Discovering a Highly Conserved S2 Epitope in SARS-CoV-2 Spike Proteins

What is it about?

This study presents a novel, highly conserved SARS-CoV-2 Spike (S) epitope recognized by antibody RAY53. The S2 domain epitope is located in the flexible hinge, and the antibody mediates antibody-dependent cellular phagocytosis and cytotoxicity against SARS-CoV-2 spike in vitro. The antibody's effectiveness against the virus is compromised by hinge epitope mutations, and certain changes in the spike opening dynamics, such as those found in Omicron BA.1, occlude the epitope and may evade preexisting serum antibodies targeting the S2 core. This work defines a third class of S2 antibodies and provides insights into the potency and limitations of S2 core epitope targeting. The study involves immunizing mice with a stabilized MERS-CoV S2 protein and boosting them with SARS-CoV-2 spike, resulting in robust serum antibody titers against the immunogen. After characterizing >80 clones binding both MERS S2 and SARS-2 spike, the most promising spike-binding clone, 3A3, and the control antibody, 3E11, were carried forward for further analysis. The study uses hydrogen-deuterium exchange mass spectrometry (HDX) and low-resolution cryo-EM to determine that antibody 3A3 binds the S2 core at the hairpin hinge, a region critical for the spike's conformational changes required for fusion of the viral envelope and target cell membrane. The hinge epitope is distinct from the previously described S2 stem and fusion peptide epitopes, providing a third class of S2 antibodies. In vitro studies reveal that antibody RAY53 binds the native hinge in MERS-CoV and SARS-CoV-2 spikes on the surface of mammalian cells and mediates antibody-dependent cellular phagocytosis and cytotoxicity against SARS-CoV-2 spike. Hinge epitope mutations that ablate antibody binding compromise pseudovirus infectivity, but changes elsewhere that affect spike opening dynamics, including those found in Omicron BA.1, occlude the epitope and may evade preexisting serum antibodies targeting the S2 core.

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Why is it important?

This research presents valuable findings on the isolation of an antibody, RAY53, which recognizes a novel, highly conserved SARS-CoV-2 Spike (S) epitope. The study provides evidence for the existence of a third class of S2 antibodies, adding to the growing repertoire of anti-S antibodies cross-reactive against human and zoonotic coronaviruses. The authors provide solid evidence supporting their claims, although the proposed antiviral mechanism of the newly described antibody requires further validation, and in vivo effectiveness remains to be determined. Key Takeaways: 1. Researchers have identified a highly conserved SARS-CoV-2 Spike (S) epitope, providing insights into the potency and limitations of S2 core epitope targeting. 2. The study adds a third class of S2 antibodies to the growing repertoire of anti-S antibodies cross-reactive against human and zoonotic coronaviruses. 3. The newly described antibody, RAY53, binds a conformational epitope at the hairpin hinge of the SARS-CoV-2 spike, offering a promising target for antiviral development, although further validation and in vivo effectiveness assessment are needed.