Defining the Antigenic Topology and Prospective Binding Breadth of Vaccination-induced SARS-CoV-2 Neutralizing Antibodies

Abstract Antibodies that neutralize SARS-CoV-2 primarily target the viral spike glycoprotein, yet the breadth of these responses is continually challenged by viral evolution. While extensive structural studies have defined epitopes across the spike protein, how antibodies elicited by the initial mRNA vaccination campaigns perform against subsequently emerging variants remains an important question. Here, we structurally and functionally characterize a panel of early plasmablast-derived human monoclonal antibodies isolated following primary mRNA vaccination, targeting both the receptor-binding domain (RBD) and the N-terminal domain (NTD) of spike. Using cryo–electron microscopy, variant-binding analyses, and viral-fusion inhibition assays, we observe that antibodies directed against immunodominant regions of the RBD and NTD are highly potent but more frequently impacted by variant-associated mutations. In contrast, antibodies engaging a conserved hydrophobic pocket within the NTD exhibit broader reactivity and neutralize through distinct molecular mechanisms. Together, these findings extend prior structural studies of spike-directed antibodies by prospectively assessing the breadth of vaccine-elicited antibodies against later variants and identifying structural features associated with differential escape sensitivity. These results contribute to a growing understanding of how early vaccine-induced antibody repertoires relate to subsequent viral evolution. One sentence summary Antibody epitopes on SARS-CoV-2 spike determine prospective breadth and vulnerability to viral evolution. Competing Interest Statement The Icahn School of Medicine at Mount Sinai has filed patent applications relating to SARS-CoV-2 serological assays, NDV-based SARS-CoV-2 vaccines influenza virus vaccines and influenza virus therapeutics which list FK as co-inventor, and FK has received royalty payments from some of these patents. Mount Sinai has spun out a company, Castlevax, to develop SARS-CoV-2 vaccines. FK is co-founder and scientific advisory board member of Castlevax. FK has consulted for Merck, GSK, Sanofi, Gritstone, Curevac, Seqirus and Pfizer and is currently consulting for 3rd Rock Ventures and Avimex. The Krammer laboratory is also collaborating with Dynavax on influenza vaccine development. The Ellebedy Lab and Infectious Disease Clinical Research Unit received funding from Moderna related to the data presented in the current study. The Ellebedy Lab received funding from Emergent BioSolutions and AbbVie that is unrelated to the data presented in the current study. A.H.E. has received consulting and speaking fees from InBios International, Fimbrion Therapeutics, RGAX, Mubadala Investment Company, Moderna, Pfizer, GSK, Danaher, Third Rock Ventures, Goldman Sachs, and Morgan Stanley and is the founder of ImmuneBio Consulting.