SARS-CoV-2 variants genotyping and diagnostic performance of a 2-genes detection assay

Cyrus Matheka, Aga Khan University
Joshua Kilonzo, Aga Khan University
Ephantus Mbugua, Aga Khan University
Zubair Munshi, Aga Khan University
Justin Nyasinga, Aga Khan University
Revathi Gunturu, Aga Khan University
Allan Njau, Aga Khan University


Background: The emergence of the COVID-19 pandemic resulted in the unprecedented expansion of molecular testing technologies. This study aimed at evaluating the performance of the FluoroType® SARS-CoV-2 plus assay for SARS-CoV-2 detection as well as describing the detection of SARS-CoV-2 variants using the FluoroType® SARS- CoV-2 varID Q kit.

Methods: The study utilized 679 archived nasopharyngeal samples. Analytical performance and the diagnostic performance of the FluoroType® SARS-CoV-2 plus assay were determined using 320 samples and reference material. Variants identification on the FluoroType® SARS-CoV-2 varID Q assay was performed on 359 samples. The study was approved by the Aga Khan University Hospital Institutional Review Board.

Results: The FluoroType® SARS-CoV-2 plus assay’s limit of detection was verified as 1.2 copies/μL. The repeatability SD and %CV were 2.45 and 9.8% while reproducibility had an SD and %CV of 1.39 and 5.68%, respectively, for the RdRP gene. The positive and negative percent agreement were determined to be 99.4% (95% CI; 98.1%–100%) and 99.4% (95% CI; 98.2%–100%) respectively. In the variants identification, samples from the original wave had no mutations identified while 12.3%, 49%, and more than 90% of the samples during the Alpha, Delta, and Omicron waves, respectively, had detectable mutations.

Conclusions: The FluoroType® SARS-CoV-2 plus assay demonstrated analytical performance comparable to the reference method with a diagnostic sensitivity and specificity of >99%. The FluoroType® SARS-CoV-2 varID Q assay achieved rapid detection of circulating variants.