The N501Y spike substitution enhances SARS-CoV-2 transmission

  1. Yang Liu
  2. Jianying Liu
  3. Kenneth S. Plante
  4. Jessica A. Plante
  5. Xuping Xie
  6. Xianwen Zhang
  7. Zhiqiang Ku
  8. Zhiqiang An
  9. Dionna Scharton
  10. Craig Schindewolf
  11. Vineet D. Menachery
  12. Pei-Yong Shi
  13. Scott C. Weaver

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Abstract

Beginning in the summer of 2020, a variant of SARS-CoV-2, the cause of the COVID-19 pandemic, emerged in the United Kingdom (UK). This B.1.1.7 variant increased rapidly in prevalence among sequenced strains, attributed to an increase in infection and/or transmission efficiency. The UK variant has 19 nonsynonymous mutations across its viral genome including 8 substitutions or deletions in the spike protein, which interacts with cellular receptors to mediate infection and tropism. Here, using a reverse genetics approach, we show that, of the 8 individual spike protein substitutions, only N501Y exhibited consistent fitness gains for replication in the upper airway in the hamster model as well as primary human airway epithelial cells. The N501Y substitution recapitulated the phenotype of enhanced viral transmission seen with the combined 8 UK spike mutations, suggesting it is a major determinant responsible for increased transmission of this variant. Mechanistically, the N501Y substitution improved the affinity of the viral spike protein for cellular receptors. As suggested by its convergent evolution in Brazil and South Africa, our results indicate that N501Y substitution is a major adaptive spike mutation of major concern.

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  1. ScreenIT

    SciScore for 10.1101/2021.03.08.434499: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board StatementIACUC: The protocol was approved by the Institutional Animal Care and Use Committee (IACUC) at UTMB.
    RandomizationStatistics: Male hamsters were randomly allocated into different groups.
    BlindingThe investigators were not blinded to allocation during the experiments or to the outcome assessment.
    Power Analysisnot detected.
    Sex as a biological variableHamster infections: Four- to six-week-old male golden Syrian hamsters, strain HsdHan:AURA (Envigo, Indianapolis, IN), were inoculated intranasally with 100 μl SARS-CoV-2.
    Cell Line AuthenticationContamination: All cell lines were verified and tested negative for mycoplasma.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Human lung adenocarcinoma epithelial Calu-3 cells (ATCC, Manassas, VA, USA) were maintained in a high-glucose DMEM containing sodium pyruvate and GlutaMAX (Gibco) with 10% FBS and 1% penicillin/streptomycin at 37°C with 5% CO2.
    Calu-3
    suggested: None
    For recovering the mutant viruses, the RNA transcripts were electroporated into Vero E6 cells.
    Vero E6
    suggested: RRID:CVCL_XD71)
    Software and Algorithms
    SentencesResources
    The sequencing reactions were purified using a 96-well plate format (EdgeBio, San Jose, CA, USA) and analyzed on a 3500 Genetic Analyzer (Applied Biosystems, Foster City, CA).
    EdgeBio
    suggested: (EdgeBio, RRID:SCR_000183)
    Analyses were performed in Prism version 9.0 (GraphPad, San Diego, CA).
    Prism
    suggested: (PRISM, RRID:SCR_005375)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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: We detected the following sentences addressing limitations in the study:
    Another limitation of our study is the models used. The hamster may be the best rodent model available8, but its ACE2 receptors differ slightly from those of humans25. Although we combined the hamster model with infection of primary human airway cells to address this limitation, the use of a primate model would be ideal to confirm our findings. In conclusion, we have used authentic SARS-CoV-2 to demonstrate that only 2 of 8 spike substitutions in the UK B.1.1.7 variant are mainly responsible for the enhanced transmission of this strain. Although mutations in other parts of the genome could also contribute to this transmission phenotype, the N501Y substitution in the spike protein in particular appears to be a major determinant of efficient transmission. This mutation is present in several regions of the world and should be closely monitored to anticipate public health measures needed to control SARS-CoV-2 spread.

    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.

    About SciScore

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  2. Version published to 10.1101/2021.03.08.434499v1 on bioRxiv