Nanobody-Functionalized Cellulose for Capturing SARS-CoV-2

  1. Xin Sun
  2. Shaobo Yang
  3. Amal A. Al-Dossary
  4. Shana Broitman
  5. Yun Ni
  6. Ming Guan
  7. Mengdi Yang
  8. Jiahe Li

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Abstract

The ongoing efforts to address the COVID-19 pandemic center around the development of diagnostics, preventative measures, and therapeutic strategies. In comparison to existing work, we have provided a complementary strategy to capture SARS-CoV-2 by functionalized cellulose materials through paper-based diagnostics as well as virus filtration in perishable samples.

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  1. Version published to 10.1128/aem.02303-21
  2. ScreenIT

    SciScore for 10.1101/2021.09.01.458653: (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
    Anti-FLAG epitope (DYKDDDDK, catalog# 637301) and horseradish peroxidase (HRP) Donkey anti-human IgG antibody (catalog #410902) were purchased from Biolegend (San Diego, CA).
    Anti-FLAG epitope (DYKDDDDK, catalog# 637301)
    suggested: None
    Anti-FLAG epitope (DYKDDDDK
    suggested: None
    anti-human IgG
    suggested: (BioLegend Cat# 410902, RRID:AB_2686937)
    The secondary antibody anti-rat IgG HRP (catalog# 7077) was bought from Cell Signaling Technology (CST, Danvers, MA).
    The secondary antibody anti-rat IgG HRP
    suggested: None
    anti-rat IgG
    suggested: (Cell Signaling Technology Cat# 7077, RRID:AB_10694715)
    Experimental Models: Cell Lines
    SentencesResources
    Cell lines: HEK293T cells expressing human angiotensin I-converting enzyme 2 (HEK293T-hACE2) were kindly provided by Dr. Jesse Bloom (Fred Hutchinson Cancer Research Center, Seattle, USA) (51).
    HEK293T
    suggested: None
    Lenti-X 293T cell line was purchased from Takara Bio USA Inc. (San Jose, CA).
    293T
    suggested: CCLV Cat# CCLV-RIE 1018, RRID:CVCL_0063)
    After 1 hr incubation, the cellulose paper treated pseudovirus was gently transferred to transfect HEK293T-hACE2 cells with 80% confluency, followed by adding polybrene to a final concentration of 8 μg/ml.
    HEK293T-hACE2
    suggested: RRID:CVCL_A7UK)
    Recombinant DNA
    SentencesResources
    Plasmids construction, protein expression and purification: Ty1 variants, including Ty1-CBD and control protein Ty1 without CBD module, were cloned into pSH200 vector (a generous gift from Prof. Xiling Shen at Duke University) containing 6 x Histidine tag (His-tag), between BamHI and XbaI sites.
    pSH200
    suggested: None
    Software and Algorithms
    SentencesResources
    Detergent compatible (DC) protein assay kit was bought from Bio-Rad Laboratories (Hercules, CA).
    Bio-Rad Laboratories
    suggested: (Bio-Rad Laboratories, RRID:SCR_008426)
    After the final wash, the cells were resuspended in 200 μL FACS buffer (5% FBS, 2mM EDTA, 0.1% sodium azide in PBS) for flow cytometric analysis in Attune™ NxT Flow Cytometer (Thermofisher) and data were analyzed by FlowJo (Franklin Lakes, NJ).
    FlowJo
    suggested: (FlowJo, RRID:SCR_008520)
    Statistical analysis: Statistical significance was evaluated using one-way ANOVA followed by Tukey post hoc test using GraphPad PRISM (San Diego, CA, USA).
    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: We detected the following sentences addressing limitations in the study:
    Despite the promises demonstrated in this study, one limitation is that only pseudovirus-containing culture media were used to characterize the fusion proteins for proof-of-concept. Therefore, it is necessary to further evaluate our approach in real specimens such as blood from COVID-19 patients in the near future.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on page 32. 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.

    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 10.1101/2021.09.01.458653v1 on bioRxiv