Confirming Multiplex RT-qPCR Use in COVID-19 with Next-Generation Sequencing: Strategies for Epidemiological Advantage
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 mutation...
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| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2022-01-01
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| Series: | Global Health, Epidemiology and Genomics |
| Online Access: | http://dx.doi.org/10.1155/2022/2270965 |
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| author | Rob E. Carpenter Vaibhav Tamrakar Harendra Chahar Tyler Vine Rahul Sharma |
| author_facet | Rob E. Carpenter Vaibhav Tamrakar Harendra Chahar Tyler Vine Rahul Sharma |
| author_sort | Rob E. Carpenter |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-88705d6512da433f8310e69cec85184b |
| institution | Kabale University |
| issn | 2054-4200 |
| language | English |
| publishDate | 2022-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | Global Health, Epidemiology and Genomics |
| spelling | doaj-art-88705d6512da433f8310e69cec85184b2025-02-03T05:49:24ZengWileyGlobal Health, Epidemiology and Genomics2054-42002022-01-01202210.1155/2022/2270965Confirming Multiplex RT-qPCR Use in COVID-19 with Next-Generation Sequencing: Strategies for Epidemiological AdvantageRob E. Carpenter0Vaibhav Tamrakar1Harendra Chahar2Tyler Vine3Rahul Sharma4Advanta GeneticsICMR-National Institute of Research in Tribal HealthRetroBioTech LLCAdvanta GeneticsAdvanta GeneticsRapid 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.http://dx.doi.org/10.1155/2022/2270965 |
| spellingShingle | Rob E. Carpenter Vaibhav Tamrakar Harendra Chahar Tyler Vine Rahul Sharma Confirming Multiplex RT-qPCR Use in COVID-19 with Next-Generation Sequencing: Strategies for Epidemiological Advantage Global Health, Epidemiology and Genomics |
| title | Confirming Multiplex RT-qPCR Use in COVID-19 with Next-Generation Sequencing: Strategies for Epidemiological Advantage |
| title_full | Confirming Multiplex RT-qPCR Use in COVID-19 with Next-Generation Sequencing: Strategies for Epidemiological Advantage |
| title_fullStr | Confirming Multiplex RT-qPCR Use in COVID-19 with Next-Generation Sequencing: Strategies for Epidemiological Advantage |
| title_full_unstemmed | Confirming Multiplex RT-qPCR Use in COVID-19 with Next-Generation Sequencing: Strategies for Epidemiological Advantage |
| title_short | Confirming Multiplex RT-qPCR Use in COVID-19 with Next-Generation Sequencing: Strategies for Epidemiological Advantage |
| title_sort | confirming multiplex rt qpcr use in covid 19 with next generation sequencing strategies for epidemiological advantage |
| url | http://dx.doi.org/10.1155/2022/2270965 |
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