Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein
The spike protein receptor-binding domain (RBD) of SARS-CoV-2 is the molecular target for many vaccines and antibody-based prophylactics aimed at bringing COVID-19 under control. Such a narrow molecular focus raises the specter of viral immune evasion as a potential failure mode for these biomedical...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
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Public Library of Science (PLoS)
2021
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| Online Access: | https://hdl.handle.net/1721.1/130548 |
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| author | Van Egeren, Debra Novokhodko, Alexander Stoddard, Madison Tran, Uyen Zetter, Bruce Rogers, Michael Pentelute, Bradley L. Carlson, Jonathan M. Hixon, Mark Joseph-McCarthy, Diane Chakravarty, Arijit |
| author2 | Massachusetts Institute of Technology. Department of Chemistry |
| author_facet | Massachusetts Institute of Technology. Department of Chemistry Van Egeren, Debra Novokhodko, Alexander Stoddard, Madison Tran, Uyen Zetter, Bruce Rogers, Michael Pentelute, Bradley L. Carlson, Jonathan M. Hixon, Mark Joseph-McCarthy, Diane Chakravarty, Arijit |
| author_sort | Van Egeren, Debra |
| collection | MIT |
| description | The spike protein receptor-binding domain (RBD) of SARS-CoV-2 is the molecular target for many vaccines and antibody-based prophylactics aimed at bringing COVID-19 under control. Such a narrow molecular focus raises the specter of viral immune evasion as a potential failure mode for these biomedical interventions. With the emergence of new strains of SARS-CoV-2 with altered transmissibility and immune evasion potential, a critical question is this: how easily can the virus escape neutralizing antibodies (nAbs) targeting the spike RBD? To answer this question, we combined an analysis of the RBD structure-function with an evolutionary modeling framework. Our structure-function analysis revealed that epitopes for RBD-targeting nAbs overlap one another substantially and can be evaded by escape mutants with ACE2 affinities comparable to the wild type, that are observed in sequence surveillance data and infect cells <jats:italic>in vitro</jats:italic>. This suggests that the fitness cost of nAb-evading mutations is low. We then used evolutionary modeling to predict the frequency of immune escape before and after the widespread presence of nAbs due to vaccines, passive immunization or natural immunity. Our modeling suggests that SARS-CoV-2 mutants with one or two mildly deleterious mutations are expected to exist in high numbers due to neutral genetic variation, and consequently resistance to vaccines or other prophylactics that rely on one or two antibodies for protection can develop quickly -and repeatedly- under positive selection. Predicted resistance timelines are comparable to those of the decay kinetics of nAbs raised against vaccinal or natural antigens, raising a second potential mechanism for loss of immunity in the population. Strategies for viral elimination should therefore be diversified across molecular targets and therapeutic modalities. |
| first_indexed | 2024-09-23T12:08:43Z |
| format | Article |
| id | mit-1721.1/130548 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T12:08:43Z |
| publishDate | 2021 |
| publisher | Public Library of Science (PLoS) |
| record_format | dspace |
| spelling | mit-1721.1/1305482022-10-01T08:29:27Z Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein Van Egeren, Debra Novokhodko, Alexander Stoddard, Madison Tran, Uyen Zetter, Bruce Rogers, Michael Pentelute, Bradley L. Carlson, Jonathan M. Hixon, Mark Joseph-McCarthy, Diane Chakravarty, Arijit Massachusetts Institute of Technology. Department of Chemistry The spike protein receptor-binding domain (RBD) of SARS-CoV-2 is the molecular target for many vaccines and antibody-based prophylactics aimed at bringing COVID-19 under control. Such a narrow molecular focus raises the specter of viral immune evasion as a potential failure mode for these biomedical interventions. With the emergence of new strains of SARS-CoV-2 with altered transmissibility and immune evasion potential, a critical question is this: how easily can the virus escape neutralizing antibodies (nAbs) targeting the spike RBD? To answer this question, we combined an analysis of the RBD structure-function with an evolutionary modeling framework. Our structure-function analysis revealed that epitopes for RBD-targeting nAbs overlap one another substantially and can be evaded by escape mutants with ACE2 affinities comparable to the wild type, that are observed in sequence surveillance data and infect cells <jats:italic>in vitro</jats:italic>. This suggests that the fitness cost of nAb-evading mutations is low. We then used evolutionary modeling to predict the frequency of immune escape before and after the widespread presence of nAbs due to vaccines, passive immunization or natural immunity. Our modeling suggests that SARS-CoV-2 mutants with one or two mildly deleterious mutations are expected to exist in high numbers due to neutral genetic variation, and consequently resistance to vaccines or other prophylactics that rely on one or two antibodies for protection can develop quickly -and repeatedly- under positive selection. Predicted resistance timelines are comparable to those of the decay kinetics of nAbs raised against vaccinal or natural antigens, raising a second potential mechanism for loss of immunity in the population. Strategies for viral elimination should therefore be diversified across molecular targets and therapeutic modalities. 2021-05-03T20:38:24Z 2021-05-03T20:38:24Z 2021-04 2021-02 Article http://purl.org/eprint/type/JournalArticle 1932-6203 https://hdl.handle.net/1721.1/130548 Van Egeren Debra et al. "Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein." PLoS ONE 16, 4 (April 2021): e0250780. © 2021 Van Egeren et al https://doi.org/10.1371/journal.pone.0250780 PLoS One Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/pdf Public Library of Science (PLoS) PLoS |
| spellingShingle | Van Egeren, Debra Novokhodko, Alexander Stoddard, Madison Tran, Uyen Zetter, Bruce Rogers, Michael Pentelute, Bradley L. Carlson, Jonathan M. Hixon, Mark Joseph-McCarthy, Diane Chakravarty, Arijit Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein |
| title | Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein |
| title_full | Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein |
| title_fullStr | Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein |
| title_full_unstemmed | Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein |
| title_short | Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein |
| title_sort | risk of rapid evolutionary escape from biomedical interventions targeting sars cov 2 spike protein |
| url | https://hdl.handle.net/1721.1/130548 |
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