Performance and cost-effectiveness of a pooled testing strategy for SARS-CoV-2 using real-time polymerase chain reaction in Uganda

Bogere, Naghib; Bongomin, Felix; Katende, Andrew; Ssebambulidde, Kenneth; Ssengooba, Willy; Ssenfuka, Henry; Kigozi, Edgar; Biraro, Samuel; Kateete, David Patrick; Andia-Biraro, Irene

doi:10.1016/j.ijid.2021.10.038

Cited by 12 publications

(7 citation statements)

References 14 publications

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“…Diagnostic tests directly diagnose the presence of virus in nasal or throat swabs; therefore, diagnostic tests are sometimes referred to as direct tests. Diagnostic tests for COVID-19 can be further subdivided into two categories [21].…”

Section: Testing For Covid-19mentioning

confidence: 99%

Gauging the Impact of Artificial Intelligence and Mathematical Modeling in Response to the COVID-19 Pandemic: A Systematic Review

Hassan

Prasad

Rani

et al. 2022

BioMed Research International

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While the world continues to grapple with the devastating effects of the SARS-nCoV-2 virus, different scientific groups, including researchers from different parts of the world, are trying to collaborate to discover solutions to prevent the spread of the COVID-19 virus permanently. Henceforth, the current study envisions the analysis of predictive models that employ machine learning techniques and mathematical modeling to mitigate the spread of COVID-19. A systematic literature review (SLR) has been conducted, wherein a search into different databases, viz., PubMed and IEEE Explore, fetched 1178 records initially. From an initial of 1178 records, only 50 articles were analyzed completely. Around (64%) of the studies employed data-driven mathematical models, whereas only (26%) used machine learning models. Hybrid and ARIMA models constituted about (5%) and (3%) of the selected articles. Various Quality Evaluation Metrics (QEM), including accuracy, precision, specificity, sensitivity, Brier-score, F1-score, RMSE, AUC, and prediction and validation cohort, were used to gauge the effectiveness of the studied models. The study also considered the impact of Pfizer-BioNTech (BNT162b2), AstraZeneca (ChAd0x1), and Moderna (mRNA-1273) on Beta (B.1.1.7) and Delta (B.1.617.2) viral variants and the impact of administering booster doses given the evolution of viral variants of the virus.

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Section: Testing For Covid-19mentioning

confidence: 99%

Gauging the Impact of Artificial Intelligence and Mathematical Modeling in Response to the COVID-19 Pandemic: A Systematic Review

Hassan

Prasad

Rani

et al. 2022

BioMed Research International

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“…Fatalities are not explicitly included in the model, but will not have any significant effects provided the total fatality rate is low and/or any fatalities are promptly replaced from the general population. Finally, we note that the method presented can obviously be used in conjunction with pooling strategies, which, whenever sample taking logistics and infection prevalence allow (see for example [ 15 , 16 ]), permit increases in the total number of daily tests.…”

Section: Resultsmentioning

confidence: 99%

On an optimal testing strategy for workplace settings operating during the COVID-19 pandemic

Hernández

Valentinotti²

2022

PLoS ONE

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High quality daily testing for the presence of the SARS-CoV-2 in workplace settings has become part of the standard and mandatory protection measures implemented widely in response to the current pandemic. Such tests are often limited to a small fraction of the attending personnel due to cost considerations, limited availability and processing capabilities and the often cumbersome requirements of the test itself. A maximally efficient use of such an important and frequently scarce resource is clearly required. We here present an optimal testing strategy which minimises the presence of pre-symptomatic and asymptomatic infected members of the population in a workplace setting, derived under a series of simplifying statistical assumptions. These assumptions however, retain many of the generalities of the problem and yield robust results, as verified through a number of numerical simulations. We show that reduction in overall infected-person-days, IPD, by significant percentages can be achieved, for fixed numbers of tests per day of 5% and 10% of the population, of 30% and 50% in the IPD numbers, respectively.

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“…Despite this, in many countries turnaround times for PCR testing were very slow, both due to limited testing capacity and shortages of testing reagents. While some countries such as the USA, the UK, and Uganda authorized two-stage traditional pooled testing 7 – 9 , pooling was not widely used to increase testing capacity and reduce costs. To the best of our knowledge, Israel was the only country in the world to validate and authorize a combinatorial single-stage pooling method for clinical use, which among other factors allowed it to offer some of the highest testing capacity per-capita in the world 2 .…”

Section: Discussionmentioning

confidence: 99%

High capacity clinical SARS-CoV-2 molecular testing using combinatorial pooling

Zismanov,

Shalem,

Margolin-Miller

et al. 2024

Commun Med

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Background The SARS-CoV-2 pandemic led to unprecedented testing demands, causing major testing delays globally. One strategy used for increasing testing capacity was pooled-testing, using a two-stage technique first introduced during WWII. However, such traditional pooled testing was used in practice only when positivity rates were below 2%. Methods Here we report the development, validation and clinical application of P-BEST - a single-stage pooled-testing strategy that was approved for clinical use in Israel. Results P-BEST is clinically validated using 3636 side-by-side tests and is able to correctly detect all positive samples and accurately estimate their Ct value. Following regulatory approval by the Israeli Ministry of Health, P-BEST was used in 2021 to clinically test 837,138 samples using 270,095 PCR tests - a 3.1fold reduction in the number of tests. This period includes the Alpha and Delta waves, when positivity rates exceeded 10%, rendering traditional pooling non-practical. We also describe a tablet-based solution that allows performing manual single-stage pooling in settings where liquid dispensing robots are not available. Conclusions Our data provides a proof-of-concept for large-scale clinical implementation of single-stage pooled-testing for continuous surveillance of multiple pathogens with reduced test costs, and as an important tool for increasing testing efficiency during pandemic outbreaks.

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Performance and cost-effectiveness of a pooled testing strategy for SARS-CoV-2 using real-time polymerase chain reaction in Uganda

Cited by 12 publications

References 14 publications

Gauging the Impact of Artificial Intelligence and Mathematical Modeling in Response to the COVID-19 Pandemic: A Systematic Review

Gauging the Impact of Artificial Intelligence and Mathematical Modeling in Response to the COVID-19 Pandemic: A Systematic Review

On an optimal testing strategy for workplace settings operating during the COVID-19 pandemic

High capacity clinical SARS-CoV-2 molecular testing using combinatorial pooling

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