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 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 9 th 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.

Background / Aim: Since the emergence of the severe acute respiratory syndrome-coronavirus-2 (SARS-COV-2) pandemic in Wuhan, China, several efforts are being focused on the development of fast and reliable diagnostic molecular tests. Real-time polymerase chain reaction (RT-PCR) based assay on respiratory specimens was recommended by the World Health Organization as the gold standard for early diagnosis of infection spread. Our study aimed to compare the analytical performance of seven commercially available RT-PCR assays. Materials and Methods: A total of 33 nasopharyngeal swabs were analyzed by: Da An, PerkinElmer, Norgen, Prestige, PhoenixDX, Bio-Speedy, and Xpert Xpress RT-PCR assays. Sensitivity and detection rates of SARS-COV-2 target genes were analyzed. Results: Da An and Xpert Xpress assays showed the highest detection rate and percentage for SARS-COV-2 target genes; (16/33) 48.5%, followed by PerkinElmer and Norgen kits (13/33) 39.4%, (10/33) 30.3%, respectively. However, Prestige, PhoenixDx, and Bio-speedy displayed the same performance (6/33) 18.2%. Conclusion: The analyzed assays showed inconsistent analytical performance. Overall, findings reported in our study may not be applicable to other RT-PCR assays or thermocyclers; analytical sensitivities and positive-negative cut-off values should be locally validated.

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