Influenza Viruses Detected in Lethal Cases in the Russian Federationin the 2023–2024 Respiratory Virus Season

Introduction: Influenza is a highly contagious disease which can cause severe complications and even death, particularly in high-risk populations. Continuous monitoring and careful testing of seasonal influenza viruses, especially for severe cases, is necessary to develop and optimize prevention and treatment. Objective: To establish genetic and antigenic characteristics of influenza viruses detected in lethal cases in the Russian Federation in the 2023–2024 respiratory virus season. Materials and methods: From September 29, 2023 to June 1, 2024, 859 specimens from influenza cases (nasopharyngeal swabs) and 101 autopsy specimens of trachea, bronchi, and lungs from lethal cases of the disease from 57 regions of the Russian Federation were analyzed by PCR. For those with a sufficient amount of genetic material, whole-genome sequencing was performed using the Illumina MiSeq platform. Results: The 2023–2024 influenza season in the Russian Federation was characterized by the dominance of A/H3N2 viruses of subclade 2a.3a.1. Influenza A/H1N1pdm09 and influenza type B viruses were detected to a lesser extent in that period. Additional diversification of A/H3N2 viruses was observed during the season with accumulation of amino acid substitutions in the hemagglutinin antigenic sites. Most lethal cases were among those at high risk and unvaccinated. No mutations associated with increased pathogenicity and virulence were identified in A/H3N2 viruses from lethal cases. No molecular markers of drug resistance to neuraminidase inhibitors and baloxavir marboxil were identified in all viruses tested in the 2023–2024 season. Conclusion: Influenza A/H3N2 viruses from the lethal cases of the diseases tested at the State Research Center for Virology and Biotechnology “Vector” in the 2023–2024 respiratory virus season were similar to those detected in recovered patients. The isolated viruses were genetically and antigenically similar to the vaccine strain and had no markers of increased pathogenicity or drug resistance.