Comparative Analysis of Influenza Viruses Isolated from Early and Severe Cases in Epidemic Seasons before and during the COVID-19 Pandemic in Russia (2019–2023)

Abstract

The influenza virus is one of the most dangerous causative agents of respiratory diseases, and its study is important for epidemiological control, especially in the case of cocirculation with SARS-CoV-2. Comparative analysis of influenza viruses isolated from early and severe cases in epidemic seasons before and during the COVID-19 pandemic in Russia. The article is based on the results of monitoring the circulation of seasonal influenza viruses obtained in 2019–2023. Samples from early and severe cases of influenza were studied using real-time PCR and whole-genome sequencing. Antigenic characterization of isolated viruses was carried out, and their sensitivity to antiviral drugs was studied. The flu season of 2019–2020 in Russia was the last epidemic season before the COVID-19 pandemic with the predominant cocirculation of influenza B and influenza A/H1 N1 pdm09 viruses. After the onset of the pandemic in the 2020–2021 season, the influenza virus was practically absent in Russia and was detected sporadically. Virus circulation resumed in the 2021–2022 season with dominance of A/H3N2 (clade 3C.2a1b.2a2) and continued in the 2022–2023 season with the dominance of A/Hi N1 pdm09 (clade 6B.1A.5a.2a) and the spread of influenza B/Victoria viruses (clade V1A.3a.2), which were antigenically different from the viruses circulating before the COVID-19 pandemic. Genetic analysis of the D222G/N mutations in the hemagglutinin of the A/H1N1pdm09 viruses, which are associated with increased disease severity, revealed an approximately equivalent selection of the D222G and D222N mutations in the 2019–2020 season and increased occurrence of the D222N variant in the 2022–2023 season. Cocirculation with SARS-CoV-2, the return of influenza circulation to epidemic levels, the emergence of new antigenic variants and pathogenicity factors emphasize the need to monitor and study influenza viruses for epidemiological analysis and prognosis, as well as for the development and application of effective measures to protect the population.