The Delta variant SARS-CoV-2 spike protein uniquely promotes aggregation of pseudotyped viral particles

  1. Jennifer D. Petersen
  2. Jianming Lu
  3. Wendy Fitzgerald
  4. Fei Zhou
  5. Paul S. Blank
  6. Doreen Matthies
  7. Joshua Zimmerberg

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Abstract

Individuals infected with the SARS-CoV-2 Delta variant, lineage B.1.617.2, exhibit faster initial infection with a higher viral load than prior variants, and pseudotyped particles bearing the SARS-CoV-2 Delta variant spike protein induce a faster initial infection rate of target cells compared to those bearing other SARS-CoV-2 variant spikes. Here, we show that pseudotyped particles bearing the Delta variant spike form unique aggregates, as evidenced by negative stain and cryogenic electron microscopy (EM), flow cytometry, and nanoparticle tracking analysis. Viral particles pseudotyped with other SARS-CoV-2 spike variants do not show aggregation by any of these criteria. The contribution to infection kinetics of the Delta spike’s unique property to aggregate is discussed with respect to recent evidence for collective infection by other viruses. Irrespective of this intriguing possibility, spike-dependent aggregation is a new functional parameter of spike-expressing viral particles to evaluate in future spike protein variants.

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  1. ScreenIT

    SciScore for 10.1101/2022.04.07.487415: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Antibodies
    SentencesResources
    Primary antibody to SARS-CoV-2 spike subunit 1 (Sino Biological, Beijing, Cat. No. 40589-T62), was diluted 1:25 in blocking solution and grids were transferred to drops of primary antibody for 30 minutes.
    SARS-CoV-2 spike subunit 1
    suggested: None
    Then, grids were transferred across two drops of blocking solution for 10 minutes before incubation with 10 nm gold-conjugated donkey-α-rabbit secondary antibody diluted 1:20 in blocking solution for 30 min.
    donkey-α-rabbit
    suggested: None
    Experimental Models: Cell Lines
    SentencesResources
    2.1 Cell culture and Production of SARS-CoV-2 Variant Spike PPs: HEK 293T cells were a gift from the laboratory of Dr. Gary Whittaker (Cornell University).
    HEK 293T
    suggested: KCB Cat# KCB 200744YJ, RRID:CVCL_0063)
    Recombinant DNA
    SentencesResources
    plasmids pCMV-MLV-gag-pol, pTG-Luc and SARS2-COV2 spike expression vector were transfected into HEK 293T cells at the ratio of 3:4:3 using Lipofectamine 3000 transfection reagent (ThermoFisher Scientific, Waltham, MA).
    pCMV-MLV-gag-pol
    suggested: None
    pTG-Luc
    suggested: None
    Software and Algorithms
    SentencesResources
    Images were prepared for display using Photoshop 2022 (Adobe).
    Photoshop
    suggested: (Adobe Photoshop, RRID:SCR_014199)
    The sizes of the Delta variant PP aggregates were measured using Fiji.
    Fiji
    suggested: (Fiji, RRID:SCR_002285)
    Data was analysed in FlowJo 10.8 (BD Biosciences, San Jose, CA).
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Each 50-frame-movie was motion corrected using SerialEM.
    SerialEM
    suggested: (SerialEM, RRID:SCR_017293)

    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.

  2. Version published to 10.1101/2022.04.07.487415 on bioRxiv