Background: Following the lifting of COVID-19 pandemic control measures, a progressive increase in influenza A virus activity, particularly the H1N1 subtype, has been observed in Jiaxing. This study systematically characterized the genomic evolution of influenza A(H1N1) viruses circulating in Jiaxing, China during the 2023-2024 epidemic seasons through whole-genome sequencing and phylogenetic analysis.

Methods: Viral RNA was detected by quantitative real-time PCR (qPCR) and 83 influenza A(H1N1) isolates (48 from 2023 and 35 from 2024 surveillance) were selected for whole-genome sequencing. Launch RDP4, MEGA11 and iTOL were used to analyze the homology, molecular evolutionary clusters and resistance sites of influenza A(H1N1) virus.

Results: The positivity rates of influenza A(H1N1) virus in Jiaxing were 10.66% in 2023 and 5.09% in 2024, respectively. Compared with vaccine strain A/Wisconsin/67/2022, the influenza A(H1N1) virus in 2023 and 2024 showed high homology, with the nucleotide homology of hemagglutinin gene ranging from 97.9% to 99.2% and that of neuraminidase gene ranging from 98.3% to 99.1%. Among 83 Jiaxing strains, 80 were classified as clade 6B.1A.5a.2a and 3 were assigned to clade 6B.1A.15a.2a.1. These strains were further categorized into subclades C.1 (45), C.1.9(17), C.1.9.3 (18), and D (3). Additionally, an HA/NA reassortant strain (A/ZJNH/SWL1331/2023) was identified in 2023, followed by an oseltamivir-resistant strain (A/ZJPH/SWL1544/2024) carrying the H275Y substitution in 2024. A total of 31 amino acid substitutions were identified in the HA1 segment of Jiaxing influenza A(H1N1) strains, affecting three antigenic sites: Ca (S137P, A139D, A141T/V, R142K, D222G), Cb (L70F, S71F), and Sb (I185S, D187N, S190G), plus an additional Ca1 substitution (K169Q).

Conclusions: During 2023-2024, multiple genomic sites of influenza A(H1N1) viruses in Jiaxing have acquired mutations, underscoring the need for enhanced continuous surveillance and prevention of H1N1 influenza.