Confirming Multiplex RT-qPCR Use in COVID-19 with Next-Generation Sequencing: Strategies for Epidemiological Advantage. (30th July 2022)

• Record Type: Journal Article
• Authors: Carpenter, Rob E.; Tamrakar, Vaibhav; Chahar, Harendra; Vine, Tyler; Sharma, Rahul
• Other Names: Mboowa Gerald Academic Editor.
• Is Part Of: Global health, epidemiology and genomics. Volume 2022(2022)
• Publication Date: 2022-07-30
• Subjects: World health -- Periodicals; Genomics -- Periodicals; Medical policy -- Periodicals; Epidemiology -- Periodicals; Global Health; Epidemiology; Genomics; Periodicals; Periodicals; Electronic journals; 362.1
• DOI: 10.1155/2022/2270965
• Languages: English
• ISSNs: 2054-4200

Abstract

Abstract : Rapid identification and tracking of emerging SARS-CoV-2 variants are critical for understanding the transmission dynamics and developing strategies for interrupting the transmission chain. Next-Generation Sequencing (NGS) is an exceptional tool for whole-genome analysis and deciphering new mutations. The technique has been instrumental in identifying the variants of concern (VOC) and tracking this pandemic. However, NGS is complex and expensive for large-scale adoption, and epidemiological monitoring with NGS alone could be unattainable in limited-resource settings. In this study, we explored the application of RT-qPCR-based detection of the variant identified by NGS. We analyzed a total of 78 deidentified samples that screened positive for SARS-CoV-2 from two timeframes, August 2020 and July 2021. All 78 samples were classified into WHO lineages by whole-genome sequencing and then compared with two commercially available RT-qPCR assays for spike protein mutation(s). The data showed good concordance between RT-qPCR and NGS analysis for specific SARS-CoV-2 lineages and characteristic mutations. RT-qPCR assays are quick and cost-effective and thus can be implemented in synergy with NGS for screening NGS-identified mutations of SARS-CoV-2 for clinical and epidemiological interest. Strategic use of NGS and RT-qPCR can offer several COVID-19 epidemiological advantages.