Performance of antigenic detection of SARS-CoV-2 in nasopharyngeal samples

  1. Catalina Lunca
  2. Cristian Cojocaru
  3. Irina Luciana Gurzu
  4. Florin Dumitru Petrariu
  5. Elena Cojocaru

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Abstract

Objectives

SARS-CoV-2 virus detection on nasopharyngeal specimens to infected individuals has become a challenge for the COVID-19 pandemic outbreak. We aim at comparing the performance of antigenic detection of SARS-CoV-2 in nasopharyngeal samples via an immunochromatographic method to molecular detection via qRT-PCR.

Materials and Methods

47 nasopharyngeal exudates were collected from suspicious COVID-19 cases. The samples were performed both via the qualitative immuno-chromatographic method for S protein detection in the SARS-CoV-2 structure, using fluorescent labelled anti-protein S antibodies and via qRT-PCR test for the qualitative detection of the screening gene E and the specific ORF1ab region of the RNA-SARS-CoV-2.

Results

There was a fair correlation between the positive antigen tests and the positive PCR assays measured through threshold cycle ORF1ab region (Ct orf). A better correlation was obtained between the antigen test results and the Ct orf when including patients with Ct orf below 25.

Conclusions

Using antigen tests as screening tests is useful on symptomatic persons during the viral replication period, therefore during the contagious period. A positive test shows a high predictive value for infection, while a negative antigen test result via immuno-chromatography must be confirmed by a qRT-PCR test.

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  1. ScreenIT

    SciScore for 10.1101/2021.07.12.21260263: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: Written informed consent and free choice were complied with, for both RT-PCR and antigen test in the same sample, as well as for this comparative study data collection.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line AuthenticationAuthentication: Samples that displayed an exponential growth curve and a cycle threshold value (Ct) <35 were considered positive, while no Ct value indicated a negative result (non-numeric value).

    Table 2: Resources

    Antibodies
    SentencesResources
    The test detected S protein in the SARS-CoV-2 structure using dye-labelled/fluorescent-labelled anti-protein S antibodies.
    anti-protein S
    suggested: None
    Software and Algorithms
    SentencesResources
    The gene E is present in all Sarbecovirus, including SARS-CoV-2.
    SARS-CoV-2
    suggested: (BioLegend Cat# 944703, RRID:AB_2890874)
    The MedCalc version 14.8.1 software was used for statistics.
    MedCalc
    suggested: (MedCalc, RRID:SCR_015044)

    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:
    Although this study provided evidence for using Fluorecare® SARS-CoV-2 Spike Protein Test Kit as antigen detection test, it has several limitations. A limitation could be generated by the lack of information related to the the time elapsed from the infectious contact and the performing of the test. Even the patients were tested immediately after symptoms onset, there could be a variable time between these moments. Another limitation is related to the antigenic test that was performed after unloading the collection buffer in the transport medium, but the inset kit allow the use of diluted sample in VTM. However, the results obtained are consistent in terms of specificity and sensitivity in patients with Ct ORF 25, the overall sensitivity was lower comparing with official data for this test. It could suggest that in cases with low viral load, the test is not sensitive.

    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 10.1101/2021.07.12.21260263v1 on medRxiv