A short report recently published in the Journal of Infectious Diseases demonstrates how spike mutations L452R and E484Q found in the variant B.1.617.1 of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) each confer modestly diminished sensitivity to Pfizer-BioNTech (BNT162b2) mRNA vaccine-elicited antibodies – with combined mutations having a similar impact as either one of them alone.
Full global control of the coronavirus disease (COVID-19) pandemic has yet to be achieved, despite the fact that highly effective vaccines against its causative agent, SARS-CoV-2, are now at our disposal. This is partly due to the emergence of new viral variants with antibody escape mutations.
Potential sources of such variants that harbor multiple mutations are chronically infected individuals who are also immune-compromised, which opens the door for their selection. Moreover, their appearance has coincided with the vaccine scale-up, endangering our success in curbing this pandemic.
One of such variants is B.1.617 that has emerged in the state of Maharashtra in the late 2020 and early 2021, subsequently spreading throughout India and to at least sixty other countries. Initially, it was labeled as a ‘double mutant’ due to the presence of both L452R and E484Q mutations.
The mutations mentioned above are found in the critical receptor-binding domain that interacts with the host cell receptor, angiotensin-converting enzyme 2 (ACE2). Furthermore, L452Rt is also associated with improved ACE2 binding, increased infectivity, and 3-6 fold drop in neutralization sensitivity after vaccination. Conversely, much less is known E484Q mutation, albeit this one is found in different variants of concern.
In this short scientific report, researchers from the Ravi Gupta group at the Cambridge Institute of Therapeutic Immunology & Infectious Disease and the Department of Medicine at the University of Cambridge (United Kingdom) aimed to appraise the exact potential of L452 and E484Q to act synergistically in the antibody evasion process.
Full use of cell cultures
First, the researchers pursued phylogenetic and structural analyses and prepared cell cultures used in this study: HEK 293T CRL-3216 (derived from a primary embryonic human kidney), Vero CCL-81 (derived from an African green monkey kidney) and HOS cells (derived from human osteosarcoma).
Then, they appraised the neutralization sensitivity of mutational combinations found in B.1.617.1 (L452R, E484Q, and P681R) using a previously reported and adequately prepared pseudotyped virus (PV) system.
Finally, with the PV system, this research group has evaluated spike-mediated entry into target HOS cells expressing ACE2 and transmembrane serine protease 2 (TMPRSS2) receptors. They have also tested the entry efficiency of the aforementioned three mutations in a wide array of target cell lines exogenously or endogenously expressing ACE2/TMPRSS2 SARS-CoV-2 receptors.
The lack of synergism between mutations
In short, this study has found modestly diminished sensitivity of the SARS-CoV-2 spike glycoprotein with RBD mutations L452R and E484Q to Pfizer–BioNTech mRNA vaccine-elicited antibodies; more specifically, this loss of sensitivity was similar in magnitude when compared to the loss conferred by either L452R or E484Q alone.
However, it has to be noted that in some sera they have found evidence for variable neutralizing activity against the L452R and E484Q PVs, which was expected as it basically reflects differential antibody responses between various individuals.
Furthermore, L452R and E484K mutant did not exhibit significantly higher entry efficiency in comparison to single mutants, while the spike triple mutant showed similar or mildly reduced entry in comparison to Wuhan-1 D614G spike glycoprotein. Also, P681R mutation did not appear to alter entry efficiency or the sensitivity to vaccine sera.
Implications for further practice
Since the emergence of the B.1.617 SARS-CoV-2 (Delta) variant in late 2020, there have been great fears that two key mutations present in the receptor-binding domain (i.e., L452R and E484Q) would have additive and compounding effects on successfully evading neutralizing antibodies.
“These data demonstrate reduced sensitivity to vaccine-elicited neutralizing antibodies by the RBD bearing L452R and E484Q but lack of synergistic loss of sensitivity”, concludes study authors in this paper.
However, although this study has shown that combined mutations have a similar impact as either of them alone, it does not mean that this will be the case for other emerging mutations. Therefore, this must be taken into consideration in our future vaccine planning efforts.