Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), since its emergence, has continuously evolved to evade host hostilities as well as increase transmission by raising new variants of concerns (VOCs). Virus host adaptation is evident by the rise of VOCs (beta, beta, gamma, and delta variants) that impede the neutralization effect of antibodies. Recently (Nov. 24th, 2021), a novel strain of SARS-CoV-2 named Omicron emerged in South Africa and quickly spread worldwide.
Currently, scientists are trying to understand how Omicron is spread, and whether current therapeutics will still be effective against it. Researchers studied the binding strength of Omicron with ACE2 and seven monoclonal antibodies either approved by the FDA or undergoing phase III clinical trials, in a study published on the bioRxiv* preprint server.
The Omicron Variant
The Omicron variant has many novel mutations in both structural and non-structural proteins. For example, scientists have observed more than 32 mutations in the Spike protein alone, with 15 of these residing in the receptor-binding domain (RBD). Such a large number of mutations have raised concerns over increased transmissibility, immune escape, and vaccine failure.
The non-structural proteins encoded by the ORF1ab contain mutations in the nsp3, nsp4, nsp5, nsp6, nsp12, and nsp14. In addition, Omicron harbors mutations in the other structural proteins, including Envelope (E), Membrane (M), and Nucleocapsid (N). Since N is highly immunogenic, these mutations could help escape the host immune response. About half of the mutations possess the potential to dampen the potency of therapeutic and enhance ACE2 binding. A significant cause for concern is that this variant can infect vaccinated people, as has been demonstrated by vaccinated people in South Africa and Hong Kong being affected.
A New Study
By conducting molecular modeling and mutational analyses, scientists sought to understand how the Omicron variant enhanced its transmissibility and whether it can escape the FDA-approved Spike-neutralizing COVID-19 therapeutic antibodies.
The researchers selected seven therapeutic antibodies, including Etesevimab, Bamlanivimab, AZD8895, AZD1061, Imdevimab, Casirivimab, and CT-p59.
The spike-ACE2 interaction: Researchers observed three deletion sites in the N-terminus domains (NTD) and at least 15 substitutions in the RBD region in the Omicron variant. The Spike also harbors mutations, such as K417, T478, E484, and N501, which have been reported in previous VOCs.
An important observation was that at least 11 (out of the 15) mutated residues could influence ACE2 binding and significantly affect the binding affinity.
The Omicron spike (compared to the prototype SARS-CoV-2) had three deletions, i.e., Δ69-70, Δ143-145, and Δ211, and one highly charged insertion at 214 positions in the Spike, i.e., ins214EPE.
In order to monitor the relative binding strength of RBD-ACE2 complexes of both the prototype Wuhan and Omicron strains, scientists used a protein design strategy and calculated binding affinity and stability changes.
Individually substituted residues were seen to have a slight effect on the local stability of the RBD-ACE2 complexes. However, a large increase in the binding affinity by T478K, Q493K, and Q498R led to an overall increase in the binding affinity of the RBDOmic with ACE2.
Researchers studied the change in electrostatic potential of the RBDOmic relative to that of RBDWT. The electrostatic energy of ACE2-RBDOmic was found to be double that of ACE2-RBDWT. The energy distribution suggested that mutations in the RBDOmic directly enhance the binding strength of amino acids in the same network. Overall, the data showed that Omicron binds to ACE2 with greater affinity, partly explaining its increased transmissibility. However, the pathogenicity of the new strain could not be predicted.
Binding of therapeutic antibodies: Scientists constructed structural models of seven mAbs bound to RBDOmic and showed a substantial drop in the total binding energies of Bamlanivimab and CT-p59. Except for AZD1061 (AstraZeneca), all other mAbs showed a significant drop.
Changes in energies were calculated for CT-p59 and Bamlanivimab to gain a better understanding of the mutations involved in weakening the RBDOmic -mAbs interactions.
It was observed that R96 and R50 of the Bamlanivimab, which establish highly stable salt bridges with the E484 of RBDWT, completely lost their binding upon E484A mutation. E102 and R104 in CDRH3 also showed a 50% reduction in binding energies. E484A, Q493K, and Y505H mutations in RBDOmic were responsible for the lowering of the bindings.
Overall, these data raise grave concerns about the efficacy of therapeutic mAbs in Omicron patients.
The Omicron variant has been proven to be more transmissible than the Delta variation, and the threat is now global. Therefore, there is an urgent need to closely monitor the COVID-19 variant and accelerate vaccination, as this could reduce COVID-19 infections dramatically. Additionally, the search for more effective therapeutics must continue.
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.