Confirming Multiplex RT-qPCR Use in COVID-19 with Next-Generation Sequencing: Strategies for Epidemiological Advantage

Conclusion:  There are two important takeaways from this study. First, the NGS data provided further evidence of the rapid evolution of SARS-CoV-2 lineages including the highly transmissible Delta variant in the East Texas region and suggests the continued threat of COVID-19. This finding is consistent with other research and further supports the need for rapid, cost-effective monitoring of variant mutations. Second, the current study endorses the potential of RT-qPCR assays as a solution for more accessible variant monitoring. )e data showed concordance with RT-qPCR and NGS analysis for specific SARS-CoV-2 lineages and characteristic mutations. Thus, the deployment of RT-qPCR testing for the detection of known SARS-CoV-2 variants may be extremely beneficial. 

The key difference between the NGS and RT-qPCR is discovery power, scalability, and throughput. Both technologies are reliable and highly sensitive. RT-qPCR can detect only known sequences with help of specific probes and primers. In contrast, NGS does not need prior information about the sequence, but NGS is less cost-effective for low target numbers and is a time-consuming method. NGS can detect thousands of targeted regions with single-base resolution. RT-qPCR is cost-effective, and its familiar workflow made the detection of a limited set of variants and low target numbers easy [34]. Accordingly, is it suggested that RT-qPCR is a quick and cost-effective alternative to sequencing for screening known mutations of SARS-CoV-2 for clinical and epidemiological interest, especially in developing countries where COVID-19 diagnostic centers are limited by regional sequencing laboratories for screening the mutations in the SARS-CoV-2 clinical samples. )e findings in this study depict great potential for RT-qPCR to be an effective strategy offering several epidemiological advantages.