Researchers in the United States have described a novel rapid method for identifying antibody-resistant mutants in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
SARS-CoV-2 is the underlying causative agent of the coronavirus disease 2019 (COVID-19) global pandemic, first identified in Wuhan, China, in December 2019. Since then, multiple variants of the virus have arisen with certain mutations allowing them to be more transmissible, or to escape neutralization from antibodies.
These escape mutations are of primary concern, as antibody-resistant viral strains may drastically reduce the efficacy of current vaccine and antibody therapies.
Now, a team of scientists at the University of Colorado and other institutions report a yeast screening method that can be used to rapidly identify escape mutants for neutralizing antibodies (nAbs).
We identified escape mutants for five nAbs, including three from the public germline class VHC-53 elicited by natural COVID-19 infection,” say the authors. “We provide libraries, methods, and software as an openly available community resource to accelerate new therapeutic strategies against SARS-CoV-2.”
A pre-print version of the research paper is available to read in full on the bioRxiv*server.
What did the researchers do?
Understanding the roles and functions of SARS-CoV-2 mutations will play a huge role in the development of sufficient vaccines, boosters, and antibody therapies. The sole viral membrane protein responsible for cell entry is the spike (S) protein, which binds to hosts through the receptor-binding domain (RBD). The researchers wished to develop a functional screening assay that would be able to identify nAb escape mutants at a large scale.
An S RBD yeast surface display (YSD) platform was created and tested to measure and predict RBD escapability. Through testing with a panel of eleven anti-S RDB antibodies, they were able to conclude that (with the exception of the S309 epitope), the yeast platform was able to “faithfully” emulate the binding interactions of neutralizing antibodies with S RBD.
The researchers then attempted to identify S RBD escape mutants, using five nAbs that were able to block ACE2 binding from SARS-CoV-2. They identified 97 S RBD mutantations in SARS-CoV-2 pseudoviruses that could escape recognition by at least one neutralizing antibody. Principally, the mutations F486I, E484K, T478R, K417N, K417T and D420K were able to completely escape neutralization from common antibodies and concurred with previous studies confirming that the N501Y mutation – present in many variants of concern – had no role in providing antibody resistance, likely instead increasing binding affinity for ACE2.
These findings were conferred using biological replicates from a public library of SARS-CoV-2 variants, confirming that escape mutants had lower rates of resistance to antibodies than other variants.
What does this mean?
The authors report some major advantages of the yeast-based screening method. Namely, that the method can precisely mimic viral infection and antibody binding, but additionally provides a safe working environment, with relatively fast identification of escape mutants, as well as a “robust and rigorous” identification algorithm of these mutants.
The team presents this new yeast screening method as an openly available community resource for scientists to aid in accelerating the development of therapeutic strategies against SARS-CoV-2, and as a new tool in identifying specific nAb-resistant mutations.
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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