Evolving Dynamics of Whole-Genome Influenza A/H3N2 Viruses Isolated in Cameroon

Background: Since 2023, Cameroon has recorded numerous cases of seasonal influenza caused by the A/H3N2 subtype, which is the strain most commonly encountered worldwide in 2024. Methods: To describe the evolutionary dynamics of influenza A/H3N2 viruses, whole genome sequencing was performed using the Oxford Nanopore Technologies sequencing platform and the SQK-LSK109, EXP-NBD196 reagent kit (Oxford Nanopore Technologies, catalog no. SQK-LSK109). Subsequently, mutational analysis was performed on the 8 genes of the H3N2 influenza strains isolated between 2023 and 2024 in Cameroon by aligning our protein sequences with the reference sequences recommended by the WHO in the northern hemisphere during the 2023-2024 influenza season using MEGA 11 software. The trimeric and tetrameric structures of the HA, NA, and M proteins were downloaded from the protein website https://www.rcsb.org/ and imported into the PyMOL Version 2.6.1 software for visualization and annotation of the observed amino acid substitutions. Results: All Cameroonian A(H3N2) strains from 2023 to 2024 belonged to clade 3c.2a. The mutations I208F, K156I, E66K, N112S, G69N, V239I, K292E, Q189R, G241D, A202D, T3A, S70R, N161S, N138D, N394S, and N120D were detected in most HA1 gene samples (Supporting Table S1). Among these mutations, the important A202D and N161S mutations in HA1 in 2023 and 2024 led to the virulence of the virus and consequently resulted in the rapid evolution of the A/H3N2 virus and the generation of the new clades 3C.2a1b.2a.2a.3 and 3c.2a1b.2a.2a.3a.1, respectively. Similarly, amino acid substitutions at sites I469T, I65V, and H275Y in the NA protein were observed compared to the 2024 vaccine strain A/Darwin/6/2021. We noted the presence of the H275Y substitution in 30% of Cameroonian strains associated with major resistance to neuraminidase inhibitors, particularly oseltamivir. In general, the number of amino acid mutations observed between circulating strains and the vaccine strain for the following year was higher, indicating that circulating strains would evolve away from vaccine strains for the year 2023-2024. Conclusions: These results highlight the evolutionary nature of the human influenza virus.