Grouping tests ("pooling", "pools"): why and for what purpose?
Text updated on 2020-10-07
Pooling is the use of a single diagnostic test to analyze a mixture of samples from different individuals. Pooling speeds up mass screening, reduces costs, and prevents epidemics in communities.
Invented in 1943 by an American statistician, Robert Dorfman, the principle of group testing is simple: rather than testing 100 samples, one can group them into ten groups (pools) of ten and test each group. If one of the groups is positive, then at least one of the samples contains the infectious agent. Conversely, if the pool is negative, then it can be concluded that each specimen in the pool must be negative as well (if there are no false negatives, i.e., a negative result when an individual is carrying the virus).
Grouping tests together, why and what for?
The method saves diagnostic reagents that are expensive and likely to be under supply demand. See the question Which test to use to find out if I am infected with SARS-CoV-2 ?
The strategy of pooled testing was used in the context of COVID-19 as early as February 2020 in the United States. Conducted at several sites in the San Francisco Bay Area, the objective was to estimate the viral prevalence, i.e., the fraction of the population infected with the SARS-CoV-2 coronavirus.
In the United States, the American Center of Disease Control (CDC) now distinguishes three types of use of the pooling technique, depending on whether it is :
1) for individual diagnosis,
2) for mass screening,
(3) for epidemic surveillance
We discuss these three uses below.
1) Use in individual diagnosis
The result of a pooled test is for all individuals in the group. To identify the infected individual(s), a first method consists of testing each of the samples from the groups identified as positive individually.
This method, known as the Dorfman method, is not the most effective, however, as it requires a new diagnostic cycle. This additional step significantly increases the individual rendering time.
Other methods allow samples to be cleverly combined into several groups in order to obtain an individual diagnosis. These methods have been applied in the context of COVID-19. The methods of matrix-pooling, hypercube and P-Best are examples of this approach. All these techniques are all the more effective the smaller the proportion of infected persons. For the Dorfman method, the optimal group size is greater than 5 if less than 5% of the individuals are infected.
Pooling is a technique that can cause false negatives due to the dilution of the viral concentration of the sample from an infected individual in the pool of samples from uninfected individuals.
2) Use for mass screening
Pool testing makes it possible, at a constant economic cost, to test a larger number of individuals and opens up the possibility of carrying out regular testing in at-risk communities (typically nursing homes or food production centres).
Pooled testing of between 5 and 30 samples was conducted in hospitals and nursing homes in Germany for epidemic prevention purposes, bringing the number of people tested in these facilities to 22,000 over a period from 13 March to 29 April. See the question What are the risks of false negatives in pooled tests?
3) Use for surveillance and epidemic prevention purposes
It may be interesting to obtain a pool result without trying to trace the contaminated individual in the test group. A positive pool result could be used to trigger an alert procedure and a reinforcement of safety procedures.
Mathematical models show how grouped tests repeated over time allow for earlier detection of pre-symptomatic or asymptomatic cases before the spread of the epidemic. This type of use of pool testing for surveillance purposes is similar to that used in wastewater.
The World Health Organization advises against pooling for the clinical diagnosis of symptomatic individuals or for the follow-up of contact cases, but the US CDC considers pooling interesting for mass screening. The Food and Drug Administration (FDA) has also approved the use of pooled virological tests for up to 4 samples.
In order to be better accepted, the samples used could be taken from saliva samples. See the question Which sample to test for the presence of coronavirus: nasopharyngeal or buccal?
In order not to overburden medical laboratories, the US CDC allows other facilities (such as research laboratories not normally licensed for clinical diagnosis) to perform these tests in groups, provided that the results are not shared with individuals.
Historical article with the optimal size in the case of a perfect test (without increasing the risk of false negatives with the size of the pool).Dorfman, R. (1943). The detection of defective members of large populations. The Annals of Mathematical Statistics, 14(4), 436-440.
C. Gollier and O. Gossner's method, published at the beginning of containment, is to use pooled testing to allow safer deconfinement and allow workers to return to their workplaces.Gollier, C., & Gossner, O. (2020). Group testing against Covid-19. Covid Economics, 2.
First use to date of pooled testing on 2,888 nasopharyngeal samples tested in groups of ten. The 3 positives detected were detected at the end of February 2020, which makes it possible to date the emergence of the viral infection in the state of California.Hogan, C. A., Sahoo, M. K., & Pinsky, B. A. (2020). Sample pooling as a strategy to detect community transmission of SARS-CoV-2. Jama, 323(19), 1967-1969.
Recommendations of the Center of Disease Control and Prevention of the United States of America, formalizing the distinction between diagnosis, screening, and surveillance.Interim Guidance for Use of Pooling Procedures in SARS-CoV-2 Diagnostic, Screening, and Surveillance Testing, Center for Disease Control and Prevention. 1st August 2020.
Implementation of Dorfman method in groups of 8; 26,576 samples from asymptomatic individuals, 31 (0.12%) samples were detected positive for CoV2-SARS. This corresponds to a 7.3-fold increase in the number of tests.Ben-Ami, R., Klochendler, A., Seidel, M., Sido, T., Gurel-Gurevich, O., Yassour, M., ... & Gertler, A. (2020). Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection. Clinical Microbiology and Infection, 26(9), 1248-1253.
Implementation and theoretical discussion of a hypercube method.Mutesa, L., Ndishimye, P., Butera, Y., Uwineza, A., Rutayisire, R., Musoni, E., ... & Musanabaganwa, C. (2020). A strategy for finding people infected with SARS-CoV-2: optimizing pooled testing at low prevalence. arXiv preprint arXiv:2004.14934.
Practical implementation of a combined pooling method (P-Best) to screen 1,115 medical staff using only 144 tests.Shental, N., Levy, S., Wuvshet, V., Skorniakov, S., Shalem, B., Ottolenghi, A., ... & Goldhirsh, M. (2020). Efficient high-throughput SARS-CoV-2 testing to detect asymptomatic carriers. Science Advances, 6(37), eabc5961.
Pooled tests (size 5 to 20) in saliva samples by the Yale University team also behind the SalivaDirect test.Watkins, A. E., Fenichel, E. P., Weinberger, D. M., Vogels, C. B., Brackney, D. E., Casanovas-Massana, A., ... & Cruz, C. S. D. (2020). Pooling saliva to increase SARS-CoV-2 testing capacity. medRxiv.
A study that conducted mass screening of SARS-CoV-2 among two cohorts of asymptomatic people in Japan, one of contact cases (161 people) and the other of individuals quarantined at airports (1,763 people). The study indicates an overall sensitivity of RT-PCR testing with nasopharyngeal (NP) swabs of 86% versus 92% with saliva samples. The specificity for both samples was greater than 99.9%.Yokota, I., Shane, P. Y., Okada, K., Unoki, Y., Yang, Y., Inao, T., ... & Nishida, M. (2020). Mass screening of asymptomatic persons for SARS-CoV-2 using saliva.
Pooled tests (size 5 to 30) in Germany, Saarland, for epidemic prevention purposes.Lohse, S., Pfuhl, T., Berkó-Göttel, B., Rissland, J., Geißler, T., Gärtner, B., ... & Smola, S. (2020). Pooling of samples for testing for SARS-CoV-2 in asymptomatic people. The Lancet Infectious Diseases.
Article on modeling the risk of false-negatives in pool testing and application to epidemiological surveillance of a closed community.Brault, V., Mallein, B., & Rupprecht, J. F. (2020). Group testing as a strategy for the epidemiologic monitoring of COVID-19. arXiv preprint arXiv:2005.06776 .
Recommendation of the World Health Organization.World Health Organization. (2020). Diagnostic testing for SARS-CoV-2: interim guidance, 11 September 2020 (No. WHO/2019-nCoV/laboratory/2020.6). World Health Organization.
Modeling the evolution of viral load and its effect on the virus detection time by a cluster testing strategy. If the virus remains detectable for an average of 14 days in an individual RT-qPCR test, it is detectable for 11.2 days in a pooled RT-qPCR test of 25 samples, i.e., a reduction of around 20% in the period of detectability of which 10% is during the latter part of the infection.Pilcher, C. D., Westreich, D., & Hudgens, M. G. (2020). Group testing for severe acute respiratory syndrome-coronavirus 2 to enable rapid scale-up of testing and real-time surveillance of incidence. The Journal of Infectious Diseases, 222(6), 903-909.