Variant-specific RT-qPCR for rapid screening of B.1.617 mutations in SARS-CoV-2

Abstract

The continuous emergence of new SARS-CoV-2 variants required rapid and reliable diagnostic methods for early detection and monitoring of the  spread of the virus, especially in lowresource countries where whole genome sequencing is not available. We aimed to evaluate and compare the  performance of two different RT-qPCR screening assays for the detection of B.1.617 lineage mutations. A total of 85 SARS-CoV-2 positive samples  were collected between 9th August and 10 September 2021 and screened by two mutation-specific RT-qPCR assays for simultaneous detection of  B.1.617.1 and B.1.617.2 lineage mutations. VIASURE Variant II PCR assay identified 2 Delta variant-specific mutations (L452R, and P681 R) in 80% of  tested samples, while the PKamp™ Variant Detect™ assay was only able to detect one Delta variant specific mutation (L452R) in 75% of tested  samples. This is the first report to show the Delta variant as the cause of the third wave in Libya. The use of multiplex RT-qPCR assays has allowed  the identification of new variants for rapid screening. However, RT-qPCR results should be confirmed by whole genome sequencing of SARS-COV-2.