Low, J. S. et al. ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies. Science 377, 735–741 (2022).
Sun, X. et al. Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2. Nat. Microbiol. 7, 1063–1074 (2022).
Qu, P. K. et al. Enhanced neutralization resistance of SARS-CoV-2 Omicron subvariants BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2. Cell Host Microbe 31, 9–17.e3 (2023).
Wang, Q. et al. Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants. Cell 186, 279–286.e278 (2023).
Chen, Y. J. et al. Broadly neutralizing antibodies to SARS-CoV-2 and other human coronaviruses. Nat. Rev. Immunol. 23, 189–199 (2023).
Ling, Z. Y., Yi, C. Y., Sun, X. Y., Yang, Z. & Sun, B. Broad strategies for neutralizing SARS-CoV-2 and other human coronaviruses with monoclonal antibodies. Sci. China Life Sci. 66, 658–678 (2023).
Dacon, C. et al. Broadly neutralizing antibodies target the coronavirus fusion peptide. Science 377, 728–735 (2022).
Bianchini, F. et al. Human neutralizing antibodies to cold linear epitopes and subdomain 1 of the SARS-CoV-2 spike glycoprotein. Sci. Immunol. 8, eade0958 (2023).
Marcink, T. C. et al. Intermediates in SARS-CoV-2 spike-mediated cell entry. Sci. Adv. 8, eabo3153 (2022).
Song, Y. T. et al. In situ architecture and membrane fusion of SARS-CoV-2 Delta variant. Proc. Natl Acad. Sci. USA 120, e2213332120 (2023).
Grunst, M. W. et al. Structure and inhibition of SARS-CoV-2 spike refolding in membranes. Science 385, 757–765 (2024).
Xing, L. et al. Early fusion intermediate of ACE2-using coronavirus spike acting as an antiviral target. Cell 188, 1297–1314.e1224 (2025).
Jackson, C. B., Farzan, M., Chen, B. & Choe, H. Mechanisms of SARS-CoV-2 entry into cells. Nat. Rev. Mol. Cell Biol. 23, 3–20 (2022).
Meng, B. et al. Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity. Nature 603, 706–714 (2022).
Willett, B. J. et al. SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nat. Microbiol. 7, 1161–1179 (2022).
Hu, B. et al. Spike mutations contributing to the altered entry preference of SARS-CoV-2 omicron BA.1 and BA.2. Emerg. Microbes Infect. 11, 2275–2287 (2022).
Kakizaki, M. et al. The respective roles of TMPRSS2 and cathepsins for SARS-CoV-2 infection in human respiratory organoids. J. Virol. 99, e0185324 (2025).
Furnon, W. et al. Phenotypic evolution of SARS-CoV-2 spike during the COVID-19 pandemic. Nat. Microbiol. 10, 77–93 (2025).
Shi, W. et al. Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane. Nature 619, 403–409 (2023).
Hoffmann, M. et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell 181, 271–280.e278 (2020).
Koch, J. et al. TMPRSS2 expression dictates the entry route used by SARS-CoV-2 to infect host cells. EMBO J. 40, e107821 (2021).
Hu, Y. B., Dammer, E. B., Ren, R. J. & Wang, G. The endosomal–lysosomal system: from acidification and cargo sorting to neurodegeneration. Transl. Neurodegener. 4, 18 (2015).
Fedotov, S., Alexandrov, D., Starodumov, I. & Korabel, N. Stochastic model of virus–endosome fusion and endosomal escape of pH-responsive nanoparticles. Mathematics 10, 375 (2022).
Li, C. et al. Broad neutralization of SARS-CoV-2 variants by an inhalable bispecific single-domain antibody. Cell 185, 1389–1401.e18 (2022).
Addetia, A. et al. Neutralization, effector function and immune imprinting of Omicron variants. Nature 621, 592–601 (2023).
Kimura, I. et al. The SARS-CoV-2 spike S375F mutation characterizes the Omicron BA.1 variant. iScience 25, 105720 (2022).
Pastorio, C. et al. Determinants of Spike infectivity, processing, and neutralization in SARS-CoV-2 Omicron subvariants BA.1 and BA.2. Cell Host Microbe 30, 1255–1268.e5 (2022).
Qu, P. et al. Determinants and mechanisms of the low fusogenicity and high dependence on endosomal entry of omicron subvariants. mBio 14, e0317622 (2023).
Walls, A. C. et al. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell 181, 281–292.e286 (2020).
Modjarrad, K. et al. Preclinical characterization of the Omicron XBB.1.5-adapted BNT162b2 COVID-19 vaccine. npj Vaccines 9, 229 (2024).
Peacock, T. P. et al. The altered entry pathway and antigenic distance of the SARS-CoV-2 Omicron variant map to separate domains of spike protein. Preprint at bioRxiv https://doi.org/10.1101/2021.12.31.474653 (2022).
Yi, C. Y. et al. Key residues of the receptor binding motif in the spike protein of SARS-CoV-2 that interact with ACE2 and neutralizing antibodies. Cell Mol. Immunol. 17, 621–630 (2020).
Yi, C. Y. et al. Comprehensive mapping of binding hot spots of SARS-CoV-2 RBD-specific neutralizing antibodies for tracking immune escape variants. Genome Med. 13, 164 (2021).
Rappazzo, C. G. et al. Broad and potent activity against SARS-like viruses by an engineered human monoclonal antibody. Science 371, 823–829 (2021).
Scheres, S. H. W. RELION: Implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012).
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
Zhang, K. Gctf: Real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016).
Bepler, T. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat. Methods 16, 1153–1160 (2019).
Tan, Y. Z. et al. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat. Methods 14, 793–796 (2017).
Pettersen, E. F. et al. UCSF chimera – a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
Sanchez-Garcia, R. et al. DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. Commun. Biol. 4, 874 (2021).
He, J. H., Li, T. & Huang, S. Y. Improvement of cryo-EM maps by simultaneous local and non-local deep learning. Nat. Commun. 14, 3217 (2023).
Mannar, D. et al. Altered receptor binding, antibody evasion and retention of T cell recognition by the SARS-CoV-2 XBB.1.5 spike protein. Nat. Commun. 15, 1854 (2024).
Waterhouse, A. et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46, W296–W303 (2018).
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of. Acta Crystallogr. D 66, 486–501 (2010).
Afonine, P. V. et al. Real-space refinement in for cryo-EM and crystallography. Acta Crystallogr. D 74, 531–544 (2018).
Chen, V. B. et al. All-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010).
Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).
Bao, Z. Pan-CoV epitope sterically occluded in an open early spike fusion intermediate. Figshare https://doi.org/10.6084/m9.figshare.31383049 (2026).

