Outwitting the foe: predicting evolved antibody escape in SARS-CoV-2

From the Bloom Lab (Basic Sciences Division)

The Covid-19 pandemic has redefined normalcy in our lives. But humans are a resilient species, and we have, though not without much pain and heartache, admirably adjusted to this ‘new normal’ a mere year after the virus’s emergence on the world stage. Unfortunately, to compound the challenges, it seems that every time we get our feet beneath us, the pandemic presents a new challenge to throw us back into uncertainty. A second wave. Airborne spread. A third wave. A vaccine. And now: B.1.1.7.; 501.V2; B.1.1.248. This cryptic code represents the latest frightening development in the pandemic – from the United Kingdom, South Africa, Brazil, reports of new and worrying mutant variants of the virus. So far, these variants appear to primarily affect virus transmissibility. But at a time when we are finally adjusting to a positive development - the beginnings of a mass vaccination campaign - they highlight an even graver concern among scientists: the evolution of a variant that can evade immune detection, rendering less effective the vaccines on which so much hope has been placed. To get ahead of this problem, Dr. Jesse Bloom’s lab in the Basic Sciences Division at Fred Hutch, co-led by graduate student Allison Greaney and postdoctoral fellow Dr. Tyler Starr in collaboration with members of the Vanderbilt Vaccine Center, report in a new paper in Cell Host & Microbe the systematic identification of possible SARS-CoV-2 mutations that can escape antibody detection.

Antibodies against the SARS-CoV-2 spike protein present an important defense against COVID-19, both in therapeutics such as convalescent plasma and monoclonal antibody therapies, and in the development of immunity after infection or vaccination. These defenses, however, have a weakness. “Viruses like SARS-CoV-2 acquire mutations [that may prevent antibody binding],” said Greaney. “But we can’t always predict what mutations might arise as a virus evolves. Thus, we set out to prospectively map how the nearly 4,000 possible mutations to the SARS-CoV-2 spike receptor-binding domain could affect antibody binding and neutralization.” To achieve this monumental task, the researchers expressed these 4,000 mutant versions of the receptor binding domain (RBD; a key antibody target on the spike protein) on the surface of yeast cells and exposed them to ten individual antibodies that had been isolated from COVID-19 patients. They then captured the cells that showed substantially impaired binding to these antibodies and performed deep sequencing to identify the RBD mutations present in these cells. This resulted in what Greaney described as a “comprehensive ‘escape map’”, showing the locations of all RBD mutations that allow the virus to escape detection by each antibody. The group identified a few locations on the protein where these escape mutations tended to cluster, and observed that these mutations tended to differ between different antibodies. An advantage of these escape maps is that they can be used to predict how the virus might evolve immune resistance, and to design improved antibody therapies against which this evolution is unlikely. “[We] used these maps to design combinations of antibodies [also known as antibody cocktails] that are escape-resistant.” Indeed, in laboratory evolution experiments, the group was very effective in blocking the evolution of escape mutants against their designer two-antibody cocktails.

Greaney says the Bloom Lab is already working on expanding this approach to address the biggest public health question related to SARS-CoV-2 evolution. “Our next steps will be to apply this approach to serum from individuals who have been vaccinated against SARS-CoV-2 to see how mutations might reduce binding and neutralization by vaccine-elicited antibodies.”

escape mapping
Mapping of the mutations that promote antibody escape onto the SARS-CoV-2 RBD using a yeast RBD expression system. Image provided by Allison Greaney.

This work was supported by the NIH, the Gates Foundation, DARPA, the Dolly Parton COVID- 19 Research Fund at Vanderbilt, the Howard Hughes Medical Institute, and Fast Grants, Mercatus Center, George Mason University.

Greaney AJ, Starr TN, Gilchuk P, Zost SJ, Binshtein E, Loes AN, Hilton SK, Huddleston J, Eguia R, Crawford KHD, Dingens AS, Nargi RS, Sutton RE, Suryadevara N, Rothlauf PW, Liu Z, Whelan SPJ, Carnahan RH, Crowe JE Jr, Bloom JD. 2021. Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition. Cell Host Microbe 29(1):44-57.e9. doi: 10.1016/j.chom.2020.11.007. PMID: 33259788