RT-qPCR Based SARS-CoV-2 Variants of Concern (VOC) Testing

This project bridges gaps in genomic surveillance by leveraging commercially available RT-qPCR assays as a rapid, cost-effective solution for SARS-CoV-2 VOC screening.

Schematic showing the study workflow and project sites.

RT-qPCR-Based SARS-CoV-2 Variants of Concern (VOC) Screening in Africa

The Africa CDC, through its Pathogen Genomics Initiative, launched a pilot project to enhance the surveillance of SARS-CoV-2 variants of concern (VOCs) across six African Union member states. This initiative addresses the urgent need for rapid, cost-effective methods to complement whole-genome sequencing (WGS) for tracking and monitoring SARS-CoV-2 VOCs.

Project Overview

The project leverages the Thermo Fisher TaqMan SARS-CoV-2 Mutation Panel Molecular Genotyping Assay to rapidly detect and genotype SARS-CoV-2 VOCs. The six participating countries—Morocco, Senegal, Kenya, Gabon, Namibia, and Sierra Leone—were selected based on their existing WGS capacity, molecular diagnostics infrastructure, and the prevalence of SARS-CoV-2 cases.

The study will utilize nasopharyngeal and oropharyngeal samples collected by the National Public Health Institutes (NPHIs) of each country. Positive samples with a cycle threshold (Ct) value ≤30 will undergo genotyping to identify SARS-CoV-2 mutations.

Objectives

      🔹 **Primary Objective:**  
         Demonstrate the feasibility of deploying the commercial TaqMan genotyping assay for VOC detection  
         in routine surveillance.  

      🔹 **Secondary Objective:**  
         Document the prevalence of circulating VOCs in the participating member states in Africa.

Outcomes This project aims to enhance Africa's capacity to detect and monitor SARS-CoV-2 VOCs efficiently, addressing the current challenges of limited genomic surveillance in the region. By complementing WGS efforts, this initiative will inform public health strategies and support the control of COVID-19 in Africa. By pioneering scalable solutions, the project highlights the importance of regional collaboration and innovation in genomic surveillance amidst ongoing public health challenges.