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bioRxiv · 10.1101/2025.07.24.666632

Emergence of an Antigenically Drifted and Reassorted Influenza B Virus at the end of the 2024-25 Influenza Season

Akin, E.·Villafuerte, D. A.·Werner, A. P.·Pinsley, M.·Fall, A.·Abdullah, O.·Norton, J. M.·Rothman, R. E.·Fenstermacher, K.·Gong, Y.-N.·Klein, E.·Mostafa, H. H.·Pekosz, A.
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Abstract

Influenza B virus (IBV) is a significant contributor to annual and severe cases of influenza, particularly in the young and elderly. Late in the 2024-25 Northern Hemisphere influenza season, a surge of IBV cases were identified in the Johns Hopkins Hospital Systems. The IBV responsible for the surge, C.3.1/re, was a clade C.3 virus that had reassorted with clade C.5.1 viruses and acquired the D197N mutation in hemagglutinin restoring a putative N-linked glycan predicted to mask a key neutralizing antibody epitope. The C.3.1/re viruses preferentially infected children but showed no significant change in disease severity. C.3.1/re viruses were poorly neutralized by pre- and post- influenza vaccination serum in a human cohort. Removal of the glycan at residue 197 restored neutralizing antibody recognition. The C.3.1/re IBV genotype that emerged late in the 2024-25 influenza season was antigenically mismatched with IBV vaccine strains for the 2025 and 2026 Southern hemisphere, as well as the 2025-26 Northern Hemisphere influenza seasons. While the 2026-27 Northern Hemisphere vaccine strain is a C.3.1/re, the egg adapted isolate selected (B/Tokyo/EIS13-175/2025) lacks the 197 glycosylation which is predicted to have poor recognition with circulating IBV clades. Phylogenetic analysis of currently circulating IBVs shows a diversification of circulating C.3 clades with multiple reassortment events between C.3 and C.5 clades in addition to independent acquisitions of D197N mutations, suggesting IBV is going through a period of significant antigenic and genetic expansion. IMPORTANCEInfluenza B viruses are undergoing a period of antigenic and genetic expansion, with several reassorted viruses emerging that also contain point mutations in key hemagglutinin antigenic sites proximal to the receptor binding domain. This has important impacts on vaccine strain choice, as only one IBV component is included in current influenza vaccines. We demonstrate a significant shift in the demographics of IBV infected individuals with the emergence of the antigenically drifted and reassorted IBV C.3.1/re. Furthermore, we show that 197 glycosylation of hemagglutinin is critical for C.3.1/re antigenic drift and we document several emergent C.3 reassortments encoding the D197N mutation. With the IBV vaccine component for the Northern Hemisphere 2026-27 season having lost a key N-linked glycan on the hemagglutinin protein, and multiple independent emergences of antigenically drifted and reassorted viruses, attention to IBV infections should be increased in the upcoming Southern and Northern hemisphere influenza seasons.

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Akin, E., Villafuerte, D. A., Werner, A. P., Pinsley, M., Fall, A., Abdullah, O., Norton, J. M., Rothman, R. E., Fenstermacher, K., Gong, Y.-N., Klein, E., Mostafa, H. H., Pekosz, A.. 2025-07-24. Emergence of an Antigenically Drifted and Reassorted Influenza B Virus at the end of the 2024-25 Influenza Season. https://doi.org/10.1101/2025.07.24.666632

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