Pseudotyped Bat Coronavirus RaTG13 is efficiently neutralised by convalescent sera from SARS-CoV-2 infected patients

  1. Diego Cantoni
  2. Martin Mayora-Neto
  3. Nazia Thakur
  4. Ahmed M. E. Elrefaey
  5. Joseph Newman
  6. Sneha Vishwanath
  7. Angalee Nadesalingam
  8. Andrew Chan
  9. Peter Smith
  10. Javier Castillo-Olivares
  11. Helen Baxendale
  12. Bryan Charleston
  13. Jonathan Heeney
  14. Dalan Bailey
  15. Nigel Temperton

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Abstract

RaTG13 is a close relative of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, sharing 96% sequence similarity at the genome-wide level. The spike receptor binding domain (RBD) of RaTG13 contains a number of amino acid substitutions when compared to SARS-CoV-2, likely impacting affinity for the ACE2 receptor. Antigenic differences between the viruses are less well understood, especially whether RaTG13 spike can be efficiently neutralised by antibodies generated from infection with, or vaccination against, SARS-CoV-2. Using RaTG13 and SARS-CoV-2 pseudotypes we compared neutralisation using convalescent sera from previously infected patients or vaccinated healthcare workers. Surprisingly, our results revealed that RaTG13 was more efficiently neutralised than SARS-CoV-2. In addition, neutralisation assays using spike mutants harbouring single and combinatorial amino acid substitutions within the RBD demonstrated that both spike proteins can tolerate multiple changes without dramatically reducing neutralisation. Moreover, introducing the 484 K mutation into RaTG13 resulted in increased neutralisation, in contrast to the same mutation in SARS-CoV-2 (E484K). This is despite E484K having a well-documented role in immune evasion in variants of concern (VOC) such as B.1.351 (Beta). These results indicate that the future spill-over of RaTG13 and/or related sarbecoviruses could be mitigated using current SARS-CoV-2-based vaccination strategies.

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  1. Version published to 10.1038/s42003-022-03325-9
  2. ScreenIT

    SciScore for 10.1101/2021.08.17.456606: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: (Study approved by Research Ethics Committee Wales, IRAS: 96194 12/WA/0148.
    Consent: All participants provided written, informed consent prior to enrolment in the study.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Recombinant DNA
    SentencesResources
    Plasmid generation: The RaTG13 construct, the chimeric expression plasmids expressing SARS-CoV-2 with the RaTG13 RBD and RaTG13 with the SARS-CoV-2 RBD as well as the individual mutants were synthesised commercially (BioBasic) and subcloned into pcDNA3.1+ expression vectors, as detailed in Conceicao et al, 2020 (7).
    pcDNA3.1+
    suggested: RRID:Addgene_117272)
    The B.1.351 (Beta) variant Spike was synthesised commercially (GeneArt) and subcloned into a pCAGGS expression vector.
    pCAGGS
    suggested: RRID:Addgene_18926)
    On the day of transfection, a DNA mix containing 1000ng of p.891 HIV Gag-Pol, 1500ng of pCSFLW luciferase and 1000ng of either SARS-CoV-2 Spike, RaTG13 Spike, Spike chimeras or B.1.351 (Beta) variant were prepared in 200µL of OptiMEM, followed by addition of transfection reagent FuGENE HD (Promega) at a 1:3 ratio and incubated for 15 minutes.
    pCSFLW
    suggested: None
    Software and Algorithms
    SentencesResources
    Data was analysed using GraphPad Prism software to derive IC50 values, as previously described (9).
    GraphPad Prism
    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: 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

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2021.08.17.456606v1 on bioRxiv