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dcyphr | Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody

Abstract

Vaccine and therapeutic research is essential to curb the spread of SARS-CoV-2. The SARS-CoV-2 Spike (S) glycoprotein helps viruses enter cells. It is the main target of neutralizing antibodies, which bind to structures on viruses and prevent them from interacting with cells. In this study, the researchers describe multiple monoclonal antibodies, which are made by identical immune cells that are clones of a unique parent cell. These antibodies target SARS-CoV-2 and were identified from memory B cells of an individual who was infected with SARS-CoV in 2003. SARS-CoV is the virus that causes SARS, which had a major outbreak in 2003 and is related to SARS-CoV-2. One antibody found called S309 effectively neutralizes SARS-CoV-2 and SARS-CoV by engaging the S receptor-binding domain. The researchers used cryo-electron microscopy and binding assays to show that S309 recognizes an antigen that is conserved within sarbecoviruses, a family of coronaviruses that includes SARS-CoV and SARS-CoV-2. Combining different antibodies with S309 enhanced SARS-CoV-2 neutralization, and could limit the emergence of resistant mutants. The results suggest that S309 and combinations of other antibodies with S309 could be used to prevent SARS-CoV-2 infection or used after exposure to limit or treat severe COVID-19.

Aims

The researchers wanted to identify neutralizing monoclonal antibodies against the SARS-CoV-2 S protein. They also wanted to test the efficacy of these antibodies in neutralizing SARS-CoV-2 infection.

Introduction

Coronavirus entry into cells is aided by the spike (S) protein. It is comprised of two functional subunits, S1 and S2. S1 is responsible for binding to the cell, while S2 promotes fusion of viral and cellular membranes. SARS-CoV and SARS-CoV-2 share 80% of S protein amino acid sequence. Previous research has shown that human-angiotensin converting enzyme 2 (hACE2) is a receptor for SARS-CoV-2 and SARS-CoV. The S1 subunit binds tightly with hACE2, which could contribute to the current rapid transmission of SARS-CoV.

The S protein has been the main target for neutralizing antibodies and vaccine/therapeutic design efforts. Using monoclonal antibodies (mAb) could provide immediate protection against SARS-CoV-2. mAb therapy has been successful in other infectious disease outbreaks, such as Ebola. Previous research has identified and isolated neutralizing mAbs in people infected with SARS-CoV and MERS-CoV, both of which are related to SARS-CoV-2.

Results

Identification of a potent SARS-CoV-2 neutralizing mAb from a SARS survivor

Previously, the researchers identified a set of SARS-CoV neutralizing mAbs from a SARS survivor. The researchers wanted to determine the potential cross-reactivity of these mAbs against SARS-CoV-2. They found 19 mAbs in a blood draw from the survivor in 2004, and 6 mAbs from a blood draw in 2013. mAbs were evaluated for binding to SARS-CoV-2 and SARS-CoV S domains. The mAbs did not bind to S domains in other coronaviruses (OC43 and MERS), suggesting there is a lack of cross-reactivity of the mAbs outside of sarbecoviruses. mAbs S303, S304, S309, and S315 bound to SARS-CoV-2 and SARS-CoV bound to S domains particularly well. 

To evaluate the neutralization efficacy of the SARS-CoV-2 cross-reactive MAbs, the researchers performed pseudovirus neutralization assays. S309 was the strongest neutralizing antibody, followed by S303, S304, and S315.

Structural basis of S309 cross-neutralization of SARS-CoV-2 and SARS-CoV

The researchers studied the mechanism of S309-mediated neutralization using cryoEM. They found that S309 recognizes an antigen of SARS-CoV SB, a subunit of the S1 protein. They also found that the SB subunit has an open and closed state. Both open and closed states are accessible to the S309 protein.

The structural data from cryoEM explains the cross-reactivity of S309 in both SARS-CoV-2 and SARS-CoV. 17 of 22 residues on the antigen that S309 recognizes are identical between the two viruses. This suggests that S309 could neutralize virtually all SARS-CoV-2 isolates and strains, as well as other sarbecoviruses.

Mechanism of S309-mediated neutralization of SARS-CoV-2 and SARS-CoV

Antibody-dependent cell cytotoxicity (ADCC), is an immune mechanism through which cells can recognize and kill antibody-coated target cells. ADCC can contribute to viral control in infected individuals. The researchers observed efficient S309-mediated ADCC of SARS-CoV-2 infected cells. These results demonstrate that in addition to neutralization, S309 could aid in additional protective mechanisms against SARS-CoV-2. However, this possibility needs to be assessed in clinical trials for antibodies and/or vaccines.

mAb cocktails enhance SARS-CoV-2 neutralization

The researchers also mapped other antibody binding sites on SARS-CoV and SARS-CoV-2 SB domains to see if other sites could be recognized by the mAbs they found. They identified 4 antigens that could be targeted by mAbs. They evaluated the neutralization efficacy of different combinations of mAbs with S309. They found that two antibodies, S315 and S304, enhanced neutralization efficacy when used with S309. This suggests that mAbs could be used in combination to prevent or control SARS-CoV-2.

Discussion

S309 is a mAb with broad neutralizing against sarbecoviruses, including SARS-CoV-2. S309 neutralizes SARS-CoV-2 by recognizing a highly conserved antigen in the SB domain. In addition, S309 can contribute to ADCC and its neutralization efficacy is boosted by other neutralizing antibodies. The results indicate the potential to discover neutralizing mAbs, define antigens to target in vaccine design, and support preparedness for future sarbecovirus outbreaks. S309 may be an effective measure against SARS-CoV-2.