Evaluation of the ID NOW among symptomatic individuals during the Omicron wave

  1. William Stokes
  2. Allison A. Venner
  3. Emily Buss
  4. Graham Tipples
  5. Byron M. Berenger

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Abstract

Introduction. Starting in December, 2020, the ID NOW was implemented throughout the province of Alberta, Canada (population 4.4 million) in various settings.

Gap statement. ID NOW’s test performance with SARS-CoV-2 Omicron variant BA.1 is unknown.

Aim. To assess the ID NOW performance among symptomatic individuals during the BA.1 Omicron wave and compare it to previous SARS-CoV-2 variant waves.

Methodology. The ID NOW was assessed in two locations among symptomatic individuals: rural hospitals and community assessment centres (AC) during the period 5–18 January 2022. Starting 5 January, Omicron represented >95 % of variants detected in our population. For every individual tested, two swabs were collected: one for ID NOW testing and the other for either reverse-transcriptase polymerase chain reaction (RT-PCR) confirmation of negative ID NOW results or for variant testing of positive ID NOW results.

Results. A total of 3041 paired samples were analysed (1139 RT-PCR positive). From this, 1873 samples were from 42 COVID-19 AC and 1168 from 69 rural hospitals. ID NOW sensitivity for symptomatic individuals presenting to community AC and rural hospitals was 96.0 % [95 % confidence interval (CI) 94.5–97.3 %, n =830 RT-PCR positive], and 91.6 % (95 % CI 87.9–94.4 %, n =309 RT-PCR positive), respectively. SARS-CoV-2 positivity rate was very high for both populations (44.3 % at AC, 26.5 % in hospital).

Conclusions. Sensitivity of ID NOW SARS-CoV-2, compared to RT-PCR, is very high during the BA.1 Omicron wave, and is significantly higher when compared to previous SARS-CoV-2 variant waves.

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  1. Version published to 10.1099/jmm.0.001669 on Access Microbiology
  2. ScreenIT

    SciScore for 10.1101/2022.05.19.22275316: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: The University of Alberta Research Ethics board approved this study (Pro00111835).
    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:
    Our study had several limitations. Due to the heterogeneity of our populations tested, it is difficult to exclude confounders that may have contributed to ID NOW performance. However, we previously observed no differences in sensitivity based on common patient, collecting and testing characteristics, including age, gender, and swab type.2 Our current study also did not demonstrate any difference in performance with these characteristics, though the sample size was not large enough to make any concrete conclusions. Another limitation is the inability to exclusively study Omicron by itself. While the Delta variant only represented 0.7% of variants detected from the assessment centres during our study period, there was still a moderately high proportion (14.5%) of delta variant still circulating within our hospitals. This study did not assess the Omicron BA.2 sublineage, as it was not circulating in our population during the study period. Other limitations include missing parallel RT-PCR results that could affect the sensitivity observed in our study. As previously mentioned, many (45.5%) ID NOW positive samples did not undergo variant testing which would affect our calculated specificity. ID NOW sensitivity may be slightly lower than we calculated due to the exclusion of 398 ID NOW negative samples that subsequently did not have a second sample tested with RT-PCR. Reasons behind missing parallel RT-PCR are multifactorial and include sample lost or discarded prior to testing, te...

    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.

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  3. Version published to 10.1101/2022.05.19.22275316v1 on medRxiv