Paired heavy and light chain signatures contribute to potent SARS-CoV-2 neutralization in public antibody responses

Banach, Bailey B.; Cerutti, Gabriele; Fahad, Ahmed S.; Shen, Chen-Hsiang; de Souza, Matheus Oliveira; Katsamba, Phinikoula S.; Tsybovsky, Yaroslav; Wang, Pengfei; Nair, Manoj S.; Huang, Yaoxing; Urdániz, Irene M. Francino; Steiner, Paul J.; Gutiérrez-González, Matias; Liu, Lihong; López Acevedo, Sheila N.; Nazzari, Alexandra; Wolfe, Jacy R.; Luo, Yang; Olia, Adam S.; Teng, I-Ting; Yu, Jian; Zhou, Tongqing; Reddem, Eswar R.; Bimela, Jude; Pan, Xiaoli; Madan, Bharat; Laflin, Amy D.; Nimrania, Rajani; Yuen, Kwon-Tung; Whitehead, Timothy A.; Ho, David D.; Kwong, Peter D.; Shapiro, Lawrence; DeKosky, Brandon J.

Understanding protective mechanisms of antibody recognition can inform vaccine and therapeutic strategies against SARS-CoV-2. We discovered a new antibody, 910-30, that targets the SARS-CoV-2 ACE2 receptor binding site as a member of a public antibody response encoded by IGHV3-53/IGHV3-66 genes. We performed sequence and structural analyses to explore how antibody features correlate with SARS-CoV-2 neutralization. Cryo-EM structures of 910-30 bound to the SARS-CoV-2 spike trimer revealed its binding interactions and ability to disassemble spike. Despite heavy chain sequence similarity, biophysical analyses of IGHV3-53/3-66 antibodies highlighted the importance of native heavy:light pairings for ACE2 binding competition and for SARS-CoV-2 neutralization. We defined paired heavy:light sequence signatures and determined antibody precursor prevalence to be ~1 in 44,000 human B cells, consistent with public antibody identification in several convalescent COVID-19 patients. These data reveal key structural and functional neutralization features in the IGHV3-53/3-66 public antibody class to accelerate antibody-based medical interventions against SARS-CoV-2. Highlights A molecular study of IGHV3-53/3-66 public antibody responses reveals critical heavy and light chain features for potent neutralization Cryo-EM analyses detail the structure of a novel public antibody class member, antibody 910-30, in complex with SARS-CoV-2 spike trimer Cryo-EM data reveal that 910-30 can both bind assembled trimer and can disassemble the SARS-CoV-2 spike Sequence-structure-function signatures defined for IGHV3-53/3-66 class antibodies including both heavy and light chains IGHV3-53/3-66 class precursors have a prevalence of 1:44,000 B cells in healthy human antibody repertoires