Antigenic and Molecular Genetic Evolution of Influenza Viruses in Kazakhstan from 2017 to 2025

Abstract

Simple Summary Influenza viruses continuously evolve, which can change their circulation patterns and reduce recognition by existing immunity and vaccine-induced antibodies. Continuous surveillance is therefore important for monitoring circulating viruses and informing influenza prevention and vaccine policy. In this study, we analyzed influenza viruses circulating in Kazakhstan over eight consecutive epidemic seasons (2017/18–2024/25) using data from the national influenza sentinel surveillance system, together with epidemiological, antigenic, molecular genetic, and phylogenetic analyses. We observed substantial changes in influenza circulation following the COVID-19 pandemic. Influenza activity was almost undetectable during the 2020/21 season, followed by A(H3N2)-dominated circulation in 2021/22. In 2022/23, influenza B predominated initially, followed by A(H1N1)pdm09, while A(H3N2) predominated in 2023/24. Genetic analysis identified 199 A(H1N1)pdm09, 157 A(H3N2), 105 B/Victoria, and 16 B/Yamagata viruses. We observed successive replacement of major genetic lineages within A(H1N1)pdm09, A(H3N2), and B/Victoria viruses. Antigenic analysis showed a 16- to 32-fold reduction in HI titers of A(H1N1)pdm09 6B.1A.5a.2 viruses when tested against antisera to earlier vaccine/reference strains. These findings demonstrate substantial changes in the timing, subtype dominance, and genetic composition of influenza viruses in Kazakhstan following the COVID-19 pandemic. Continuous integrated epidemiological, genetic, and antigenic surveillance is important for detecting changes in circulating viruses, assessing vaccine relevance, and supporting national influenza prevention and control strategies.