The ongoing threat of zoonotic coronavirus spillover into humans, exemplified by severe acute respiratory syndrome virus 2 (SARS-CoV-2), underscores the urgent need for pan-coronavirus therapeutics that can be deployed to mitigate future pandemics.
Here, we identified monoclonal antibodies from COVID-19 convalescent donors that target two conserved epitopes in the S2 domain of the coronavirus Spike glycoprotein: the central helix (CH) and a membrane-proximal epitope in the heptad repeat 2 (HR2), which we designate the lower stalk (LS).
CH-directed antibodies exhibited broad cross-reactivity across betacoronaviruses, whereas LS-directed antibodies demonstrated reactivity primarily within sarbecoviruses. Using cryogenic electron microscopy (cryo-EM), we determined sub-4 Å structures of three cross-reactive CH antibodies–ch.005, ch.007, and ch.010–bound to the prefusion-stabilized SARS-CoV-2 S2 protein, revealing distinct binding poses and contact residues relative to previously described CH antibodies. In parallel, X-ray crystallography studies yielded a sub-2 Å structure of the ls.019 Fab in complex with the LS peptide, providing, to our knowledge, the first structural visualization of a human monoclonal antibody engaging this epitope.
Together, these findings advance our knowledge of two conserved and structurally vulnerable sites within the coronavirus S2 subunit—the central helix and the lower stalk—that can guide the development of broad-spectrum antibody therapeutics and vaccines against current and emerging coronaviruses.
Howard Hughes Medical Institute
Vaccines and Immunotherapy (VAC)
Adonis A. Rubio, M. Abernathy, Davide F. Robbiani et al.· Journal of Immunology· 0 citations
SARS-CoV-2 evolution has reduced the efficacy of clinical monoclonal antibodies, underscoring the need for therapeutics targeting conserved viral regions. The Spike (S) heptad repeat 2 (HR2) stem helix is highly conserved across SARS-CoV-2 variants and related betacoronaviruses. Although antibodies to this region can neutralize infection, their natural occurrence and evolution remain poorly understood. We previously identified human neutralizing antibodies to a conserved peptide within this region (HR2 coldspot). Here, we show that plasma IgG reactivity to this region remains rare, even after repeated antigen exposure. Longitudinal analysis over 30 months revealed continued somatic hypermutation of HR2-specific antibodies, yet none surpassed the potency or breadth of hr2.016, which emerged shortly after primary infection. Crystal structures of four HR2 stem helix antibodies revealed convergent recognition across distinct antibody lineages. Comparison of hr2.016 with its non-neutralizing clonal relative hr2.086 showed that structural convergence masks distinct binding kinetics. Surface plasmon resonance and molecular dynamics simulations revealed a more stable interaction network for hr2.016, with slower dissociation and prolonged S residence time. Neutralization required the IgG format, supporting an avidity-driven mechanism. Together, these findings define kinetic and avidity constraints governing neutralization at the HR2 stem helix and position hr2.016 as a resilient therapeutic candidate.
Virginia Crivelli, Concetta Guerra, M. Abernathy et al.· bioRxiv· 0 citations
Two human-derived monoclonal antibodies are characterized that recognize conserved epitopes on the SARS-CoV-2 RBD and retain activity across antigenically distinct variants, and conserved, mutationally constrained epitopes may serve as targets for vaccines designed to elicit antibody responses resilient to ongoing SARS-CoV-2 evolution and future sarbecovirus emergence.
M. Abernathy, William B. Foreman, Jasmyn A. Lopez et al.· bioRxiv· 0 citations