Sample pooling methods for efficient pathogen screening: Practical implications

Abstract

Due to the large number of negative tests, individually screening large populations for rare pathogens can be wasteful and expensive. Sample pooling methods improve the efficiency of large-scale pathogen screening campaigns by reducing the number of tests and reagents required to accurately categorize positive and negative individuals. Such methods rely on group testing theory which mainly focuses on minimizing the total number of tests; however, many other practical concerns and tradeoffs must be considered when choosing an appropriate method for a given set of circumstances. Here we use computational simulations to determine how several theoretical approaches compare in terms of (a) the number of tests, to minimize costs and save reagents, (b) the number of sequential steps, to reduce the time it takes to complete the assay, (c) the number of samples per pool, to avoid the limits of detection, (d) simplicity, to reduce the risk of human error, and (e) robustness, to poor estimates of the number of positive samples. We found that established methods often perform very well in one area but very poorly in others. Therefore, we introduce and validate a new method which performs fairly well across each of the above criteria making it a good general use approach.

Digital PCR Applications in the SARS-CoV-2/COVID-19 Era: a Roadmap for Future Outbreaks

“…Since its introduction in 1943 by Robert Dorfman ( 155 ), “pooling of samples” has become a commonly used method for the detection and diagnosis of infectious diseases ( 156 – 159 ). Specifically, pooling of samples means that different samples are mixed to form a pool before tests are performed on that pool as a single sample ( 160 – 162 ).…”

Double Batched DNA Sequencing is a reliable, cost-effective and scalable approach to genomic population screening

“…Lately, combinatorial pooling strategies, like DoBSeq, have received increased attention as a theoretical alternative to the extensive and costly population screening for the SARS-Cov-2 virus 25 . While the methods appear similar, a crucial difference is that, a disease may be caused by a myriad of distinct genetic variants, whereas SARS-Cov-2 tests, by and large, are positive in the same way.…”

Cost analysis of coronavirus disease 2019 test strategies using pooled reverse transcriptase‐polymerase chain reaction technique

“…16,17 In addition to simple pooling testing (e.g., Dorfman testing or hierarchical group testing), more complicated methodologies such as nonhierarchical group testing or array testing have also been developed. [18][19][20] Recently, these pooling strategies have been adopted to efficiently detect SARS-CoV-2 by speeding up the tests and increasing the testing capacity, and have thus been recommended by the US FDA as well. 21 Several simulation studies tried to determine the optimal pooling strategy by taking into account relevant parameters such as pool size and positive rate (PR).…”

“…Accordingly, strategies for pooling diagnostic specimens, which have been applied in screening donated blood samples for blood‐borne pathogens such as hepatitis B virus, 14,15 were introduced to reduce the cost of screening large populations 16,17 . In addition to simple pooling testing (e.g., Dorfman testing or hierarchical group testing), more complicated methodologies such as nonhierarchical group testing or array testing have also been developed 18–20 . Recently, these pooling strategies have been adopted to efficiently detect SARS‐CoV‐2 by speeding up the tests and increasing the testing capacity, and have thus been recommended by the US FDA as well 21…”