Rapid and Flexible RT-qPCR Surveillance Platforms To Detect SARS-CoV-2 Mutations.

Area of Science:

• Virology
• Molecular Biology
• Public Health

Background:

• Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) possess multiple mutations enhancing transmission, severity, and immune evasion.
• Specific mutations (ΔH69/V70, L452R, E484K, N501Y) in the spike glycoprotein are crucial for identifying VOCs.

Purpose of the Study:

• To develop and validate flexible reverse transcription-quantitative PCR (RT-qPCR) platforms for detecting SARS-CoV-2 VOCs based on mutational signatures.
• To provide adaptable screening tools for both small and large-scale variant detection, complementing whole-genome sequencing (WGS).

Main Methods:

• Development of two RT-qPCR platforms: one for small-scale and one for large-scale screening of SARS-CoV-2 mutations.
• Validation of the large-scale platform through pairwise matching with whole-genome sequencing (WGS) data to assess specificity and sensitivity.

Main Results:

• The large-scale RT-qPCR platform demonstrated high specificity and sensitivity when compared to WGS.
• Both developed RT-qPCR platforms effectively detect key mutations associated with SARS-CoV-2 VOCs.
• The mutational signature approach was successfully implemented in the Danish public health system.

Conclusions:

• The developed RT-qPCR platforms are valuable tools for the rapid detection and surveillance of SARS-CoV-2 VOCs.
• These platforms complement WGS, offering flexibility for laboratories with varying infrastructure.
• The mutational signature strategy aids in controlling SARS-CoV-2 outbreaks and managing public health crises.