In Russia, during the COVID-19 pandemic, a decrease in influenza circulation was initially observed. Influenza circulation re-emerged with the dominance of new clades of A(H3N2) viruses in 2021–2022 and A(H1N1)pdm09 viruses in 2022–2023. In this study, we aimed to characterize influenza viruses during the 2022–2023 season in Russia, as well as investigate A(H1N1)pdm09 HA-D222G/N polymorphism associated with increased disease severity. PCR testing of 780 clinical specimens showed 72.2% of them to be positive for A(H1N1)pdm09, 2.8% for A(H3N2), and 25% for influenza B viruses. The majority of A(H1N1)pdm09 viruses analyzed belonged to the newly emerged 6B.1A.5a.2a clade. The intra-sample predominance of HA-D222G/N virus variants was observed in 29% of the specimens from A(H1N1)pdm09 fatal cases. The D222N polymorphic variant was registered more frequently than D222G. All the B/Victoria viruses analyzed belonged to the V1A.3a.2 clade. Several identified A(H3N2) viruses belonged to one of the four subclades (2a.1b, 2a.3a.1, 2a.3b, 2b) within the 3C.2a1b.2a.2 group. The majority of antigenically characterized viruses bore similarities to the corresponding 2022–2023 NH vaccine strains. Only one influenza A(H1N1)pdm09 virus showed reduced inhibition by neuraminidase inhibitors. None of the influenza viruses analyzed had genetic markers of reduced susceptibility to baloxavir.

The circulation of seasonal influenza in 2020–2021 around the world was drastically reduced after the start of the COVID-19 pandemic and the implementation of mitigation strategies. The influenza virus circulation reemerged in 2021–2022 with the global spread of the new genetic clade 3C.2a1b.2a.2 of A(H3N2) viruses. The purpose of this study was to characterize influenza viruses in the 2021–2022 season in Russia and to analyze the receptor specificity properties of the 3C.2a1b.2a.2 A(H3N2) viruses. Clinical influenza samples were collected at the local Sanitary-and-Epidemiological Centers of Rospotrebnadzor. Whole genome sequencing was performed using NGS. The receptor specificity of hemagglutinin was evaluated using molecular modeling and bio-layer interferometry. Clinical samples from 854 cases of influenza A and B were studied; A(H3N2) viruses were in the majority of the samples. All genetically studied A(H3N2) viruses belonged to the new genetic clade 3C.2a1b.2a.2. Molecular modeling analysis suggested a higher affinity of hemagglutinin of 3C.2a1b.2a.2. A(H3N2) viruses to the α2,6 human receptor. In vitro analysis using a trisaccharide 6’-Sialyl-N-acetyllactosamine receptor analog did not resolve the differences in the receptor specificity of 3C.2a1b.2a.2 clade viruses from viruses belonging to the 3C.2a1b.2a.1 clade. Further investigation of the A(H3N2) viruses is required for the evaluation of their possible adaptive advantages. Constant monitoring and characterization of influenza are critical for epidemiological analysis.

Outbreaks of influenza, which is a contagious respiratory disease, occur throughout the world annually, affecting millions of people with many fatal cases. The D222G/N mutations in the hemagglutinin (HA) gene of A(H1N1)pdm09 are associated with severe and fatal human influenza cases. These mutations lead to increased virus replication in the lower respiratory tract (LRT) and may result in life-threatening pneumonia. Targeted NGS analysis revealed the presence of mutations in major and minor variants in 57% of fatal cases, with the proportion of viral variants with mutations varying from 1% to 98% in each individual sample in the epidemic season 2018–2019 in Russia. Co-occurrence of the mutations D222G and D222N was detected in a substantial number of the studied fatal cases (41%). The D222G/N mutations were detected at a low frequency (less than 1%) in the rest of the studied samples from fatal and nonfatal cases of influenza. The presence of HA D222Y/V/A mutations was detected in a few fatal cases. The high rate of occurrence of HA D222G/N mutations in A(H1N1)pdm09 viruses, their increased ability to replicate in the LRT and their association with fatal outcomes points to the importance of monitoring the mutations in circulating A(H1N1)pdm09 viruses for the evaluation of their epidemiological significance and for the consideration of disease prevention and treatment options.

The WHO has developed a tool to assess the risk of newly emerging influenza viruses with pandemic potential (TIPRA). According to TIPRA, the main parameters for assessing the risk of human-to-human transmission of a novel influenza virus are its ability to bind to human cell receptors of the upper respiratory tract (URT) and transmit in model animals. The aim of this study was to quantify airborne transmission of human and animal influenza viruses in the ferret model. The transmission of influenza viruses was studied in the ferret model in an aerobiology chamber. Airborne particles concentration and fractional composition in the aerobiology chamber were measured using an aerosol particle counter and analytical aerosol filters. Viral load in ferret nasal washings and aerosol filters was determined by titration in MDCK cells and quantitative RT-PCR. Genetic analysis of influenza viruses was performed using virus genome sequences obtained by NGS. After intranasal infection, human and animal influenza viruses replicated in the cells of nasal mucosa in ferrets. The level of virus airborne particles contamination provided by infected animals depends on the infectious dose and differs significantly between influenza virus strains. The studied avian influenza viruses show insufficient transmission in the ferret model, while human and swine influenza viruses are highly transmitted in ferrets. We propose a quantitative model of airborne transmission of influenza virus from donor to recipient ferrets. Level of influenza virus transmission in the ferret model correlates with genetic markers of virus receptor specificity and the level of virus airborne particle contamination induced by donor ferrets.

The purpose of the present work was to evaluate population immunity to influenza and molecular genetic analysis of influenza viruses detected in the Russian Federation over 2020-2022. In this study, 1344 samples of blood serum collected prior to the 2021-2022 flu season in Siberian, Southern, Far Eastern, Volga and Ural Federal Districts were studied. Seropositivity to the A/Victoria/2570/2019 vaccine strain (H1N1) pdm09 was detected in 25% to 31% of samples from the four federal districts, and in 8% of samples from the Far Eastern Federal District. Seropositivity to the A/Cambodia/e0826360/2020 strain (H3N2) was detected in 24% to 37% of the samples. The lowest population immunity was revealed to the influenza B/Washington/02/2019 vaccine strain (Victoria lineage), with < 10% of serum samples reactive to the studied strain. Since March 2020, the worldwide turnover of all seasonal respiratory viruses has sharply decreased, except of rhinoviruses. From March 2020 to June 2021, we have identified six B/Victoria influenza viruses from sporadic cases of influenza. From June 2021 to the end February 2022, the State Research Center “Vector” received 901 samples positive for influenza A(H3N2) virus RNA, two specimens positive for A(H1N1) pdm09 virus RNA, and 17 samples positive for influenza B. All studied A(H3N2) viruses belonged to the 3C.2a1b.2a2 subclade (Bangladesh group). The two verified A(H1N1) pdm09 influenza viruses belonged to the 6B.1A.5a clade. All studied influenza B viruses were assigned to the B/Victoria genetic lineage, and to 1A.3a2 subclade. The genomes of all identified viruses did not contain mutations of the NA gene responsible for drug resistance to neuraminidase inhibitors, or mutations in РA gene responsible for baloxavir resistance. All viruses tested by fluorescence assay were sensitive to oseltamivir and zanamivir. The worldwide frequency of influenza isolates resistant to antineuraminidase drugs does not exceed 1-2% of cases. Hence, oseltamivir and zanamivir provide effective treatment for seasonal influenza.

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.