Antigenic seniority and convergent haemagglutinin evolution shaped the immune landscape preceding influenza B/Yamagata’s extinction
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Background
In 2020, the B/Yamagata lineage of influenza B disappeared from circulation. Understanding the immunological conditions preceding this loss can help explain why the lineage disappeared and has implications for our understanding of viral evolution and ongoing vaccine policies.
Methods
We measured neutralising antibody responses in age- and sex-matched blood donor cohorts collected in 2020, 2023, and 2025 (n=114 per cohort) against a panel of pseudotyped influenza B viruses spanning 79 years of evolution, validated against live virus neutralisation assays. We performed antibody pulldown assays using full-length and head domain HA proteins from B/Yamagata (B/Phuket/3073/2013) and B/Victoria (B/Washington/02/2019) lineages, testing purified antibodies against chronologically distinct pseudotyped viruses. We used Bayesian network analysis, and LASSO regression to identify potential molecular determinants of cross-lineage neutralisation which were then confirmed via site-directed mutagenesis, and epitope-specific peptide pulldowns.
Findings
In 2020, population immunity was asymmetrically focused on B/Yamagata viruses. Despite no B/Yamagata circulation after 2020, neutralisation of recent B/Yamagata strains increased in 2023 while B/Victoria responses remained unchanged, consistent with antigenic seniority directing recall responses toward B/Yamagata. This trend inverted by 2025, with B/Yamagata immunity declining and B/Victoria immunity increasing. Antigen-specific purified antibodies showed lineage-biased potency, neutralising B/Yamagata viruses more effectively than B/Victoria viruses. We identified the 120-loop of the HA head domain as a critical cross-lineage epitope, with the charge state at a single convergently evolving residue at position 131 determining cross-reactive potency between lineages.
Interpretation
B/Yamagata’s acquisition of a positively charged residue at position 131, shared with B/Victoria, likely increased its cross-neutralisation by Victoria-raised immunity preceding its disappearance. Although antigenic seniority sustained cross-reactive responses to B/Yamagata after its extinction, the waning of this effect by 2025 suggests that population immunity to B/Yamagata is now declining. This has implications for influenza B vaccine policy.
Funding
CPT and UO were funded by a joint grant by the British Council and the Israeli Ministry of Innovation, Science & Technology, under the ISPF scheme [grant number 47650215]. N.C.R. is supported by a Royal Society Dorothy Hodgkin Research Fellowship [grant number DHR00620]. RG was funded by The Institute for Global Pandemic Planning at the University of Warwick, UK, as part of a philanthropically supported doctoral programme. M.L. was funded via the Medical Research Council doctoral training programme grant.
Evidence before this study
We searched PubMed and bioRxiv for articles published between Jan 1, 2010 and Apr 1, 2026, using the terms ‘influenza B’, ‘B/Yamagata’ or ‘B/Victoria’ combined with ‘cross-reactivity’, ‘extinction’, ‘disappearance’ or ‘antigenic seniority’, without language restrictions. Evidence quality was assessed by study design, reproducibility across independent datasets, and sample size. Assessment of these manuscripts confirmed that prior work had established that cross-lineage neutralising antibodies exist between influenza B lineages. Vaccination studies in humans and mice demonstrated that these cross-reactive responses are asymmetrically focused on B/Yamagata. Studies of first-infection history suggested that the initial lineage encountered can shape lifelong antibody profiles through antigenic imprinting. Global surveillance confirmed B/Yamagata’s absence from circulation after 2020, prompting its removal from quadrivalent vaccines. However, whether this asymmetry observed in vaccination settings extends to population-level immunity shaped by natural infection, the specific molecular determinants of cross-lineage neutralisation, and how population immunity has evolved since B/Yamagata’s disappearance remained unknown.
Added value of this study
Using age-and sex-matched blood donor cohorts from 2020, 2023 and 2025, we demonstrate that population immunity was asymmetrically focused on B/Yamagata in 2020, widening further by 2023 consistent with antigenic seniority. An inversion of this pattern was seen by 2025 as B/Yamagata-specific responses waned. Among singleton positions unambiguously identifiable by LASSO, position 131 showed the strongest temporal increase, governing cross-reactive potency. B/Yamagata’s evolution to a positively charged residue at this position, matching the charge state of B/Victoria, likely increased its vulnerability to Victoria-raised immunity in the years preceding its disappearance.
Implications of all the available evidence
The waning of antigenic seniority-reinforced immunity to B/Yamagata by 2025 indicates that population protection against this lineage is declining. Should a B/Yamagata-like virus re-emerge, the population may face substantially reduced lineage-specific protection. Ongoing serological surveillance will be needed to determine when this declining immunity reaches a threshold warranting reconsideration of vaccine composition.
