Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants

  1. Yongfei Cai
  2. Jun Zhang
  3. Tianshu Xiao
  4. Christy L. Lavine
  5. Shaun Rawson
  6. Hanqin Peng
  7. Haisun Zhu
  8. Krishna Anand
  9. Pei Tong
  10. Avneesh Gautam
  11. Shen Lu
  12. Sarah M. Sterling
  13. Richard M. Walsh
  14. Sophia Rits-Volloch
  15. Jianming Lu
  16. Duane R. Wesemann
  17. Wei Yang
  18. Michael S. Seaman
  19. Bing Chen

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Abstract

Several fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have become the dominant circulating strains that continue to fuel the COVID-19 pandemic despite intensive vaccination efforts throughout the world. We report here cryo-EM structures of the full-length spike (S) trimers of the B.1.1.7 and B.1.351 variants, as well as their biochemical and antigenic properties. Mutations in the B.1.1.7 protein increase the accessibility of its receptor binding domain and also the binding affinity for receptor angiotensin-converting enzyme 2 (ACE2). The enhanced receptor engagement can account for the increased transmissibility and risk of mortality as the variant may begin to infect efficiently infect additional cell types expressing low levels of ACE2. The B.1.351 variant has evolved to reshape antigenic surfaces of the major neutralizing sites on the S protein, rendering complete resistance to some potent neutralizing antibodies. These findings provide structural details on how the wide spread of SARS-CoV-2 enables rapid evolution to enhance viral fitness and immune evasion. They may guide intervention strategies to control the pandemic.

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  1. ScreenIT

    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
    SentencesResources
    Western blot: Western blot was performed using an anti-SARS-COV-2 S antibody following a protocol described previously (42).
    anti-SARS-COV-2 S
    suggested: None
    Alkaline phosphatase conjugated anti-Rabbit IgG (1:5000) (Sigma-Aldrich, St. Louis, MO) was used as a secondary antibody.
    anti-Rabbit IgG
    suggested: None
    Control sensors with no Spike protein or antibody were also dipped in the ACE2 or Spike protein solutions and the running buffer as references.
    ACE2
    suggested: None
    For 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 IgG
    suggested: None
    For ACE2615-foldon T27W staining, APC conjugated anti-HIS antibody (Miltenyi Biotec, Auburn, CA) was used as secondary antibody at 1:50 dilution.
    anti-HIS
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    Briefly, Expi293F cells transfected with monomeric ACE2 or dimeric ACE2 expression construct and the supernatant of the cell culture was collected.
    Expi293F
    suggested: 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).
    HEK293T
    suggested: 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/17
    suggested: 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.
    293T
    suggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)
    Software and Algorithms
    SentencesResources
    Africa/KRISP-EC-MDSH925100/2020 (GISAID accession ID: EPI_ISL_736980) were synthesized by GENEWIZ (South Plainfield, NJ).
    GENEWIZ
    suggested: (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.
    SerialEM
    suggested: (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.
    MotionCor2
    suggested: (MotionCor2, RRID:SCR_016499)
    For the RBD-up class of the B.1.351 sample, data processing was primarily carried out in cryoSPARC (37).
    cryoSPARC
    suggested: (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.
    RELION
    suggested: (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.
    coot
    suggested: (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.
    Phenix
    suggested: (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.
    • 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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  2. Version published to 10.1101/2021.04.13.439709 on bioRxiv