The outbreak of COVID-19 caused by SARS-CoV-2 virus has now become a pandemic, but there is currently very little understanding of the antigenicity of the virus.

Source Science

A recent study has shown that CR3022 can also bind to the RBD of SARS-CoV-2 . This finding provides an opportunity to uncover a cross-reactive epitope. Therefore the crystal structure of CR3022 with the SARS-CoV-2 RBD was determined.

The researchers therefore determined the crystal structure of CR3022, a neutralizing antibody previously isolated from a convalescent SARS patient, in complex with the receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein to 3.1 Å.

SARS-CoV-2 uses the same host receptor, angiotensin I converting enzyme 2 (ACE2) as SARS-CoV. Interestingly, the epitope of CR3022 does not overlap with the ACE2- binding site.

Structural alignment of the CR3022- SARS-CoV-2 RBD complex with the ACE2-SARS-CoV-2 RBD complex further indicates that binding of CR3022 would not clash with ACE2.

This analysis implies that the neutralization mechanism of CR3022 for SARS-CoV does not depend on direct blocking of receptor binding, which is consistent with the observation that CR3022 does not compete with ACE2 for binding to the RBD.

Unlike CR3022, most known SARS RBD-targeted antibodies compete with ACE2 for binding to RBD. The epitopes of these antibodies are very different from that of CR3022.

In fact, it has been shown that CR3022 can synergize with other RBD-targeted antibodies to neutralize SARS-CoV. Although CR3022 itself cannot neutralize SARS-CoV-2 in this in vitro assay, whether CR3022 can synergize with other SARSCoV-2 RBD-targeted monoclonal antibodies for neutralization remains to be determined.

CR3022 targets a highly conserved epitope, distal from the receptor-binding site, that enables cross-reactive binding between SARS-CoV-2 and SARS-CoV.

Structural modeling further demonstrates that the binding epitope can only be accessed by CR3022 when at least two RBD on the trimeric S protein are in the “up” conformation and slightly rotated.

The study provides insight into how SARS-CoV-2 can be targeted by the humoral immune response and revealed a conserved, but cryptic epitope shared between SARSCoV-2 and SARS-CoV.

Recently, researchers have identified a conserved epitope on influenza A virus hemagglutinin (HA) that is located in the trimeric interface and is only exposed through protein “breathing”, which is somewhat analogous to the epitope of CR3022.

Antibodies to this influenza HA trimeric interface epitope do not exhibit in vitro neutralization activity but can confer in vivo protection.
Similarly, antibodies to another conserved epitope that partially overlaps with the influenza HA trimeric interface also are non-neutralizing in vitro, but protective in vivo.

Examples of antibodies that do not have in vitro neutralization activity but confer in vivo protection, have also been reported
for influenza virus, herpesvirus, cytomegalovirus, alphavirus and dengue virus.

Therefore, although CR3022 does not neutralize SARS-CoV-2 in vitro, it is possible that this epitope can confer in vivo protection. Further studies will require suitable animal models, which have yet to be established.

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