Prospective mapping of viral mutations that escape antibodies used to treat COVID-19
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Abstract
Several antibodies are in use or under development as therapies to treat COVID-19. As new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants emerge, it is important to predict whether they will remain susceptible to antibody treatment. Starr et al. used a yeast library that covers all mutations to the SARS-CoV-2 receptor-binding domain that do not strongly disrupt binding to the host receptor (ACE2) and mapped how these mutations affect binding to three leading anti–SARS-CoV-2 antibodies. The maps identify mutations that escape antibody binding, including a single mutation that escapes both antibodies in the Regeneron antibody cocktail. Many of the mutations that escape single antibodies are circulating in the human population.
Science , this issue p. 850
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SciScore for 10.1101/2020.11.30.405472: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources Antibodies: Publicly available antibody variable domain sequences were acquired for REGN10933, REGN10987, and LY-CoV016 (also known as JS016, LY3832479, or CB6). LY3832479suggested: NoneCB6suggested: NoneSpecifically, antibody variable domains were cloned with the human IgG1 heavy chain and human IgK (REGN10933 and LY-CoV016) or human IgL2 (REGN10987) constant regions into pcDNA3.4 vector, and transfected into HD 293F cells maintained at 37°C with 8% CO2 on an orbital shaker. human IgKsuggested: NoneAntibody-escape mapping: Antibody selection experiments were performed in biological duplicate using a … SciScore for 10.1101/2020.11.30.405472: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources Antibodies: Publicly available antibody variable domain sequences were acquired for REGN10933, REGN10987, and LY-CoV016 (also known as JS016, LY3832479, or CB6). LY3832479suggested: NoneCB6suggested: NoneSpecifically, antibody variable domains were cloned with the human IgG1 heavy chain and human IgK (REGN10933 and LY-CoV016) or human IgL2 (REGN10987) constant regions into pcDNA3.4 vector, and transfected into HD 293F cells maintained at 37°C with 8% CO2 on an orbital shaker. human IgKsuggested: NoneAntibody-escape mapping: Antibody selection experiments were performed in biological duplicate using a deep mutational scanning (mutational antigenic profiling) approach (8) using previously described duplicate mutant RBD libraries (7). Antibody-escapesuggested: NoneLabeled cells were washed with ice-cold PBS-BSA followed by secondary labeling for 1 h at 4°C in 2.5 mL 1:200 PE-conjugated goat anti-human-IgG (Jackson ImmunoResearch 109-115-098) to label for bound antibody, and 1:100 FITC-conjugated anti-Myc (Immunology Consultants Lab, CYMC-45F) to label for RBD surface expression. anti-human-IgGsuggested: Noneanti-Mycsuggested: NoneExperimental Models: Organisms/Strains Sentences Resources LY-CoV016 (CB6) sequence was reported by Shi et al. (11), Genbank Accessions MT470196 and MT470197. LY-CoV016suggested: NoneSoftware and Algorithms Sentences Resources The deep sequencing data have been deposited on the Sequence Read Archive under BioProject accession PRJNA681234. BioProjectsuggested: (NCBI BioProject, RRID:SCR_004801)Following filtering, reads were aligned to the Wuhan-Hu-1 reference with BWA-MEM (31). BWA-MEMsuggested: (Sniffles, RRID:SCR_017619)S4C) over the last three timepoints, we used a custom Python script that counted the co-occurrence of nonsynonymous variants in read-pairs. Pythonsuggested: (IPython, RRID:SCR_001658)The static structural views in the paper were rendered in PyMOL using antibody-bound RBD structures PDB 6XDG (9) and PDB 7C01 (11) PyMOLsuggested: (PyMOL, RRID:SCR_000305)Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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SciScore for 10.1101/2020.11.30.405472: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources See also Fig. 3. B) For each antibody, sites were classified as direct antibody contacts (non-hydrogen atoms within 4Å of antibody), antibody-proximal (4-8Å), or antibody-distal (>8Å) antibody-proximal (4-8Å),suggested: Noneantibody-distalsuggested: NoneAntibodies Publicly available antibody variable domain sequences were acquired for REGN10933, REGN10987, and … SciScore for 10.1101/2020.11.30.405472: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources See also Fig. 3. B) For each antibody, sites were classified as direct antibody contacts (non-hydrogen atoms within 4Å of antibody), antibody-proximal (4-8Å), or antibody-distal (>8Å) antibody-proximal (4-8Å),suggested: Noneantibody-distalsuggested: NoneAntibodies Publicly available antibody variable domain sequences were acquired for REGN10933, REGN10987, and LY-CoV016 (also known as JS016, LY3832479, or CB6). LY3832479suggested: NoneCB6suggested: NoneSpecifically, antibody variable domains were cloned with the human IgG1 heavy chain and human IgK (REGN10933 and LY-CoV016) or human IgL2 (REGN10987) constant regions into pcDNA3.4 vector, and transfected into HD 293F cells maintained at 37°C with 8% CO2 on an orbital shaker. human IgKsuggested: NoneAs described in (8), these libraries were sorted to eliminate variants that lose ACE2 binding prior to mapping the antibody-escape variants antibody-escapesuggested: NoneLabeled cells were washed with ice-cold PBS-BSA followed by secondary labeling for 1 h at 4°C in 2.5 mL 1:200 PE-conjugated goat anti-human-IgG (Jackson ImmunoResearch 109-115-098) to label for bound antibody, and 1:100 FITC-conjugated anti-Myc (Immunology Consultants Lab, CYMC-45F) to label for RBD surface expression. anti-human-IgGsuggested: Noneanti-Mycsuggested: NoneDeep mutational scanning method to map antibody-escape mutations. (A) Experimental approach to map antibody-escape mutations (8). antibody-escape mutations.suggested: None( B) We then performed neutralization assays using the REGN-COV2 antibodies / cocktail with the indicated spike mutants, using a dilution range that spanned higher antibody concentration ranges to maximize the resolution on changes in IC50 for escape mutations. REGN-COV2suggested: NoneSoftware and Algorithms Sentences Resources Intra-patient single-nucleotide polymorphisms (SNPs) were identified with an automated variant-calling pipeline (https://github.com/jbloomlab/SARS-CoV-2_chronic-infection-seq) created with Snakemake (29). Snakemakesuggested: (Snakemake, RRID:SCR_003475)Following filtering, reads were aligned to the Wuhan-Hu-1 reference with BWA-MEM (31). BWA-MEMsuggested: (Sniffles, RRID:SCR_017619)S4C) over the last three timepoints, we used a custom Python script that counted the co-occurrence of nonsynonymous variants in read-pairs. Pythonsuggested: (IPython, RRID:SCR_001658)The static structural views in the paper were rendered in PyMOL using antibody-bound RBD structures PDB 6XDG (9) and PDB 7C01 (11) PyMOLsuggested: (PyMOL, RRID:SCR_000305)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
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