SARS-CoV-2 variants detection using TaqMan SARS-CoV-2 mutation panel molecular (genotyping) assays

PURPOSE: For rapid detection and tracking of SARS-CoV-2, alternative method for screening in few hours is highly desirable. Here, we evaluated performance characteristics of TaqMan SARS-CoV-2 mutation panel genotyping molecular assay for detection of most common published SARS-CoV-2 variants using specific RT-PCR assays targeting single nucleotide polymorphisms (SNP). METHODS & MATERIALS: A total of 150 SARS-CoV-2 positive samples from March to July were included for this study. In addition, five controls comprised of synthetic RNA B.1.1.7_601443, B.1.351_678597, B.1.351_678597, P.1_792683, B.1.617.1_1662307 and MN908947.3-Wuhan-hu-1 from Twist bioscience and B.1.1.7 (England/204820464/2020) and B.1.351 (South Africa/KRISP-K005325/2020) from (Zeptometrix, NY, USA) were used for validation. RNA from all specimens were extracted using Omega Bio-Tek Mag-Bind Viral RNA Xpress Extraction Kit and tested for known SARS-CoV2 variants using ThermoFisher TaqMan SARS-CoV-2 mutation panel molecular assay on the Quant Studio 12K Flex. Nine representative samples have been compared with sequencing. Data were analyzed by genotype calling using QuantStudio(TM) design and analysis software v2.5 with the genotyping analysis module. RESULTS: All validation controls were tested in triplicate and repeated in singlet on three different days and all reported variants were matching as expected. Out of 150 SARS-CoV-2 positive specimens, 69 (46%) were B.1.617.2, 49 (32.7%) were B.1.1.7, P.1 and P.2 were 4 (2.7%) each and B.1.351 and B.1.427/B.1429 were 2 (1.3%) each. 3 (2%) were B.1.526, and 17 (11.3%) have mutation in D614G. Genotyping results from present study showing B.1.617.2, B.1.1.7 and B.1.526 variants and their mutation genes were concordance with sequencing results. CONCLUSION: Our study indicates that TaqMan SARS-CoV-2 mutation panel molecular (genotyping) assays detects and differentiate all published common variants B.1.617.2 (Delta), B.1.1.7 (Alpha), B.1.526 (Iota), B.1.351 (Beta), P.1 (Gamma), B.1.617.1 (Kappa) and B.1.427/ B.1.429 (Epsilon) that can be used for surveillance and epidemic control and prevention.