Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants
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Abstract
As battles to contain the COVID-19 pandemic continue, attention is focused on emerging variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus that have been deemed variants of concern because they are resistant to antibodies elicited by infection or vaccination or they increase transmissibility or disease severity. Three papers used functional and structural studies to explore how mutations in the viral spike protein affect its ability to infect host cells and to evade host immunity. Gobeil et al . looked at a variant spike protein involved in transmission between minks and humans, as well as the B1.1.7 (alpha), B.1.351 (beta), and P1 (gamma) spike variants; Cai et al . focused on the alpha and beta variants; and McCallum et al . discuss the properties of the spike protein from the B1.1.427/B.1.429 (epsilon) variant. Together, these papers show a balance among mutations that enhance stability, those that increase binding to the human receptor ACE2, and those that confer resistance to neutralizing antibodies. —VV
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SciScore for 10.1101/2021.04.13.439709: (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 Western blot: Western blot was performed using an anti-SARS-COV-2 S antibody following a protocol described previously (42). anti-SARS-COV-2 Ssuggested: NoneAlkaline phosphatase conjugated anti-Rabbit IgG (1:5000) (Sigma-Aldrich, St. Louis, MO) was used as a secondary antibody. anti-Rabbit IgGsuggested: NoneControl sensors with no Spike protein or antibody were also dipped in the ACE2 or Spike protein solutions and the running buffer as references. ACE2suggested: NoneFor antibody staining, an Alexa Fluor 647 conjugated donkey anti-human IgG Fc F(ab’)2 fragment (Jackson ImmunoResearch, West Grove, PA) was … SciScore for 10.1101/2021.04.13.439709: (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 Western blot: Western blot was performed using an anti-SARS-COV-2 S antibody following a protocol described previously (42). anti-SARS-COV-2 Ssuggested: NoneAlkaline phosphatase conjugated anti-Rabbit IgG (1:5000) (Sigma-Aldrich, St. Louis, MO) was used as a secondary antibody. anti-Rabbit IgGsuggested: NoneControl sensors with no Spike protein or antibody were also dipped in the ACE2 or Spike protein solutions and the running buffer as references. ACE2suggested: NoneFor antibody staining, an Alexa Fluor 647 conjugated donkey anti-human IgG Fc F(ab’)2 fragment (Jackson ImmunoResearch, West Grove, PA) was used as secondary antibody at 5 μg/ml concentration. anti-human IgGsuggested: NoneFor ACE2615-foldon T27W staining, APC conjugated anti-HIS antibody (Miltenyi Biotec, Auburn, CA) was used as secondary antibody at 1:50 dilution. anti-HISsuggested: NoneExperimental Models: Cell Lines Sentences Resources Briefly, Expi293F cells transfected with monomeric ACE2 or dimeric ACE2 expression construct and the supernatant of the cell culture was collected. Expi293Fsuggested: RRID:CVCL_D615)Briefly, various amount of the full-length SARS-CoV2 (D614, G614, UK and South Afirca) S construct (0.025-10 μg) and the α fragment of E. coli β-galactosidase construct (10 μg), or the full-length ACE2 construct (10 μg) together with the ω fragment of E. coli β-galactosidase construct (10 μg), were transfected to HEK293T cells using Polyethylenimine (PEI) (80 μg). HEK293Tsuggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)Pseudotyped virus particles were produced in 293T/17 cells (ATCC) by co-transfection of plasmids encoding codon-optimized SARS-CoV-2 full-length Spike constructs, packaging plasmid pCMV DR8.2, and luciferase reporter plasmid pHR’ CMV-Luc. 293T/17suggested: ATCC Cat# CRL-11268, RRID:CVCL_1926)The 293T cell line stably overexpressing the human ACE2 cell surface receptor protein was kindly provided by Drs. 293Tsuggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)Software and Algorithms Sentences Resources Africa/KRISP-EC-MDSH925100/2020 (GISAID accession ID: EPI_ISL_736980) were synthesized by GENEWIZ (South Plainfield, NJ). GENEWIZsuggested: (GENEWIZ, RRID:SCR_003177)Automated data collection was carried out using SerialEM version 3.8.6 (43) at a nominal magnification of 105,000× and the K3 detector in counting mode (calibrated pixel size, 0.825 Å) at an exposure rate of 20.21 (for B.1.1.7) or 20.50 (for B.1.351) electrons per pixel per second. SerialEMsuggested: (SerialEM, RRID:SCR_017293)Image processing and 3D reconstructions: Drift correction for cryo-EM images was performed using MotionCor2 (44), and contrast transfer function (CTF) was estimated by CTFFIND4 (45) using motion-corrected sums without dose-weighting. MotionCor2suggested: (MotionCor2, RRID:SCR_016499)For the RBD-up class of the B.1.351 sample, data processing was primarily carried out in cryoSPARC (37). cryoSPARCsuggested: (cryoSPARC, RRID:SCR_016501)All density maps from RELION were corrected from the modulation transfer function of the K3 detector and then sharpened by applying a temperature factor that was estimated using post-processing in the program. RELIONsuggested: (RELION, RRID:SCR_016274)The maps with a resolution lower than 4.0Å were primarily modeled manually in coot and by rigid body fitting, as the local resolution of many regions is higher than 4.0Å. cootsuggested: (Coot, RRID:SCR_014222)Iteratively, refinement was performed in both Phenix (real space refinement) and ISOLDE (49), and the Phenix refinement strategy included minimization_global, local_grid_search, and adp, with rotamer, Ramachandran, and reference-model restraints, using 7KRQ and 7KRR as the reference model. Phenixsuggested: (Phenix, RRID:SCR_014224)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
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: Please consider improving the rainbow (“jet”) colormap(s) used on pages 27 and 29. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
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- No protocol registration statement was detected.
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