New insight into impact of SARS-CoV-2 mutations on receptor binding

By Dr. Tomislav Meštrović, MD, Ph.D.Aug 9 2021

A recent study by Canadian researchers, currently available on the bioRxiv* preprint server, contributes to the growing body of literature on emerging variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by appraising the impact of single mutations on their overall antigenicity and binding affinity for the angiotensin-converting enzyme 2 (ACE2) receptor.

Study: Contribution of single mutations to selected SARS-CoV-2 emerging variants Spike antigenicity. Image Credit: Design_Cells

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources

The replication cycle of SARS-CoV-2, a causative agent of the ongoing coronavirus disease 2019 (COVID-19) pandemic, starts with the virus attaching to the target cell by using ACE2 receptor before fusion between viral and cellular membranes takes place. This is mediated by the spike glycoprotein present on the surface of viral particles.

The latter structure represents a major target of the cellular and humoral responses prompted by natural infection. It is then of no wonder that the antigen utilized in currently approved vaccines is actually the stabilized form of the SARS-CoV-2 spike glycoprotein.

However, this structure is under high selective pressure to break away from host immune response, improve affinity for the ACE2 receptor, evade antibody recognition and increase transmissibility. As a result, mutations in the viral genetic code that provide a fitness increase are rapidly selected in most emerging variants.

For example, the N501Y substitution initially seen in the B.1.1.7 (UK) lineage can improve binding of SARS-CoV-2 to the ACE2 receptor; this mutation is now also observed in B.1.351, P.1, and P.3 lineages. On the other hand, certain mutations can improve immune evasion from antibodies.

Consequently, a recent study first-authored by Dr. Shang Yu Gong from McGill University in Montreal (Canada) described binding and neutralization experiments with plasma from vaccinated and naturally infected individuals and provided a meticulous analysis of the spike glycoprotein antigenicity from selected SARS-CoV-2 variants of concern.

Different ways to assess ACE2 binding

In this paper, human embryonic kidney (HEK) 293 cell line was used to explore SARS-CoV-2 full spike glycoprotein harboring single or combined mutations from emerging variants. In addition, a specific type of conformationally independent monoclonal antibody has been used to normalize the expression of spike glycoprotein.

Furthermore, the researchers have determined the contribution of individual mutations on ACE2 binding in order to discern the ones contributing to the increased receptor affinity of emerging variants. For that purpose, plasma from vaccinated and previously infected pre- and post-first-dose vaccination donors has been collected.

Biolayer interferometry was utilized to measure the binding kinetics of selected mutants to soluble ACE2 after biosensors were coated with recombinant receptor-binding domain (RBD) of spike glycoprotein and exposed to increasing concentrations of soluble ACE2.

Cells expressing spike glycoprotein were incubated at either 4 ºC or 37 ºC, while their binding with antibodies has been measured by flow cytometry. Finally, the neutralization profile of different emerging variants has been obtained with the use of a pseudoviral neutralization assay.

Robust vaccine protection

The researchers have observed that spike glycoprotein from a sundry of different SARS-CoV-2 variants (B.1.1.7, B.1.351, P.1, B.1.429, B.1.526, B.1.617 and B.1.617.2) showed increased ACE2 interaction; this includes a rise in ACE2 binding at cold temperatures (i.e., 4 ºC).

However, an interesting observation was that spike glycoproteins from tested emerging variants bind better to ACE2 at 37°C when compared to the D614G variant present in earlier variants, which contains a point mutation that gives rise to a substitution outside of the RBD.

The study has also demonstrated that plasma from vaccinated individuals (previously infected and non-infected) with SARS-CoV-2) efficiently recognized spike glycoproteins from emerging variants. Still, as demonstrated previously, plasma from vaccinated individuals previously infected showed a higher and much more robust recognition of all tested spike glycoproteins.

Keeping track of emerging variants

In short, this study offers a comparative view appraising ACE2 binding properties of selected SARS-CoV-2 circulating variants and also shows what impact single mutations have on plasma binding. This is important, as antigenic drift has been and remains a big concern of the ongoing COVID-19 pandemic.

“Altogether, our results highlight the difficulty in predicting the phenotype of an emerging variant’s spike, either related to ACE2 interaction, antigenic profile, infectivity and transmission based on the sum of the phenotype of single mutants making that particular spike”, further elaborate study authors in this bioRxiv paper.

Therefore, close monitoring of the functional properties characteristic for emerging variants remains one of the key aspects of vaccine design and implementing adequate preventive interventions that will control the spread of the highly transmissible virus.

This news article was a review of a preliminary scientific report that had not undergone peer-review at the time of publication. Since its initial publication, the scientific report has now been peer reviewed and accepted for publication in a Scientific Journal. Links to the preliminary and peer-reviewed reports are available in the Sources section at the bottom of this article. View Sources