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

Area of Science:

• Virology
• Genomics
• Epidemiology

Background:

• Next-Generation Sequencing (NGS) is vital for tracking SARS-CoV-2 variants and mutations.
• NGS is complex and costly, limiting its use in resource-limited settings for widespread epidemiological monitoring.
• Effective strategies require rapid identification and tracking of emerging SARS-CoV-2 variants.

Purpose of the Study:

• To explore the application of RT-qPCR for detecting SARS-CoV-2 variants identified by NGS.
• To assess the concordance between RT-qPCR assays and whole-genome sequencing for specific mutations and lineages.
• To evaluate RT-qPCR as a complementary tool for epidemiological surveillance of SARS-CoV-2.

Main Methods:

• Analyzed 78 SARS-CoV-2 positive samples from August 2020 and July 2021.
• Classified all samples into WHO lineages using whole-genome sequencing (NGS).
• Compared NGS results with two commercial RT-qPCR assays targeting spike protein mutations.

Main Results:

• Demonstrated good concordance between RT-qPCR and NGS for specific SARS-CoV-2 lineages and mutations.
• RT-qPCR assays proved effective in identifying characteristic mutations.
• The study confirmed the utility of RT-qPCR in detecting variants identified by NGS.

Conclusions:

• RT-qPCR assays are quick, cost-effective, and suitable for screening NGS-identified SARS-CoV-2 mutations.
• Integrating RT-qPCR with NGS enhances clinical and epidemiological surveillance capabilities.
• Strategic use of both NGS and RT-qPCR offers significant advantages for COVID-19 epidemiological monitoring.