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Boosting SARS-CoV-2 detection combining pooling and multiplex strategies
Isadora Alonso Correa1,2, Tamires de Souza Rodrigues3,4, Alex Queiroz3,4
1Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-617, Brazil.
Scientific Reports
|May 23, 2022
Summary
Pooling samples for reverse transcription quantitative polymerase chain reaction (RT-qPCR) significantly increases SARS-CoV-2 testing capacity and reduces costs. This strategy maintains high test sensitivity, crucial for managing new variants and large populations.
Area of Science:
- Molecular Biology
- Virology
- Public Health
Background:
- Reverse transcription quantitative polymerase chain reaction (RT-qPCR) is the standard for SARS-CoV-2 detection but faces challenges with long turnaround times and high costs.
- Increased demand for SARS-CoV-2 testing, particularly for monitoring vaccinated populations against emerging variants, necessitates strategies for enhanced capacity and cost-efficiency.
Purpose of the Study:
- To evaluate the feasibility and effectiveness of RT-qPCR sample pooling strategies for SARS-CoV-2 detection.
- To assess the impact of pooling on test sensitivity, cost savings, and overall testing capacity.
Main Methods:
- In-silico statistical modeling and validation using specimen samples from a mass testing program.
- Evaluation of RT-qPCR pooling in simplex and multiplex assays with varying pool sizes (up to 32 samples).
- Analysis of cost savings and reagent consumption associated with pooling strategies.
Main Results:
- High test sensitivity was maintained when pooling up to 16 or 8 samples in simplex assays.
- Pooling 4 or 8 samples in a triplex RT-qPCR assay (targeting N and E genes) was feasible without sensitivity loss.
- A cost saving of 51.5% was achieved in a mass testing program, even accounting for individual pool re-testing.
Conclusions:
- RT-qPCR pooling, especially in multiplex assays, offers a viable strategy for cost-effective mass SARS-CoV-2 testing.
- This approach significantly increases testing capacity and reduces reagent consumption, aiding in pandemic control.
- Pooling strategies are essential for managing high testing demands and monitoring viral spread effectively.
