Implementation of an efficient SARS-CoV-2 specimen pooling strategy for high throughput diagnostic testing.

Area of Science:

• Virology
• Epidemiology
• Biotechnology

Background:

• Controlling SARS-CoV-2 spread requires rapid identification of infected individuals.
• Frequent testing is crucial for early detection, especially in asymptomatic cases, to intercept transmission.
• RT-PCR, the gold standard for SARS-CoV-2 diagnosis, is costly, limiting widespread application.

Purpose of the Study:

• To evaluate hypercube sample pooling strategies for cost-effective SARS-CoV-2 detection.
• To assess the reliability and sensitivity of pooled RT-PCR testing for a professional sports team.
• To automate the sample pooling process for efficient large-scale testing.

Main Methods:

• Implementation of 3-D and 4-D hypercube pooling strategies for sample collection.
• RT-PCR testing of pooled samples from a professional sports team in South Africa.
• Automation of sample pooling using a liquid-handling robot and a web interface.

Main Results:

• Reliable detection of infected samples within groups of 27 and 81 individuals.
• Minimal loss of assay sensitivity for samples with individual Ct values up to 32.
• Successful automation of the sample pooling and positive sample identification process.

Conclusions:

• Hypercube pooling offers a reliable and cost-effective method for RT-PCR detection of SARS-CoV-2.
• This approach significantly reduces costs compared to individual testing and lateral flow antigen tests.
• Automated hypercube pooling facilitates efficient mass testing strategies for infectious disease control.