Genetic characterization and whole-genome sequencing-based genetic analysis of influenza B in Shandong Province during 2015–2024

Influenza B virus (IBV) remains a significant concern due to its role in seasonal epidemics, frequently leading to localized outbreaks characterized by high morbidity and mortality rates. This study analyzed 109 IBV strains isolated in Shandong Province using phylogenetic and amino acid variation analyses. These sequences were aligned with vaccine strains and representative isolates obtained from the GISAID influenza database. Phylogenetic trees were constructed using the maximum likelihood (ML) method in MEGA software, while amino acid substitutions were visualized using MegAlign software, and potential N-glycosylation sites were predicted using NetNGlyc 1.0. Compared with contemporary vaccine strains, the 109 IBV strains isolated in Shandong Province exhibited genetic homology ranging from 96.2% to 100.0%, with a trend of increasing evolutionary divergence over time. Annual amino acid substitutions in the HA gene were observed, particularly within critical antigenic epitopes, including the 120-loop, 150-loop, 160-loop, and 190-helix, as well as in receptor-binding domains. A total of 30 antigenically drifted strains were identified. Notably, one strain carried the H273Y mutation in the NA gene, which is associated with resistance to neuraminidase (NA) inhibitors. Additional mutations were detected in genes encoding NP, PA, NS1, PB2, and PB1, suggesting their potential involvement in viral replication and immune evasion. Furthermore, one B/Victoria strain was identified with an NP gene derived from the B/Yamagata lineage, indicating possible reassortment between lineages. The genomic evolution of Shandong’s IBV strains between 2015 and 2024 was driven by both antigenic drift and genetic reassortment. The suboptimal antigenic match between circulating strains and vaccine components, along with the emergence of drug-resistant variants, underscores the urgent need for continuous vaccine updates and strategic selection of antiviral drugs. Sustained surveillance of IBV epidemiology and genetic evolution remains essential for providing early warnings of potential pandemic threats.