Performance Evaluation of the SAMBA II SARS-CoV-2 Test for Point-of-Care Detection of SARS-CoV-2

  1. Sonny M. Assennato
  2. Allyson V. Ritchie
  3. Cesar Nadala
  4. Neha Goel
  5. Cuijuan Tie
  6. Lourdes M. Nadala
  7. Hongyi Zhang
  8. Rawlings Datir
  9. Ravindra K. Gupta
  10. Martin D. Curran
  11. Helen H. Lee

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Abstract

Nucleic acid amplification for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in respiratory samples is the standard method for diagnosis. The majority of this testing is centralized and therefore has turnaround times of several days. Point-of-care (POC) testing with rapid turnaround times would allow more effective triage in settings where patient management and infection control decisions need to be made rapidly. The inclusivity and specificity of the Simple AMplification-Based Assay (SAMBA) II SARS-CoV-2 test were determined by both in silico analyses of the primers and probes and wet testing.

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  1. Version published to 10.1128/jcm.01262-20
  2. ScreenIT

    SciScore for 10.1101/2020.05.24.20100990: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Single round of VSV-G pseudotyped lentiviruses were produced by transfecting HEK-293T cells in a 3-plasmid transfection system (HIV Gag-pol expresser under a CMV promoter, luciferase genome reporter and VSV-g envelope) as previously described [14].
    HEK-293T
    suggested: None
    Software and Algorithms
    SentencesResources
    Virus inactivation in SAMBA SCoV
    SAMBA
    suggested: (Samba, RRID:SCR_006557)
    In silico inclusivity analysis: The SAMBA-SARS-CoV-2 primers and probes for Orf1ab and N regions were individually evaluated using in-silico analysis with respect to 157 SARS-CoV-2 sequences in the NCBI database.
    NCBI
    suggested: (NCBI, RRID:SCR_006472)

    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:
    Potential limitations of this study include that the virus inactivation study was carried out using a constructed pseudovirus rather than a SARS-CoV-2 or other coronavirus due to availability. Also clinical samples were collected in VTM and diluted 1:2 in SCoV buffer rather than collected directly into SCoV buffer, which may affect the sensitivity.

    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

    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 10.1101/2020.05.24.20100990 on medRxiv