• Mwada Jallul, Khaled Ibrahim, Ahmed Zaghdani, Mohamed Musbah Abdusalam, Samira M Al Dwigen, Wafya S Atwair, Mohamed Elbasir, Inas Alhudiri, Salah Edin El Meshri, and Adam Elzagheid.
• Genetic Engineering Department, Libyan Biotechnology Research Center, Tripoli, Libya.
• Libyan J Med. 2022 Dec 1; 17 (1): 2121252.

AbstractThe 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 low-resource 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.

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