Genomic and Antigenic Evolution of Influenza A(H3N2) After the COVID-19 Era: A Scoping Review with Focus on J and K Subclades and Implications for Vaccine Effectiveness
A scoping review was conducted across six databases in January 2026, including studies on genomic surveillance, antigenic characterization, and vaccine effectiveness (VE), which indicated diminished VE against drifted strains, though no consistent increase in clinical severity was observed.
Abstract
Post-COVID-19, influenza A(H3N2) has re-emerged with accelerated genetic diversification. The rise in antigenically drifted subclades raises concerns regarding immune escape and vaccine mismatch. To synthesize the available evidence on the post-pandemic evolution of influenza A(H3N2), with particular attention to emerging subclades and their potential public health implications, a scoping review (PRISMA-ScR) was conducted across six databases in January 2026, including studies on genomic surveillance, antigenic characterization, and vaccine effectiveness (VE). Twenty studies were included. While clade 2a.3a.1 (J lineage) predominated, reports highlighted the rapid emergence of the antigenically distinct K subclade (formerly J.2.4.1). Genetic and laboratory assays (HI/neutralization) confirmed immune escape and reduced vaccine match. Observational estimates indicated diminished VE against drifted strains, though no consistent increase in clinical severity was observed. Post-pandemic A(H3N2) is defined by rapid drift and diversification. Emerging variants like the K subclade challenge vaccine selection and seasonal preparedness. Integrated surveillance remains vital for timely vaccine updates and mitigating public health impact.
Due to the continuous evolution of Influenza A viruses (IAVs), novel strains with efficient human-to-human transmission may emerge and cause future pandemics. Among these, highly pathogenic avian influenza (HPAI) H5N1 remains a major concern because of its impact on wildlife, livestock, and human health. The widespread circulation of H5N1 clade 2.3.4.4b, detected in hundreds of bird species and numerous mammals worldwide, highlights important changes in viral ecology and transmission, increasing its zoonotic and pandemic potential. This review summarizes current evidence on cross-reactive and cross-protective immunity to H5N1 in humans, focusing primarily on humoral immune responses. We examine the presence of pre-existing H5N1-reactive antibodies in individuals without known exposure and discuss how previous seasonal influenza infection or vaccination may contribute to their development. Particular attention is given to antibodies targeting conserved regions of hemagglutinin (HA), especially the stalk domain, as well as neuraminidase (NA), which may provide heterosubtypic protection. We also evaluate the ability of seasonal influenza vaccines and infections to induce cross-reactive responses against H5N1 and their potential role in partial protection or immune priming. Finally, we review current and emerging H5N1 vaccination strategies, including adjuvanted and mRNA-based platforms, and identify priorities for surveillance, population immunity assessment, and the development of broadly protective influenza vaccines.
Iván Sanz-Muñoz, Carlos J. Ciria-Gil, Marta Hernández et al.· Journal of Infection· 0 citations
ABSTRACT Enterovirus D68 (EV-D68) has re-emerged over the past decade as a significant respiratory pathogen associated with severe respiratory disease and acute flaccid myelitis. Its circulation has typically followed a biennial pattern, with predominance in late summer and early fall, a pattern that was temporarily disrupted during the COVID-19 pandemic. Surveillance in 2025 revealed off-season circulation of EV-D68. This study describes the genomic characteristics of the 2025 EV-D68 viruses and the clinical features of affected patients. Between May and December 2025, remnant respiratory specimens positive for rhinovirus/enterovirus were screened for EV-D68 and subjected to whole-genome sequencing. Phylogenetic analyses were performed using maximum-likelihood methods. Recombination was assessed using subgenomic phylogenies, SimPlot similarity and BootScan analyses, and read-level inspection. Among 1,321 patients tested, 147 (11.1%) were EV-D68-positive, and 119 (81.0%) yielded complete genomes. EV-D68 positivity increased in July 2025, peaked in August (~21%), and remained elevated through September and October, exceeding levels observed in 2024. Patients had a median age of 36 years, with infections disproportionately affecting older adults. Phylogenetic analysis demonstrated exclusive circulation of subclade A2. Five genomes formed a distinct recombinant lineage (A2-Re). Subgenomic phylogenies showed clustering with A2 viruses in the P1 region and with B3 viruses in the P2–P3 regions. SimPlot and BootScan analyses identified a recombination breakpoint near the 2A/2B junction (~nt 3,700). The recombinant lineage was associated with temporally clustered cases in September–October. These findings demonstrate recombination between distinct EV-D68 subclades and underscore the importance of whole-genome surveillance for accurate viral characterization. Continued genomic monitoring is essential for detecting emerging variants with potential implications for transmissibility, pathogenicity, and public health preparedness. IMPORTANCE This study highlights an increased off-season circulation of Enterovirus D68 (EV-D68) and a higher burden of disease in adults in 2025. The identification of a novel A2–B3 recombinant lineage provides evidence of ongoing viral evolution through recombination, a mechanism that may alter transmissibility, virulence, or immune responses. Detection of this lineage in temporally clustered cases suggests local transmission and underscores the potential for rapid spread of newly emerged variants. These findings emphasize the limitations of partial genomic approaches and the critical role of whole-genome sequencing in accurately characterizing circulating strains and identifying recombination events. Enhanced genomic surveillance is essential to detect emerging variants in real time, inform diagnostic assay performance, and support public health responses. Continued monitoring of EV-D68 evolution will be important for anticipating changes in disease burden, guiding clinical awareness, and strengthening preparedness for future outbreaks. This study highlights an increased off-season circulation of Enterovirus D68 (EV-D68) and a higher burden of disease in adults in 2025. The identification of a novel A2–B3 recombinant lineage provides evidence of ongoing viral evolution through recombination, a mechanism that may alter transmissibility, virulence, or immune responses. Detection of this lineage in temporally clustered cases suggests local transmission and underscores the potential for rapid spread of newly emerged variants. These findings emphasize the limitations of partial genomic approaches and the critical role of whole-genome sequencing in accurately characterizing circulating strains and identifying recombination events. Enhanced genomic surveillance is essential to detect emerging variants in real time, inform diagnostic assay performance, and support public health responses. Continued monitoring of EV-D68 evolution will be important for anticipating changes in disease burden, guiding clinical awareness, and strengthening preparedness for future outbreaks.
A. Fall, C. Morris, O. Elgazayerly et al.· Microbiology spectrum· 0 citations
Background: Enteric fever, caused by Salmonellaenterica serovars Typhi and Paratyphi A, remains a major concern in low- and middle-income countries, with treatment increasingly complicated by antimicrobial resistance. Typhoid conjugate vaccines (TCVs) offer a promising intervention, but their impact on circulating lineages and population structure remains poorly understood. Nepal introduced a nationwide TCV programme in April 2022, shortly after the COVID-19 pandemic disrupted healthcare delivery and surveillance. Methods: We sequenced 350 S. Typhi and 114 S. Paratyphi A isolates collected in Nepal between 2018 and 2024 and analyzed them alongside1,797 previously published Nepal genomes (2005-2018). We characterized genotype distribution, antimicrobial resistance determinants, phylogenetic relationships and lineage-specific phylodynamics across three epidemiological periods: pre-pandemic (before 2020), pandemic/pre-vaccine (2020-2022), and post-vaccine introduction (2022-2024). Results: Sixteen S. Typhi genotypes were identified, dominated by 4.3.1.2 (28%), 3.3.2 (20.3%) and 3.3.1 (16.9%); S. Paratyphi A was dominated by genotypes 2.4.3 (57.0%) and 2.4.2 (25.4%). Multidrug resistance was rare, but fluoroquinolone non-susceptibility was widespread (70.6% of S. Typhi; 99.1% of S. Paratyphi A), with high-level resistance confined to a single S. Typhi 4.3.1.2.1 clade dating to 2008. Phylodynamic reconstruction revealed asymmetric lineage trajectories: S. Typhi H58 contracted sharply during the pandemic, lineage 3.3 contracted specifically post-TCV, and S. Paratyphi A (not vaccine-targeted) showed only a modest pandemic-era decline. Post-TCV, the age distribution of cases shifted older and the adult genotype mix shifted toward lineage 3.3. We found no evidence of vaccine-driven escape at the Vi capsule or O-antigen in Nepal or across a cross-country cohort. Conclusions: Both S. Typhi and S. Paratyphi A populations in Nepal underwent recent declines in effective population size, coinciding with the COVID-19 pandemic and TCV introduction. Persistent fluoroquinolone resistance, particularly among S. Paratyphi A, underscores ongoing AMR challenges and highlights the need for expanded vaccine strategies targeting both pathogens.
K. D. da Silva, S. Naga, N. Katuwal et al.· medRxiv· 0 citations
Research on regional circulation and evolution of influenza A viruses before and after the COVID-19 pandemic is crucial for informing vaccine updates and antiviral drug development. This study generated 260 new genomic sequences of influenza A(H1N1)pdm09 viruses collected in Yunnan province, China, between 2018 and 2023. Comparative genomics analyses elucidated their evolutionary characteristics and dynamics. Epidemiological analysis identified key risk factors (sex, age, occupation) for influenza infection. Phylogenetic analyses revealed the sequence divergences between the vaccine strains and Yunnan circulating strains, especially in the 2020-2024 influenza seasons. The subclade reassortment events were extremely limited among these sequenced Yunnan strains, suggesting the reassortment may be not a major contributor for the circulation and evolution of influenza A(H1N1)pdm09 viruses in Yunnan during these influenza seasons. We detected the elevated evolutionary pressures acting on the specific gene segments, reflected in increased dN/dS ratios, particularly for envelope proteins. Furthermore, numerous amino acid substitutions (e.g., S185I/T) within HA antigenic epitopes and receptor binding sites were identified in most Yunnan strains, indicating potential roles of antigenic drift in modulating viral antigenicity and host adaptation. Notably, 17 amino acid substitutions in HA and NA (including HA: N156K) accumulated to higher frequencies during the 2022-2023 and 2023-2024 seasons. These changes likely represented the molecular signature of contemporary A(H1N1)pdm09 viruses in Yunnan. Collectively, this study explored the molecular evolutionary dynamics of A(H1N1)pdm09 viruses in Yunnan province during diverse influenza seasons, providing new regional data for studying molecular characterization and evolution of A(H1N1)pdm09 within the global surveillance framework.
Meiling Zhang, Xiuping Zhang, Ruize Ni et al.· Virology Journal· 0 citations
The H3 subtype avian influenza virus (AIV) poses a substantial global public health threat due to its high host adaptability and ongoing evolution. The recent emergence of novel H3N8 and H3N3 AIVs associated with cross-species transmission underscores the urgent need for enhanced epidemiological surveillance. In this study, we conducted surveillance and characterization of H3 AIVs based on a total of 737 poultry samples collected across 21 Chinese provinces from November 2022 to December 2023. Of these, 69 (9.4%) tested positive for H3 AIV by RT-qPCR, and one H3N8 isolate and ten H3N3 isolates were obtained for whole-genome characterization. We performed whole-genome sequencing, phylogenetic analysis, reassortment inference, and evaluation of key amino acid substitutions, alongside antigenic characterization using hemagglutination inhibition (HI) assays and an in vivo mouse challenge experiment. The H3N8 isolate was identified as a triple-reassortant virus possessing the Eurasian avian H3 gene, the North American avian N8 gene, and H9N2-derived internal genes. The H3N3 isolates represented reassortant viruses that had acquired the HA gene from the novel H3N8 AIV lineage, the NA gene from H10N3 AIV, and internal genes from H9N2 AIV. All isolates exhibited HA cleavage sites characteristic of low pathogenic avian influenza viruses. Additionally, several amino acid substitutions previously associated with enhanced mammalian adaptation were identified, including L89V and I292V in PB2 and H436Y in PB1. In a BALB/c mouse challenge experiment, the representative H3N8 virus established infection without prior adaptation and replicated predominantly in the upper respiratory tract, with detectable viral RNA in respiratory tissues and limited extrapulmonary dissemination. Antigenic analysis revealed no cross-reactivity between the novel H3 AIVs and H5, H7, or H9 AIVs as measured by HI. Based on molecular and phylogenetic characterization, antigenic assessment, and preliminary mammalian infection data, our findings provide evidence suggesting a potential public health risk. We recommend intensified surveillance of H3 AIVs in poultry and accelerated vaccine development to curb viral spread and improve public health preparedness.
Xue Wang, Hao Shi, Peidong Li et al.· The Veterinary Journal· 0 citations
Influenza A(H3N2) remains a significant public health threat due to its rapid antigenic drift, which often compromises vaccine effectiveness. This study characterized the molecular and epidemiological profile of hemagglutinin (HA) variants circulating in Western Mexico throughout 2022. Among 476 positive cases, A(H3N2) was the predominant subtype (88%), with infection peaks during epidemiological weeks (EW) 1, 45, and 46. Sanger sequencing of the HA gene identified 64 amino acid substitutions, with 85.9% of the substitutions located in the HA1 subunit, primarily within the receptor-binding domain (RBD). Homology modeling and molecular docking were performed on five representative variants: C156S, D158N, Y159N, C136S, and L227P. All variants exhibited a slight decrease in binding affinity for sialic acid compared to the 1HGE reference. Notably, while mutations such as D158N and Y159N remodeled the interaction network, Glu190 and His183 remained critical for stabilizing the HA-ligand complex through hydrogen bonds and non-covalent interactions in the structural models. These structural findings suggest that contemporary mutations in the RBD may contribute to changes in receptor-binding interactions while preserving key structural features associated with host cell attachment.
Karen M Hernandez-Gonzalez, A. S. Carranza-Aranda, J. Muñóz-Valle et al.· International Journal of Mol...· 0 citations