Identification of specific anti-SARS-CoV-2 antibodies with cross-neutralization potency

A team of scientists from the USA and Canada recently characterized the cross-neutralizing potency of anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies isolated from coronavirus disease 2019 (COVID-19) patients. The findings reveal that some of the isolated antibodies targeting the spike receptor-binding domain (RBD) and the S2 subunit are capable of cross-neutralizing other members of the human beta-coronavirus family. The study is currently available on the bioRxiv* preprint server.

Background

SARS-CoV-2, the causative pathogen of COVID-19, is an enveloped, positive-sense, single-stranded RNA virus of the Coronaviridae family. The viruses belonging to the Coronaviridae family are capable of zoonotic transmission as observed in the current COVID-19 pandemic, as well as in previous outbreaks of SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV).

Given the 54% sequence similarity between different coronavirus strains, many studies have been conducted to investigate the cross-reactive potency of anti-SARS-CoV-2 antibodies. In this context, it has been observed that only a small fraction of antibodies isolated from SARS-CoV-2 infected patients are capable of cross-neutralizing SARS-CoV, MERS-CoV, or other beta (OC43 and HKU1) and alpha (229E and NL63) coronaviruses.

In the current study, the scientists have isolated and characterized a total of 198 monoclonal antibodies targeting SARS-CoV-2 spike protein. Specifically, they have explored the cross-neutralizing potency of these antibodies against different strains of coronaviruses.  

For antibody isolation, serum samples and peripheral blood mononuclear cells have been collected from four COVID-19 positive patients 3 to 7 weeks after the symptom onset.

Important observations

The analysis of serum samples using Enzyme-linked Immunosorbent assay (ELISA) revealed that all enrolled patients developed significant levels of anti-RBD bindings and neutralizing antibodies in response to SARS-CoV-2 infection. The highest virus neutralization potency was observed in samples collected at later timepoints.

By conducting a series of experiments using patient-obtained spike+ and RBD+ B cells (IgG+), the scientists finally isolated 198 anti-SARS-CoV-2 monoclonal antibodies. Moreover, they isolated 59 monoclonal antibodies from healthy individuals as experimental controls. By comparing relative frequencies of each heavy and light chain variable region sequence of patients and healthy controls, they observed that naïve B cell clones preferentially recognized the viral spike protein at the initial stages of infection. In contrast, the anti-spike B cell response predominated 3 – 7 weeks after the symptom onset. Moreover, they noticed that the sequences of heavy and light chain variable regions derived from later-timepoint samples harbored higher amino acid mutations than early-timepoint samples. This indicates that the evolution of B cells occurs continuously during SARS-CoV-2 infection.

Cross-reactive potency of anti-SARS-CoV-2 antibodies

Using various recombinant proteins, including spike S1 and S2 subunits, RBD, and N-terminal domain (NTD), the scientists observed that only a small fraction of isolated monoclonal antibodies recognized and bound the RBD. While exploring the cross-reactivity against SARS-CoV, MERS-CoV, OC43 and HKU1 beta-coronaviruses, and NL63 and 229E alpha-coronaviruses, they noticed that 81 out of 198 monoclonal antibodies bound various subdomains of SARS-CoV spike protein, with RBD being the highly recognized region. In contrast, a significantly lower cross-reactivity was observed against other coronaviruses.

Cross-neutralizing potency of anti-SARS-CoV-2 antibodies

Of 198 monoclonal antibodies, only 14 showed SARS-CoV-2 neutralization potency; of which, one targeted the NTD, one targeted the S2 subunit, and 12 targeted the RBD. Regarding cross-neutralization, only 4 out of 14 antibodies were found to effectively neutralize SARS-CoV. Of all cross-neutralizing antibodies, three were specific to the RBD, and one was specific to the S2 subunit. Importantly, all cross-neutralizing antibodies were found to effectively neutralize the South African variant of SARS-CoV-2 (lineage: B.1.351).  

The mechanistic analysis conducted in the study revealed that the most potent anti-RBD antibodies neutralized SARS-CoV-2 by blocking the angiotensin-converting enzyme 2 (ACE2)-RBD interaction. Moreover, there was an association between the degree of ACE2-RBD binding inhibition and the robustness of neutralization. A similar mechanism was observed for SARS-CoV neutralization.

Interestingly, the analysis revealed that the two most potent anti-SARS-CoV-2 neutralizing antibodies failed to neutralize SARS-CoV. This could be because these two antibodies interacted with the receptor-binding motif in the RBD, which is structurally not similar to that of SARS-CoV RBD.

To explore the infection preventing abilities of neutralizing antibodies, the scientists initially immunized the mice with a panel of neutralizing antibodies with different epitope specificities, followed by experimental infection with SARS-CoV-2. By analyzing the viral RNA in lung samples two days post-infection, they observed that only antibodies with high neutralization efficiency could provide protection against infection.

Study significance

The study reveals that the expansion of B cell populations expressing particular pairs of variable domains is not a prerequisite for generating SARS-CoV-2 and SARS-CoV cross-neutralizing antibodies. The study also identifies one epitope in the spike S2 subunit that is specific to at least four human beta-coronaviruses. Monoclonal antibodies targeting this S2 epitope have cross-neutralization potency.  

*Important Notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:
Dr. Sanchari Sinha Dutta

Written by

Dr. Sanchari Sinha Dutta

Dr. Sanchari Sinha Dutta is a science communicator who believes in spreading the power of science in every corner of the world. She has a Bachelor of Science (B.Sc.) degree and a Master's of Science (M.Sc.) in biology and human physiology. Following her Master's degree, Sanchari went on to study a Ph.D. in human physiology. She has authored more than 10 original research articles, all of which have been published in world renowned international journals.

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