Saliva swabs are the preferred sample for Omicron detection
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Abstract
The Omicron variant is characterised by more than 50 distinct mutations, the majority of which are located in the spike protein. The implications of these mutations for disease transmission, tissue tropism and diagnostic testing are still to be determined. We evaluated the relative performance of saliva and mid-turbinate swabs as RT-PCR samples for the Delta and Omicron variants. The positive percent agreement (PPA) of saliva swabs and mid-turbinate swabs to a composite standard was 71% (95% CI: 53-84%) and 100% (95% CI: 89-100%), respectively, for the Delta variant. However, for the Omicron variant saliva and mid-turbinate swabs had a 100% (95% CI: 90-100%) and 86% (95% CI: 71-94%) PPA, respectively. This finding supports ex-vivo data of altered tissue tropism from other labs for the Omicron variant. Reassessment of the diagnostic testing standard-of-care may be required as the Omicron variant become the dominant variant worldwide.
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SciScore for 10.1101/2021.12.22.21268246: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources The assays in used by this laboratory during the study period were the Allplex™ 2019-nCoV assay (Seegene, South Korea) (n=343), the Abbott RealTime SARS-CoV-2 assay (Abbott Laboratories, USA) (n=7) and the Abbott Alinity m SARS-CoV-2 assay (Abbott Laboratories, USA) (n=32). Abbott Laboratoriessuggested: NoneThe Abbott assay were run as per kit package inserts and subject to the operational requirements of a South African National Accreditation System (SANAS) accredited diagnostic virology laboratory. Abbottsu…SciScore for 10.1101/2021.12.22.21268246: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics not detected. Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources The assays in used by this laboratory during the study period were the Allplex™ 2019-nCoV assay (Seegene, South Korea) (n=343), the Abbott RealTime SARS-CoV-2 assay (Abbott Laboratories, USA) (n=7) and the Abbott Alinity m SARS-CoV-2 assay (Abbott Laboratories, USA) (n=32). Abbott Laboratoriessuggested: NoneThe Abbott assay were run as per kit package inserts and subject to the operational requirements of a South African National Accreditation System (SANAS) accredited diagnostic virology laboratory. Abbottsuggested: (Abbott, RRID:SCR_010477)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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.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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