Characterizing SARS-CoV-2 Omicron Variants

Nasopharyngeal sites were swabbed from 150 consecutive outpatients presenting to the CoVID-19 Triage and Test Center at UHB for SCoV2 specific NAT testing from January 25^th to February 28^th 2022 (6 (link)). Swabs were collected in universal transport medium (UTM; Copan; Brescia, Italy), and analyzed using the cobas SARS-CoV-2 test on the cobas6800 platform (Roche) as described (3 (link)). Cobas SARS-CoV-2 Target 1 (ORF1a/b) Ct-values were used to assess RAT performance. Omicron BA.1 was confirmed in the 100 SCoV2-positive nasopharyngeal swabs. As Omicron BA.2 and BA.5 harbor the additional nucleocapsid mutation S413R, we obtained 100 Omicron BA.2 and 100 Omicron BA.5 positive nasopharyngeal swabs from consecutive outpatients at UHB from March 8 to July 15, 2022.

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Leuzinger K., Roloff T., Egli A, & Hirsch H.H. (2022). Impact of SARS-CoV-2 Omicron on Rapid Antigen Testing Developed for Early-Pandemic SARS-CoV-2 Variants. Microbiology Spectrum, 10(4), e02006-22.

Publication 2022

cobas6800 platform

Covid 19 Mutation Nasopharyngeal Nucleocapsid Outpatients Sars cov 1 Sars cov 2

Corresponding Organization : University of Basel

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Variable analysis

independent variables

Type of SARS-CoV-2 variant (Omicron BA.1, Omicron BA.2, Omicron BA.5)

dependent variables

Cobas SARS-CoV-2 Target 1 (ORF1a/b) Ct-values

control variables

Nasopharyngeal swab collection method
Universal transport medium (UTM) used for swab collection
Cobas SARS-CoV-2 test on the cobas6800 platform (Roche) for analysis

positive controls

100 Omicron BA.1 positive nasopharyngeal swabs
100 Omicron BA.2 positive nasopharyngeal swabs
100 Omicron BA.5 positive nasopharyngeal swabs

negative controls

Not explicitly mentioned

Annotations

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