MORBIDITY DYNAMICS AND GENETIC ANALYSIS OF SARS-COV-2 AND INFLUENZA VIRUSES STRUCTURE IN MOSCOW POPULATION

The paper aims to define the genetic structure (strains, serotypes) of coronavirus SARS-CoV-2 and influenza viruses as well as assess the infection rate among the Moscow population and suggest measures for effective management of the epidemiological situation. Patients with upper respiratory tract infections (URTI) symptoms undergo naso-oropharyngeal swabbing procedure. The taken samples are used in polymerase chain reaction (PCR) testing and next generation sequencing (NGS) by means of MiSeq system (Illumina, US) for SARS-CoV-2 and influenza А and В viruses detection. The authors perform a bioinformatic analysis of genome sequences using Iterative Refinement Meta-Assembler (IRMA 1.2.1), Basic Local Alignment Search Tool (BLAST 6), and Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN). From late 2021 to early 2022, the genetic structure of COVID-19 diagnosed in Moscow residents changed. Thus, the sublineage BA of the Omicron variant replaced the sublineage AY of the SARS-CoV-2 Delta strain. Consequently, the infection rate rose to 3700 per 100,000 people. Associated with the appearance of less virulent Omicron sublineages (XBB, JN.1, FliRT, KS1, LR1, LF, FL1), the rate between the end of 2022 and the start of 2025 stood at 100–500 per 100,000 individuals. Between late 2022 and early 2023, 64.3–97.6% of the specified population was infected with the H1N1 strain of influenza A. However, since January 23, 2023, the B variant became prevalent, counting 52.36–97.37% of all test swabs in early 2023. From the end of 2023 to the beginning of 2024, Moscow citizens contracted 2 novel H3N2 strains of influenza A: A/Massachusetts/01/2020 and A/Massachusetts/38/2019. From late 2024 to early 2025, Moscow residents were diagnosed with a newly emerged subclone of influenza A strain, i.e. H1N1, Hawaii/25/2020, and the Texas/43/2019 variant of influenza B. The outcomes of this research hold the potential to advance the modernization of PCR-based diagnostic kits, aid in the selection of vaccine strain candidates, and evaluate the effectiveness of established vaccines and antiviral treatments.

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