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Virus EvolutionMicrobiologyPeer-reviewed journal article

Near real-time data on the human neutralizing antibody landscape to influenza virus as of early 2026 to inform vaccine-strain selection

Caroline KikawaiD, John HuddlestoniD, Samuel A. Turner, Andrea N. LoesiD, Jiaojiao LiuiD, Sydney GangiD, Tachianna Griffiths, Elizabeth M. DrapeauiD, Benjamin John CowlingiD, Faith C. S. HoiD, Nancy LeungiD, Janet A. EnglundiD, Kirsten LacombeiD, Shinji WatanabeiD, Hideki HasegawaiD, Michael Paul BuschiD, Lanteri Marion, Mars StoneiD, Bryan Spencer, Richard A. NeheriD, Derek J. SmithiD, Trevor BedfordiD, Scott E. HensleyiD, Jesse D. BloomiD

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Abstract

Twice each year, a decision is made on whether to update the strains included in the seasonal influenza vaccine to better match the most recent circulating viral strains. To characterize the antigenic properties of current seasonal influenza A strains to inform the upcoming decision about which strains to include in the 2026-2027 Northern Hemisphere vaccine, here we perform high-throughput sequencing-based neutralization assays using a library of 57 H3N2 and 34 H1N1 influenza hemagglutinins reflecting the circulating diversity of strains in late 2025 to early 2026. We assay this library against 302 human sera collected in late 2025. The resulting data set encompasses 27,409 titers, and provides a near real-time portrait of the human neutralizing antibody landscape against influenza virus. We find that many human sera have lower titers against the K subclade of H3N2 and the D.3.1.1 subclade of H1N1; these subclades have recently become dominant among their respective subtypes. Our measurements also reveal variability in titers to different subvariants within the K subclade of H3N2, with titers especially low to subclade K strains with additional mutations in antigenic regions D and E. We make all our data and accompanying visualizations publicly available to enable their use in vaccine-strain selection and analyses of influenza evolution and immunity.

In-depth summary

Claude Sonnet 4.6 · xhigh effort · 8 Nov 2026 · from the full text of version 2 (14 Jul 2026) · CC BY 4.0

Sequencing-based neutralization of 91 H3N2 and H1N1 hemagglutinins against 302 human sera (27,409 titers) shows reduced titers to H3N2 subclade K and H1N1 D.3.1.1.

Vaccine-strain selection depends on serology plus sequence data, and human-serum measurements are increasingly used because human antibody specificities are more complex than those of singly infected ferrets. This work supplies near real-time human titers against the strains circulating in early 2026, ahead of the 2026-2027 Northern Hemisphere decision.

Key results

  1. ShownMedian human titers varied across recent H3N2 strains, and subclade K strains had the lowest titers, below the J.2:S145N 2025-2026 vaccine strain and the J.2.4 strain chosen for the 2026 Southern Hemisphere vaccine.

    17,142 H3N2 titers; median titers differed by more than three-fold across recent H3N2 strains, and the lowest-titer strains were in subclade K. · Neutralizing antibody landscapes to recent H3N2…

  2. SuggestedWithin subclade K, strains with extra mutations in antigenic region D (sites 96, 207, 223) or E (site 261) had the lowest titers, suggesting neutralization is further eroded beyond canonical K.

    Lowest-titer K strains carried region D or E mutations (Figures 4 and 5); a few J.2.4 strains with 135N (added glycosylation site) had similarly low titers. · Neutralizing antibody landscapes to recent H3N2…; Discussion

  3. ShownFor H1N1, nearly all the lowest-median-titer strains were in subclade D.3.1.1, and all six D.3.1.1 strains sat below both the 2025-2026 Northern Hemisphere and 2026 Southern Hemisphere vaccine strains; titer spread was smaller than for H3N2.

    10,267 H1N1 titers; median variation about two-fold; all six D.3.1.1 strains lower than the C.1.1 (2025-2026 NH vaccine) and D.3.1 (2026 SH vaccine) strains. · Neutralizing antibody landscapes to recent H1N1…

  4. SuggestedTiter patterns differed by age: adolescents and young adults had reduced H1N1 titers to strains mutated at sites 155 or 157, and children had lower H3N2 titers to J.2.3, J.2.4 and K than to J.2, J.2.2 and G.1.3.1.

    H1N1 comparison uses sera from ages 10 to 25 years (Figure 6B); the H3N2 child trend comes from the Seattle Children's Hospital (SCH) set versus adult sets. No statistical tests reported. · Neutralizing antibody landscapes to recent H3N2…; Neutralizing antibody landscapes to recent H1N1…; Figure legends

  5. ShownThe 2025-2026 egg-based trivalent vaccine raised titers only modestly, and increases were smaller for the newest H3N2 subclades (K, J.2.4, J.2.3) and for G155E-containing H1N1 strains.

    59 PENN individuals, pre vs 28 days post: H3N2 median fold change ~1.5 to 2.5; base K ~2-fold vs ~1.5-fold for K strains with region D mutations; H1N1 ~1.4-2-fold. · Changes in neutralization titers after…

Methods, data and reproducibility

Pooled libraries of barcoded influenza viruses, each carrying a natural human H3N2 or H1N1 hemagglutinin, were neutralized by serial serum dilutions and read out by barcode sequencing. Titers are the reciprocal dilution giving 50% neutralization, with the median taken across barcodes per strain.

  • Barcoded virus library: 186 barcodes covering 53 recent H3N2, 30 recent H1N1, 4 historical H3N2 and 4 historical H1N1 vaccine-strain HAs · Influenza A virus (H3N2, H1N1) · n = 91 HAs; 186 barcodes
  • Human sera/plasma from five sets (CTS, HKU, NIID, PENN, SCH), mostly collected October to November 2025, ages 0 to 103 years · human · n = 302 sera; 27,409 titers
  • PENN pre- and 28-day post-vaccination sera after the 2025-2026 Northern Hemisphere egg-based trivalent vaccine · human · n = 59 individuals
  • HKU (EPI-HK cohort) sera tested, including 35 follow-up participants, 7 replacements and one post-infection serum reported · human · n = 48 sera tested
Methods & tools
Sequencing-based neutralization assay, seqneut-pipeline v6.2.0, Nextstrain pdmH1N1 and H3N2 6-month builds, pick_library_strains.py (nextstrain/seasonal-flu), Nextstrain Community builds (protein trees), nextstrain-prot-titers-tree, Twist Biosciences gene synthesis
Software & environment
Analysis run with seqneut-pipeline version 6.2.0; parameters set in the repository config.yml.
Limitations (4)
  • How to account for the heterogeneity in titers across sera and within subclades when forecasting evolution and choosing vaccine strains remains an open question. · stated by the authors
  • Many sera come from people with unknown or incomplete infection and vaccination histories, and the sera sets differ in geography and age, so set-to-set and age comparisons are descriptive and may be confounded. · noted in this summary
  • Library coverage was reduced in practice: most egg-passaged H1N1 vaccine strains were dropped for poor growth, and quality control cut recent strains from 58 to 53 (H3N2) and 48 to 30 (H1N1). · stated by the authors
  • Findings are descriptive medians without reported statistical tests or confidence intervals, and the link between low titers and subclade expansion is correlational. Viruses carry WSN/1933 internal genes, so titers reflect HA-specific neutralization only. · noted in this summary

Read this if you need human-serum neutralization data on current H3N2 and H1N1 strains for 2026-2027 vaccine-strain selection or analyses of influenza antigenic evolution.

Citations
4
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top 1%

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