Optimizing and evaluating PCR-based pooled screening during COVID-19 pandemics

Abstract

Population screening played a substantial role in safely reopening the economy and avoiding new outbreaks of COVID-19. PCR-based pooled screening makes it possible to test the population with limited resources by pooling multiple individual samples. Our study compared different population-wide screening methods as transmission-mitigating interventions, including pooled PCR, individual PCR, and antigen screening. Incorporating testing-isolation process and individual-level viral load trajectories into an epidemic model, we further studied the impacts of testing-isolation on test sensitivities. Results show that the testing-isolation process could maintain a stable test sensitivity during the outbreak by removing most infected individuals, especially during the epidemic decline. Moreover, we compared the efficiency, accuracy, and cost of different screening methods during the pandemic. Our results show that PCR-based pooled screening is cost-effective in reversing the pandemic at low prevalence. When the prevalence is high, PCR-based pooled screening may not stop the outbreak. In contrast, antigen screening with sufficient frequency could reverse the epidemic, despite the high cost and the large numbers of false positives in the screening process.

Taking a step back from testing: Preanalytical considerations in molecular infectious disease diagnostics

“…Although sample pooling is common for blood banks, this was an adaptive solution to meet the exponential demands for testing with unreliable access to resources. There are a number of downsides to sample pooling for a prevalent infectious disease: 1) the possibility of false negative results due to diluted samples [108] ; and, 2) increased TAT when individual samples from a pool must be re-run to confirm presence of infection.…”

Projections of the transmission of the Omicron variant for Toronto, Ontario, and Canada using surveillance data following recent changes in testing policies

“…The easy availability of cheap rapid test kits can help to maintain hospitalization caps under critical level ( Grundel et al, 2022 ). Studies have shown that antigen screening with sufficient frequency could reverse the epidemic, while PCR-based pooled screening may not stop the outbreak ( Smith et al, 2022 ; Yu et al, 2021 ). However, all the available studies look at the implementation of a single type of test.…”

Practical considerations to establish a validated platform for pooled detection of SARS-CoV-2 by droplet digital PCR

“…Practical experience shows that countries that carried out massive testing campaigns were the most effective in controlling the pandemic [13]. Therefore, pool testing has become an appealing method that has been explored by many laboratories using RT-qPCR [13][14][15][16][17][18][19][20][21][22][23][24].…”

“…Even when it possesses several advantages (it is cost-effective at low prevalence of the virus [15] and expands screening capacities [21]), pool testing by RT-qPCR also presents limitations like low sensitivity due to dilution effect [15] and inhibitions [16] associated to this method. Both limitations could be circumvented by a third-generation PCR: the droplet digital PCR (ddPCR).…”