Do viruses have heads, shoulders, knees, and toes?

From the Stamatatos, Pancera and McGuire labs, Vaccine and Infectious Disease Division

While coronaviruses do not have heads, shoulders, knees, and toes, they do employ dynamic movement, similar to how a knee joint bends, to gain access to host cells. The Stamatatos, Pancera and McGuire labs from the Fred Hutchinson Cancer Center Vaccine and Infectious Disease Division mapped the interaction domain of a broadly neutralizing antibody to the “knee joint” of the spike protein, a viral protein essential for entry into host cells. This research was published recently in Communications Biology.

The spike protein on the outside of the coronavirus particle is essential for infection of host cells but is exposed for detection by our adaptive immune system and for this reason, among others, is the target for all the COVID-19 vaccines. One arm of the adaptive immune response relies on antibodies which are produced by B cells and can mediate neutralization of viruses by binding to specific epitopes, or parts of a protein, to block entry of the virus into cells. Whether these neutralizing antibodies are produced by your body following a previous infection or vaccination or separately introduced as a therapeutic, they can reduce disease severity following infection. To date, there are six known neutralizing antibodies that bind to the spike protein at the stem-helix region or “knee joint”: B6, 1.6C7,28D9, IgG22, CC40.8, S2P6, and CV3-25. Several of these antibodies interact with the hydrophobic, exposed surface of the stem-helix but CV3-25 interacts with the opposite, buried hydrophilic surface of the amphipathic, containing both hydrophilic and hydrophobic surfaces, “knee joint”. The “CV3-25 [antibody] is interesting because it binds a site of the SARS-CoV-2 spike protein that so far is not mutated in variants,” said Dr. Nick Hurlburt, a co-first author of the study and postdoctoral fellow in the Pancera lab. This is a critical finding, as this epitope is highly conserved across coronaviruses and may represent a targetable vulnerability.

The CV3-25 antibody can neutralize SARS-CoV-1, several SARS-CoV-2 variants, and a distant bat sarbecovirus WIV1 by binding to the spike stem-helix “knee joint” and restricting entry of the virus into host cells.
The CV3-25 antibody can neutralize SARS-CoV-1, several SARS-CoV-2 variants, and a distant bat sarbecovirus WIV1 by binding to the spike stem-helix “knee joint” and restricting entry of the virus into host cells. Image provided by Dr. Hurlburt

To follow-up on this idea of a pan-coronavirus or multi-coronavirus neutralizing antibody, the researchers tested how well CV3-25 neutralized several SARS-CoVs and a more distant sarbecovirus from bats. This assay was conducted using pseudoviruses that have a shared virus backbone with different, virus specific spike proteins decorating the outside of the non-coronavirus particle. Intriguingly, the CV3-25 antibody was “able to neutralize pseudoviruses for all of the [SARS-CoV-2] variants of concern, as well as SARS-CoV-1 and a SARS-like bat CoV, WIV1,” stated Dr. Hurlburt. A key feature of these tested viruses is that they all use the angiotensin converting enzyme 2 (ACE2) receptor to gain access to cells. When coronaviruses bind to a receptor on the surface of the cell, conformational changes in the spike protein on the virus particle enable cell entry. Therefore, coronaviruses that use different receptors to enter cells may differ in conformation or structure of the spike protein during entry, altering exposed epitopes for antibody binding. For this reason, the researchers tested the ability of CV3-25 to bind the conserved spike epitopes and neutralize coronaviruses that utilize different receptors for host cell entry. Although CV3-25 could bind linear, conserved peptides of various spike proteins including those of human coronavirus (HCoV) OC43 and MERS-CoV, this antibody could not neutralize pseudoviruses with OC43 and MERS-CoV spike proteins. These data suggest that, while this epitope is highly conserved across coronaviruses, the dynamic movement and structure of the spike “knee joint” may differ depending on the receptor used for entry into the host cell. These findings illustrate another layer of virus evasion of the host immune system. Specifically, by varying the receptor used to gain access to cells, coronaviruses can maintain high conservation of the spike “knee joint” sequence while using dynamic structural changes to restrict neutralization by an antibody that recognizes this conserved epitope. Together, the collaborating labs mapped the binding site of CV3-25 to a highly conserved region on the spike protein and characterized antibody-mediated neutralization of various spike proteins by CV3-25. This work identified previously unknown vulnerabilities of the spike “knee joint” that may prove useful in the future design of a pan-coronavirus vaccine.

The spotlighted research was supported by donations to the Fred Hutch COVID-19 Research Fund, Fast Grants, a Fred Hutch COVID pilot award, the M.J. Murdock Charitable Trust, and the Bill and Melinda Gates Foundation.

UW/Fred Hutch Cancer Consortium member Andrew McGuire contributed to this work.

Hurlburt NK, Homad LJ, Sinha I, Jennewein MF, MacCamy AJ, Wan YH, Boonyaratanakornkit J, Sholukh AM, Jackson AM, Zhou P, Burton DR, Andrabi R, Ozorowski G, Ward AB, Stamatatos L, Pancera M, McGuire AT. 2022. Structural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit. Commun Biol. 5(1):342.