations in variants, especially in the receptor-binding domain RBD. According to the literature, amino acid substitutions led to an S protein conformational alteration which, in turn, increased the affinity of RBD binding to ACE2 and resulted in a milder disease and higher contagiousness compared with earlier SARS-CoV-2 variants.