Abstract
Background
The genomic surveillance of SARS-CoV-2 is challenging in high-volume, resource-limited settings. Faster and less expensive methods are required for the prompt detection of variants of interest. This study aimed to validate and implement the TaqMAMA RT-PCR method for the detection of SARS-CoV-2 variants.
Methods
We developed the TaqMAMA RT-PCR method for SARS-CoV-2 variants. From the viral genomes obtained from the GISAID database, fluorescent amplification probes and oligonucleotides were designed to detect two specific mutations for each variant. The study consisted of an assay validation phase comparing the newly designed method to WGS in COVID-19-positive samples, followed by a large-scale implementation phase to calculate its performance.
Results
During the assay validation phase, we included 232 samples for analysis using TaqMAMA and WGS. TaqMAMA identified 82.3% as positive, and had sensitivities of 82%, 100%, and 50%, specificities of 91%, 99%, and 100%, with PPVs of 99%, 75%, and 100%, and NPVs of 20%, 100%, and 100% for the Delta, Alpha, and Gamma variants, respectively. For the implementation phase, we included 1315 samples, TaqMAMA identified 68% positive samples, 97.5% as delta. The predicted performance using Bayesian statistics was 95%, 55%, and 0% for the positive, and 29%, 0%, and < 1% for the negative delta, alpha, and gamma variants, respectively.
Conclusions
The diagnostic performance of TaqMAMA RT-PCR was acceptable for the detection of the most prevalent SARS-CoV-2 variants of interest. This method offers a cost and time-saving alternative for the genomic surveillance of SARS-CoV-2 in high-volume settings.