Structural basis of diverse antibody recognition of conserved coronavirus spike S2 epitopes that contribute to protective immunity
- 1Stanford University
Abstract
Conserved epitopes within the coronavirus spike S2 domain elicit broadly reactive antibodies, yet many characterized responses show limited neutralizing and variable protective activity, leaving their contribution to antiviral immunity unclear. Building on our previous mapping of evolutionarily conserved spike coldspots, we isolated human monoclonal antibodies targeting four conserved epitopes in the spike S2 domain: the internal fusion peptide (iFP), the central helix (CH), the connector domain (CD), and a membrane-proximal epitope in the heptad repeat 2 that we term the lower stalk (LS). A crystal structure of an LS-directed antibody defined a previously unresolved mode of antibody recognition of this membrane-proximal epitope, while cryogenic electron microscopy (cryo-EM) structures revealed that genetically diverse CH-specific antibodies use distinct binding modes to converge on conserved features of the prefusion S2 apex. Despite minimal neutralizing activity, CH- and LS-directed antibodies exhibited distinct antiviral functions. LS-directed antibodies mediated Fc{gamma} receptor-dependent effector activity in vitro, whereas the broadly reactive CH-directed antibody ch.007 lacked detectable antibody-dependent cellular cytotoxicity (ADCC) or cellular phagocytosis (ADCP) activity yet protected mice from lethal SARS-CoV-2 MA10 challenge, with protection abrogated by Fc{gamma} receptor-silencing mutations. Together, these findings expand the genetic, structural and functional landscape of human antibody responses to conserved coronavirus S2 epitopes and demonstrate that CH-directed antibodies can contribute to protective immunity through Fc-dependent mechanisms not predicted by in vitro neutralization or conventional in vitro Fc effector assays.
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BibTeX
@misc{rubio2026structural,
title = {{Structural basis of diverse antibody recognition of conserved coronavirus spike S2 epitopes that contribute to protective immunity}},
author = {A. A. Rubio and V. Crivelli and V. Hönig and M. Cizkova and T. Cervantes Rincon and M. E. Abernathy and M. K. Parada and D. Vahdat and Y. E. Lee and M. Eso and J. Cantergiani and S. G. Moro and D. Jarrossay and C. Guerra and B. Cena and M. Minculescu and V. Gradauskaite and M. Biggiogero and V. Calvaruso and A. F. Pellanda and A. Cavalli and C. Garzoni and M. Palus and D. F. Robbiani and C. O. Barnes},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.13.750764},
url = {https://www.biorxiv.org/content/10.64898/2026.09.13.750764v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Structural basis of diverse antibody recognition of conserved coronavirus spike S2 epitopes that contribute to protective immunity
AU - A. A. Rubio
AU - V. Crivelli
AU - V. Hönig
AU - M. Cizkova
AU - T. Cervantes Rincon
AU - M. E. Abernathy
AU - M. K. Parada
AU - D. Vahdat
AU - Y. E. Lee
AU - M. Eso
AU - J. Cantergiani
AU - S. G. Moro
AU - D. Jarrossay
AU - C. Guerra
AU - B. Cena
AU - M. Minculescu
AU - V. Gradauskaite
AU - M. Biggiogero
AU - V. Calvaruso
AU - A. F. Pellanda
AU - A. Cavalli
AU - C. Garzoni
AU - M. Palus
AU - D. F. Robbiani
AU - C. O. Barnes
PY - 2026
DA - 2026/09/13
PB - bioRxiv
DO - 10.64898/2026.09.13.750764
UR - https://www.biorxiv.org/content/10.64898/2026.09.13.750764v1
AB - Conserved epitopes within the coronavirus spike S2 domain elicit broadly reactive antibodies, yet many characterized responses show limited neutralizing and variable protective activity, leaving their contribution to antiviral immunity unclear. Building on our previous mapping of evolutionarily conserved spike coldspots, we isolated human monoclonal antibodies targeting four conserved epitopes in the spike S2 domain: the internal fusion peptide (iFP), the central helix (CH), the connector domain (CD), and a membrane-proximal epitope in the heptad repeat 2 that we term the lower stalk (LS). A crystal structure of an LS-directed antibody defined a previously unresolved mode of antibody recognition of this membrane-proximal epitope, while cryogenic electron microscopy (cryo-EM) structures revealed that genetically diverse CH-specific antibodies use distinct binding modes to converge on conserved features of the prefusion S2 apex. Despite minimal neutralizing activity, CH- and LS-directed antibodies exhibited distinct antiviral functions. LS-directed antibodies mediated Fc{gamma} receptor-dependent effector activity in vitro, whereas the broadly reactive CH-directed antibody ch.007 lacked detectable antibody-dependent cellular cytotoxicity (ADCC) or cellular phagocytosis (ADCP) activity yet protected mice from lethal SARS-CoV-2 MA10 challenge, with protection abrogated by Fc{gamma} receptor-silencing mutations. Together, these findings expand the genetic, structural and functional landscape of human antibody responses to conserved coronavirus S2 epitopes and demonstrate that CH-directed antibodies can contribute to protective immunity through Fc-dependent mechanisms not predicted by in vitro neutralization or conventional in vitro Fc effector assays.
ER -