1. Reverse mutational scanning of SARS-CoV-2 spike BA.2.86 identifies epitopes contributing to immune escape from polyclonal sera.
- Author
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Bdeir N, Lüddecke T, Maaß H, Schmelz S, Rand U, Jacobsen H, Metzdorf K, Kulkarni U, Cossmann A, Stankov MV, Hoffmann M, Pöhlmann S, Blankenfeldt W, Dopfer-Jablonka A, Behrens GMN, and Čičin-Šain L
- Subjects
- Humans, COVID-19 Vaccines immunology, Neutralization Tests, HEK293 Cells, Spike Glycoprotein, Coronavirus immunology, Spike Glycoprotein, Coronavirus genetics, SARS-CoV-2 immunology, SARS-CoV-2 genetics, Antibodies, Neutralizing immunology, Antibodies, Neutralizing blood, Antibodies, Viral immunology, Antibodies, Viral blood, Immune Evasion genetics, Immune Evasion immunology, COVID-19 immunology, COVID-19 virology, Epitopes immunology, Epitopes genetics, Mutation
- Abstract
The recently detected Omicron BA.2.86 lineage contains more than 30 amino acid mutations relative to BA.2. BA.2.86 and its JN.1 derivative evade neutralization by serum antibodies of fully vaccinated individuals. In this study, we elucidate epitopes driving the immune escape of BA.2.86 and JN.1 via pseudovirus neutralization. Here we generate 33 BA.2.86 mutants, each reverting a single mutation back to BA.2. We use this library in an approach that we call reverse mutational scanning to define distinct neutralization titers against each epitope. Mutations within the receptor binding domain at K356T, V483Δ, and to a lesser extent N460K, A484K, and F486P enhance immune escape. Interestingly, 16insMPLF within the spike N-terminal domain and P621S within S1/S2 also significantly contribute to antibody escape of BA.2.86. Upon XBB.1.5 booster vaccination, neutralization titers against JN.1 and BA.2.86 improve considerably, and residual immune escape is driven by 16insMPLF, N460K, E554K, and to a lesser extent P621S, and A484K., Competing Interests: Competing interests: L.C.-S. served as an advisor to Sanofi unrelated to this work. G.M.N.B. served as advisor for Moderna unrelated to this work, A.D.-J. served as an advisor for Pfizer unrelated to this work, S.P. and M.H. conducted contract research (testing of vaccinee plasma for neutralizing activity against SARS-CoV-2) for Valneva unrelated to this work. S.P. served as advisor for BioNTech, unrelated to this work. H.J. served as advisor on COVID neutralization assays for WHO and CEPI, unrelated to this work. The other authors declare no competing interests., (© 2025. The Author(s).)
- Published
- 2025
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