Performance study of a point-of-care antigen test during the SARS-CoV-2 Delta to Omicron variant transition in the USA

  1. Paul K Drain
  2. Gregory Chiklis
  3. Poppy Guest
  4. Nigel M Lindner
  5. Jayne E Ellis

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Abstract

Introduction

Concerns have been raised regarding the accuracy of diagnostic antigen testing for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant. We compared the performance of the LumiraDx SARS-CoV-2 Antigen Test between symptomatic participants recruited prospectively during the Delta to Omicron variant transition in the USA.

Methods

Two paired anterior nasal swabs were collected from each participant (adults and children) within 12 days of symptom onset between November 24 th , 2021 and February 1 st , 2022, during which time Omicron replaced Delta as the dominant variant in the sample population. Swabs were tested by the LumiraDx SARS-CoV-2 Antigen Test and compared using real-time polymerase chain reaction (RT-PCR) reference testing. Reference samples identified as positive were sequenced to identify the SARS-CoV-2 variant. Positive percent agreement (PPA) was calculated, with results stratified by RT-PCR cycle threshold (Ct).

Results

Of the 38 participants for whom LumiraDx SARS-CoV-2 Antigen Test results were available, 36 were confirmed positive by RT-PCR. Overall, PPA of the LumiraDx SARS-CoV-2 Antigen Test was 94.7% (95% confidence interval: 82.3%, 99.4%) and PPA was 100% for samples with a Ct <33. Sufficient viral load for sequencing was present in nine samples (six Delta, three Omicron), all of which returned a positive result using the LumiraDx SARS-CoV-2 Antigen Test. There were no performance differences observed between participants with the Delta and Omicron variants.

Conclusions

SARS-CoV-2 differences between Delta and Omicron variant mutations did not affect the performance of the LumiraDx SARS-CoV-2 Antigen Test which detects the nucleocapsid protein antigen. The LumiraDx SARS-CoV-2 Antigen Test can be a useful antigen test to diagnose emerging variants of coronavirus disease 2019.

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  1. ScreenIT

    SciScore for 10.1101/2022.05.11.22274962: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: The study received ethical approval from the Diagnostics Investigational Review Board (IRB project #1021-14).
    Consent: All participants, or parents or guardians of minor participants, provided informed consent.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    No key resources detected.

    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:
    A limitation of this study was that not all of the collected samples could be sequenced, due to a minimal viral load requirement for sequencing; samples with a Ct>28 could not be sequenced. Of the collected samples, only 23% contained sufficient sample for sequencing. However, during the period of testing, Omicron replaced Delta as the dominant SARS-CoV-2 variant in the state of Massachusetts[15]. State-wide, Omicron accounted for only 1% of sequenced SARS-CoV-2 samples in the week commencing November 29th, 2021. However, this increased to 99% of sequenced cases in the week commencing January 10th, 2022 [15]. Figure 2 highlights the shift in SARS-CoV-2 variant dominance from Delta to Omicron over time, indicating that the tested samples were a mixture of the two variants (Figure 2), as confirmed by the sequenced samples.

    Results from TrialIdentifier: We found the following clinical trial numbers in your paper:

    IdentifierStatusTitle
    NCT04557046RecruitingPerformance Evaluation of LumiraDx COVID-19 (SARS-CoV-2) Ag …

    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 10.1101/2022.05.11.22274962v1 on medRxiv