Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta

  1. Lorenz Ulrich
  2. Nico Joel Halwe
  3. Adriano Taddeo
  4. Nadine Ebert
  5. Jacob Schön
  6. Christelle Devisme
  7. Bettina Salome Trüeb
  8. Bernd Hoffmann
  9. Manon Wider
  10. Xiaoyu Fan
  11. Meriem Bekliz
  12. Manel Essaidi-Laziosi
  13. Marie Luisa Schmidt
  14. Daniela Niemeyer
  15. Victor Max Corman
  16. Anna Kraft
  17. Aurélie Godel
  18. Laura Laloli
  19. Jenna N. Kelly
  20. Brenda M. Calderon
  21. Angele Breithaupt
  22. Claudia Wylezich
  23. Inês Berenguer Veiga
  24. Mitra Gultom
  25. Sarah Osman
  26. Bin Zhou
  27. Kenneth Adea
  28. Benjamin Meyer
  29. Christiane S. Eberhardt
  30. Lisa Thomann
  31. Monika Gsell
  32. Fabien Labroussaa
  33. Jörg Jores
  34. Artur Summerfield
  35. Christian Drosten
  36. Isabella Anne Eckerle
  37. David E. Wentworth
  38. Ronald Dijkman
  39. Donata Hoffmann
  40. Volker Thiel
  41. Martin Beer
  42. Charaf Benarafa

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Abstract

Emerging variants of concern (VOCs) are driving the COVID-19 pandemic 1,2 . Experimental assessments of replication and transmission of major VOCs and progenitors are needed to understand the mechanisms of replication and transmission of VOCs 3 . Here we show that the spike protein (S) from Alpha (also known as B.1.1.7) and Beta (B.1.351) VOCs had a greater affinity towards the human angiotensin-converting enzyme 2 (ACE2) receptor than that of the progenitor variant S(D614G) in vitro. Progenitor variant virus expressing S(D614G) (wt-S 614G ) and the Alpha variant showed similar replication kinetics in human nasal airway epithelial cultures, whereas the Beta variant was outcompeted by both. In vivo, competition experiments showed a clear fitness advantage of Alpha over wt-S 614G in ferrets and two mouse models—the substitutions in S were major drivers of the fitness advantage. In hamsters, which support high viral replication levels, Alpha and wt-S 614G showed similar fitness. By contrast, Beta was outcompeted by Alpha and wt-S 614G in hamsters and in mice expressing human ACE2. Our study highlights the importance of using multiple models to characterize fitness of VOCs and demonstrates that Alpha is adapted for replication in the upper respiratory tract and shows enhanced transmission in vivo in restrictive models, whereas Beta does not overcome Alpha or wt-S 614G in naive animals.

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  1. Version published to 10.1038/s41586-021-04342-0
  2. ScreenIT

    SciScore for 10.1101/2021.06.28.450190: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: The studies were approved either by the Geneva Cantonal Ethics Commission (2020-00516) or by the ethics committee of Charité-Universitätsmedizin Berlin (EA2/066/20, EA4/244/20, EA2/092/20, and EA4/245/20).
    IACUC: Animal experimentation ethics declarations: All ferret and hamster experiments were evaluated by the responsible ethics committee of the State Office of Agriculture, Food Safety, and Fishery in Mecklenburg–Western Pomerania (LALLF M-V) and gained governmental approval under registration number LVL MV TSD/7221.3-1-004/21.
    Field Sample Permit: Mouse studies were conducted in compliance with the Swiss Animal Welfare legislation and approved by the commission for animal experiments of the canton of Bern under license BE-43/20.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Immunohistochemistry (IHC) was performed using an anti-SARS nucleocapsid antibody (Novus Biologicals #NB100-56576, dilution 1:200) according to standardized avidin-biotin-peroxidase complex-method producing a red labelling and hematoxylin counterstain.
    anti-SARS
    suggested: (Novus Cat# NB100-56576, RRID:AB_838838)
    Experimental Models: Cell Lines
    SentencesResources
    Cell lines: Vero E6 cells (kindly provided by Doreen Muth, Marcel Müller, and Christian Drosten, Charité, Berlin, Germany) or Vero-TMPRSS2 22 (kindly provided by Stefan Pöhlmann, German Primate Center - Leibniz Institute for Primate Research, Göttingen, Germany) were propagated in Dulbecco’s Modified Eagle Medium-GlutaMAX™ supplemented with 1 mM sodium pyruvate, 10% (v/v) heat-inactivated fetal bovine serum (FBS), 100 μg/ml streptomycin, 100 IU/ml penicillin, 1% (w/v) nonessential amino acids, and 15 mM HEPES (Gibco, Gaithersburg, Maryland, United States of America).
    Vero E6
    suggested: RRID:CVCL_XD71)
    Contemporary clinical isolates from the B.1.160 (SD614G) (EPI_ISL_414019), B.1.1.7 (EPI_ISL_2131446, EPI_ISL_751799 (L4549)) and B.1.351 (EPI_ISL_803957 (L4550)) were isolated and minimal passaged upon Vero E6 cells. B.1.351 (EPI_ISL_981782) was initially isolated on A549 cells expressing hACE2 before passaging on Vero E6 cells.
    A549
    suggested: NCI-DTP Cat# A549, RRID:CVCL_0023)
    Isogenic viruses were grown on Vero-TMPRSS2 cells, after one passage on human bronchial airway epithelial cells.
    Vero-TMPRSS2
    suggested: JCRB Cat# JCRB1818, RRID:CVCL_YQ48)
    Vero-E6 cells were washed 1x with PBS and inoculated with the virus serum/plasma mixture for 1h.
    Vero-E6
    suggested: None
    Experimental Models: Organisms/Strains
    SentencesResources
    SARS-CoV-2 B.1.1.7 (L4549) and B.1.351 (L4550) 18 were received from the Robert-Koch-Institut Berlin,
    SARS-CoV-2 B.1.1.7
    suggested: None
    Protein expression, purification, and biolayer interferometry assay: SARS-CoV-2 spike protein expression plasmids were constructed to encode the ectodomain of spike protein S614G or SB.1.1.7 (residues 1–1208, with a mutated furin cleavage site and K986P/V987P substitutions) followed by a T4 foldon trimerization domain and a polyhistidine purification tag.
    SB.1.1.7
    suggested: None
    Evaluation and interpretation was performed by board-certified veterinary pathologists (DiplECVP) (AB, IBV).
    AB
    suggested: RRID:BDSC_203)
    Mouse studies: Homozygous hACE2 knock-in mice (B6.Cg-Ace2tm1(ACE2)Dwnt; henceforth hACE2-KI) and hemizygous transgenic mice (Tg(K18-hACE2)2Prlmn; henceforth hACE2-K18Tg) were described previously 4, 16.
    B6.Cg-Ace2tm1 ( ACE2)Dwnt; henceforth hACE2-KI )
    suggested: None
    Tg(K18-hACE2)2Prlmn; henceforth hACE2-K18Tg
    suggested: None
    One day after inoculation, infected hACE2-K18Tg mice were placed in the cage of another hACE2-K18Tg contact mouse.
    hACE2-K18Tg
    suggested: None
    Software and Algorithms
    SentencesResources
    Statistical Analysis: Statistical analysis was performed using the GraphPad Prism version 8 or R (version 4.1).
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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.

    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.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

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  3. Version published to 10.1101/2021.06.28.450190v1 on bioRxiv