Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition

Greaney, Allison J; Starr, Tyler N; Gilchuk, Pavlo; Zost, Seth J.; Binshtein, Elad; Loes, Andrea N; Hilton, Sarah K; Huddleston, John; Eguia, Rachel; Crawford, Katharine H.D.; Dingens, Adam S.; Nargi, Rachel S.; Sutton, Rachel E.; Suryadevara, Naveen Chandra; Rothlauf, Paul W.; Liu, Zhuoming; Whelan, Sean P. J.; Carnahan, Robert H.; Bloom, Jesse D

doi:10.1016/j.chom.2020.11.007

Cited by 975 publications

(860 citation statements)

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“…As described in ( 8 ), these libraries were sorted to eliminate variants that lose ACE2 binding prior to mapping the antibody-escape variants. Antibody labeling and selection was performed essentially as described in ( 8 ). Specifically, OD aliquots of RBD libraries were thawed and grown overnight at 30°C 275 rpm in 45mL SD-CAA (6.7 g/L Yeast Nitrogen Base, 5.0 g/L Casamino acids, 1.065 g/L MES, and 2% w/v dextrose).…”

Section: Supplementary Materialsmentioning

confidence: 99%

“…Analysis of mutant library deep sequencing and computation of per-mutant escape fractions Escape fractions were computed as described in ( 8 ), with minor modifications as noted below. Specifically, we used the dms_variants package ( https://jbloomlab.github.io/dms_variants/ , version 0.8.2) to process Illumina sequences into counts of each barcoded RBD variant in each pre-sort and antibody-escape population using the barcode/RBD look-up table from ( 7 ).…”

Section: Supplementary Materialsmentioning

confidence: 99%

“…For each antibody selection, we then computed the "escape fraction" for each barcoded variant using the deep sequencing counts for each variant in the original and antibody-escape populations and the total fraction of the library that escaped antibody binding via the formula provided in Greaney et al ( 8 ). These escape fractions represent the estimated fraction of cells expressing that specific variant that fall in the antibody escape bin, so a value of 0 means the variant is always bound by antibody and a value of 1 means that it always escapes antibody binding.…”

Section: Supplementary Materialsmentioning

confidence: 99%

“…Next, we removed any variants that had poor RBD expression or ACE2 binding, or contained mutations that individually cause poor RBD expression and ACE2 binding, the logic being that this would eliminate misfolded or non-expressing RBDs. Specifically, we removed variants that had (or contained mutations with) ACE2 binding scores < -2.35 or expression scores < -1, using the variant-and mutation-level deep mutational scanning scores from Starr et al ( 8 ). Note that these filtering criteria are slightly more stringent than those used in Greaney et al ( 8 ).…”

Section: Supplementary Materialsmentioning

confidence: 99%

“…Specifically, we removed variants that had (or contained mutations with) ACE2 binding scores < -2.35 or expression scores < -1, using the variant-and mutation-level deep mutational scanning scores from Starr et al ( 8 ). Note that these filtering criteria are slightly more stringent than those used in Greaney et al ( 8 ). A markdown rendering of the computation of the variant-level escape fractions and the variant filtering is at https://github.com/jbloomlab/SARS-CoV-2-RBD_MAP_clinical_Abs/blob/main/results/summar y/counts_to_scores.md .…”

Section: Supplementary Materialsmentioning

confidence: 99%

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Prospective mapping of viral mutations that escape antibodies used to treat COVID-19

Starr

Greaney

Addetia

et al. 2020

Preprint

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258

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Antibodies are becoming a frontline therapy for SARS-CoV-2, but the risk of viral evolutionary escape remains unclear. Here we map how all mutations to SARS-CoV-2's receptor-binding domain (RBD) affect binding by the antibodies in Regeneron's REGN-COV2 cocktail and Eli Lilly's LY-CoV016. These complete maps uncover a single amino-acid mutation that fully escapes the REGN-COV2 cocktail, which consists of two antibodies targeting distinct structural epitopes. The maps also identify viral mutations that are selected in a persistently infected patient treated with REGN-COV2, as well as in lab viral escape selections. Finally, the maps reveal that mutations escaping each individual antibody are already present in circulating SARS-CoV-2 strains. Overall, these complete escape maps enable immediate interpretation of the consequences of mutations observed during viral surveillance.

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Section: Supplementary Materialsmentioning

confidence: 99%

Section: Supplementary Materialsmentioning

confidence: 99%

Section: Supplementary Materialsmentioning

confidence: 99%

Section: Supplementary Materialsmentioning

confidence: 99%

Section: Supplementary Materialsmentioning

confidence: 99%

See 3 more Smart Citations

Prospective mapping of viral mutations that escape antibodies used to treat COVID-19

Starr

Greaney

Addetia

et al. 2020

Preprint

Self Cite

258

395

View full text Add to dashboard Cite

show abstract

Engineering Extracellular Vesicles Enriched with Palmitoylated ACE2 as COVID‐19 Therapy

Xie

Pan

et al. 2021

Advanced Materials

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Angiotensin converting enzyme 2 (ACE2) is a key receptor present on cell surfaces that directly interacts with the viral spike (S) protein of the severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2). It is proposed that inhibiting this interaction can be promising in treating COVID‐19. Here, the presence of ACE2 in extracellular vesicles (EVs) is reported and the EV‐ACE2 levels are determined by protein palmitoylation. The Cys141 and Cys498 residues on ACE2 are S‐palmitoylated by zinc finger DHHC‐Type Palmitoyltransferase 3 (ZDHHC3) and de‐palmitoylated by acyl protein thioesterase 1 (LYPLA1), which is critical for the membrane‐targeting of ACE2 and their EV secretion. Importantly, by fusing the S‐palmitoylation‐dependent plasma membrane (PM) targeting sequence with ACE2, EVs enriched with ACE2 on their surface (referred to as PM‐ACE2‐EVs) are engineered. It is shown that PM‐ACE2‐EVs can bind to the SARS‐CoV‐2 S‐RBD with high affinity and block its interaction with cell surface ACE2 in vitro. PM‐ACE2‐EVs show neutralization potency against pseudotyped and authentic SARS‐CoV‐2 in human ACE2 (hACE2) transgenic mice, efficiently block viral load of authentic SARS‐CoV‐2, and thus protect host against SARS‐CoV‐2‐induced lung inflammation. The study provides an efficient engineering protocol for constructing a promising, novel biomaterial for application in prophylactic and therapeutic treatments against COVID‐19.

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Charge Matters: Mutations in Omicron Variant Favor Binding to Cells

et al. 2022

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Evidence is strengthening to suggest that the novel SARS-CoV-2 mutant Omicron, with its more than 60 mutations, will spread and dominate worldwide. Although the mutations in the spike protein are known, the molecular basis for why the additional mutations in the spike protein that have not previously occurred account for Omicron's higher infection potential, is not understood. We propose, based on chemical rational and molecular dynamics simulations, that the elevated occurrence of positively charged amino acids in certain domains of the spike protein (Delta: + 4; Omicron: + 5 vs. wild type) increases binding to cellular polyanionic receptors, such as heparan sulfate due to multivalent charge-charge interactions. This observation is a starting point for targeted drug development.

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Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition

Abstract: Highlights d Develop system to map all SARS-CoV-2 RBD mutations that escape antibody binding d Escape maps predict which mutations emerge when virus grown in presence of antibody d Escape maps inform surveillance for possible antigenic evolution

Cited by 975 publications

References 98 publications

Prospective mapping of viral mutations that escape antibodies used to treat COVID-19

Prospective mapping of viral mutations that escape antibodies used to treat COVID-19

Engineering Extracellular Vesicles Enriched with Palmitoylated ACE2 as COVID‐19 Therapy

Charge Matters: Mutations in Omicron Variant Favor Binding to Cells

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