Study reveals how SARS-CoV-2 variants of concern modulate receptor and antibody binding

In a trailblazing engineering effort, Canadian and US researchers indicate that the emergence of novel variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) stems from the mutations of spike glycoprotein that confer either increased affinity for the host cell receptor or increased antibody evasion. The paper is currently available on the bioRxiv* preprint server while it undergoes peer review.

Genomic surveillance efforts that are used to track the global spread of SARS-CoV-2, a causative agent of the ongoing coronavirus disease 2019 (COVID-19) pandemic, pinpointed the emergence and rapid spread of several notable viral variants, also known as variants of concern.

These variants have several mutations primarily in the receptor-binding domain (RBD) of the spike glycoprotein that protrudes from the viral surface and enables viral entry into cells by using its binding receptor on the human cells – angiotensin-converting enzyme 2 (ACE2).

Furthermore, RBD of the spike glycoprotein also represents a prime target of the humoral immune response and the region targeted by a majority of neutralizing antibodies. As a result, vaccines that are currently being used basically exploit this protein as their principal antigenic constituent.

Naturally, a problem with mutations within the RBD of the viral spike protein is that they may confer enhanced viral fitness and increased protein expression. This is the reason why a research group from the University of British Columbia in Canada and the University of Pittsburgh Medical Center in the US aimed to understand specific aspects of RBD mutations on common SARS-CoV-2 variants of concern.

Structural and biochemical experiments

By utilizing eleven SARS-CoV-2 spike glycoproteins with diverse complements of mutations, this research group led by Dr. Dhiraj Mannar and Dr. James W. Saville systematically appraised the contributions of major known variants of concern towards increasing ACE2 affinity and evading neutralizing antibodies.

This was primarily done with the use of cryogenic electron microscopy structural analysis; however, the researchers have also developed novel and hitherto unreported mutation combinations to explore the properties of variants that may possibly emerge in the future.

More specifically, spike proteins were engineered to express these RBD variant of concern mutations either as isolated traits or in different combinations. Subsequently, structural analysis with cryogenic electron microscopy in combination with biochemical assays has been used to analyze the effects.

ACE2 affinity and antibody binding effects

In short, their results have shown that individual SARS-CoV-2 RBD mutations may be categorized as resulting in either increased affinity for the ACE2 receptor alone, reduced ACE2 affinity and reduced antibody binding or a concurrent increase in ACE2 affinity and reduced antibody binding. However, these mutations can be combined with preserved individual effects.

It has to be noted that the majority of developed human-derived neutralizing antibodies can bind the RBD with footprints that span at least one of the positions corresponding to RBD mutation in variants of concern, which will be an important consideration in developing future treatment modalities.

The study has also shown that novel combinations of RBD mutations are able to retain antibody evasive properties when tested for antibody binding with a panel of monoclonal antibodies.

Elucidating evolutionary trajectory

“Overall, our findings suggest that the emergence of new SARS-CoV-2 variant spikes can be rationalized as the result of mutations that confer either increased ACE2 affinity, increased antibody evasion, or both, providing a framework to dissect the molecular factors that drive variant of concern evolution”, emphasize study authors in this bioRxiv paper.

Although we have focused the present study on RBD mutations present within variants of concern, it is possible that mutations elsewhere in the spike glycoprotein (particularly in the N-terminal domain) also play a significant role in antibody evasion and may affect ACE2 binding”, they caution.

With only several small exceptions, these results that describe the effects on ACE2 binding and antibody evasion as a result of RBD mutations in the tested SARS-CoV-2 variants of concern are highly in agreement with other recently published scientific reports.

Moreover, the study implies that RBD evolution basically follows a trajectory aimed towards a concomitant increase of receptor affinity and reduction of neutralizing antibody binding. Future studies will be needed to further elucidate these pertinent aspects of SARS-CoV-2 infection.

*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.

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