In the past few months we have seen a lot of papers reporting antibodies that they found to bind to SARS-CoV-2 (a database can be found here: http://opig.stats.ox.ac.uk/webapps/covabdab/). Some of them were from the analysis of a patient’s immune system. Some of them come with crystal structures to show where they bind. Some don’t have structures, but they have the sequences and some competition assay data to show approximately where on the spike protein they bind. The main focus is around an area called the Receptor Binding Domain (RBD) which is where the spike protein engages the human ACE2 receptor and causes the downstream problems. In this paper, the authors ran a complete mutagenesis on the RBD of the SARS-CoV-2 spike protein.
On a high level, the authors mutated specific locations of the RBD and evaluated the binding efficiency of 10 of the reported SARS-CoV-2 binders. They used a traditional yeast system to express all the mutants. The misfolded proteins were sorted by FACS, and only the correctly folded ones were retained. They then compared 10 anti-SARS-CoV-2 antibodies, and found the antibody sequences that were enriched in each of the antigen mutants. With this information, they constructed a matrix of each of the mutants and whether this mutation “fooled” the antibody and reduced its neutralisation strength – the antigen escape pattern.
They have also used electron microscopy to reconstruct the binding modes of these antibodies. In the specific case study of COV2-2165 and COV2-2832, they claimed that even though in the EM structure these two antibodies bind to very similar epitopes, their antigen escape pattern (from the mutagenesis study) is different. This leads to a key argument in the manuscript: structures may be not as informative as the mutagenesis study.
Since the start of the pandemic, a number of SARS-CoV-2 strains have been uncovered, containing mutations that vary the degree of severity and infection rate in different geography. It would be interesting to see if the complete mutagenesis sheds any light on the escape pattern and our natural antibody defence. The authors reviewed all the reported SARS-CoV-2 strains and highlighted their effect on the 10 reported antibodies. From the matrix, they designed a cocktail and proved that it may be possible to devise a cocktail of antibodies to target this virus with varying escape mechanisms through its mutation.
The major significance of this work is to provide a rather good quality epitope mapping dataset that could be useful for us to describe the binding of these antibodies. It is rare to have such complete datasets, from screening, in vitro assays to structural studies.
Preprint: Greaney, A.J., Starr, T.N., Gilchuk, P., Zost, S.J., Binshtein, E., Loes, A.N., Hilton, S.K., Huddleston, J., Eguia, R., Crawford, K.H. and Dingens, A.S. (2020) Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition. bioRxiv.
