Challenges and issues of SARS-CoV-2 pool testing
Authors: Jens N Eberhardt, Nikolas P Breuckmann, Christiane S Eberhardt
Journal: The Lancet Infectious Diseases (2020)

We read with interest the Correspondence by Stefan Lohse and colleagues,1Lohse S Pfuhl T Berkó-Göttel B et al.Pooling of samples for testing for SARS-CoV-2 in asymptomatic people.Lancet Infect Dis. 2020; (published online April 28.)https://doi.org/10.1016/S1473-3099(20)30362-5Summary Full Text Full Text PDF PubMed Scopus (231) Google Scholar who evaluated the practicability of pool testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Pooling of samples yields considerable savings of test kits when the prevalence of infection is low because pools with all-negative samples can be discarded with a single test. Lohse and colleagues' findings suggest that pooling up to 30 samples is technically feasible with currently used and commercially available SARS-CoV-2 RT-PCR kits.1Lohse S Pfuhl T Berkó-Göttel B et al.Pooling of samples for testing for SARS-CoV-2 in asymptomatic people.Lancet Infect Dis. 2020; (published online April 28.)https://doi.org/10.1016/S1473-3099(20)30362-5Summary Full Text Full Text PDF PubMed Scopus (231) Google Scholar But is bigger always better? Is it really efficient to pool 30 samples? First discussed around 80 years ago by Dorfman2Dorfman R The detection of defective members of large populations.Ann Math Statist. 1943; 14: 436-440Crossref Google Scholar in the context of large-scale syphilis testing, the matter is complex and optimal pool sizes depend on the prevalence of infection in the population. Furthermore, there are more sophisticated pooling schemes than the one originally discussed by Dorfman, which use multiple stages of pooling or test samples in rows and columns of a matrix.3Phatarfod RM Sudbury A The use of a square array scheme in blood testing.Stat Med. 1994; 13: 2337-2343Crossref PubMed Scopus (82) Google Scholar We propose an adaptive approach that uses different pooling schemes depending on the estimated prevalence in a population.4Eberhardt JN Breuckmann NP Eberhardt CS Multi-stage group testing improves efficiency of large-scale COVID-19 screening.J Clin Virol. 2020; 128104382Crossref PubMed Scopus (66) Google Scholar Our exhaustive comparison of testing schemes shows that three different schemes with initial pool sizes of 16, nine, and three samples are optimal for a prevalence of up to 3·5%, 3·5–12%, and 12–30%, respectively (appendix). The first two schemes are three-staged, meaning that if a pool tests positive it is further divided into sub-pools of four or three samples, before then testing samples individually. These schemes have a consistently higher testing efficiency than the method proposed by Lohse and colleagues, who used a three-staged scheme with initial pools of 30 samples and sub-pools of ten samples (appendix). For a prevalence of 2%, as in the population tested by Lohse and colleagues,1Lohse S Pfuhl T Berkó-Göttel B et al.Pooling of samples for testing for SARS-CoV-2 in asymptomatic people.Lancet Infect Dis. 2020; (published online April 28.)https://doi.org/10.1016/S1473-3099(20)30362-5Summary Full Text Full Text PDF PubMed Scopus (231) Google Scholar our proposed testing scheme (pool size of 16 and four sub-pools of four samples) uses around 20% fewer tests. At higher prevalence, differences become even more pronounced and smaller pool sizes are optimal. For prevalence over 18%, pools of 30 samples are even less efficient than individual testing, whereas small pool sizes of three samples still yield a considerable improvement in efficiency (appendix). Hence bigger is not always better. Rather, it is preferable to choose one of the three proposed testing schemes based on the estimated underlying prevalence. We declare no competing interests. Download .pdf (.27 MB) Help with pdf files Supplementary appendix Challenges and issues of SARS-CoV-2 pool testing – Authors' replyWe appreciate the comments on our letter,1 in which we described a strategy to identify asymptomatic people infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in large populations of uninfected people when testing capacity is low and laboratory infrastructure is overwhelmed. We proposed pool testing to screen for individuals who might spread SARS-CoV-2 without showing any symptoms. He and colleagues2 reported temporal patterns of viral shedding and inferred from their data that viral load peaks 0·7 days before symptom onset and estimated that 44% of SARS-CoV-2 infections occur during the pre-symptomatic stage of the index case. Full-Text PDF Pooling of samples for testing for SARS-CoV-2 in asymptomatic peopleThe ongoing coronavirus disease 2019 (COVID-19) pandemic is a substantial challenge for health-care systems and their infrastructure. RT-PCR-based diagnostic confirmation of infected individuals is crucial to contain viral spread because infection can be asymptomatic despite high viral loads. Sufficient molecular diagnostic capacity is important for public health interventions such as case detection and isolation, including for health-care professionals.1 Full-Text PDF Challenges and issues of SARS-CoV-2 pool testingWe read with interest Stefan Lohse and colleagues' Correspondence about sample pooling for testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in asymptomatic people.1 Some of the findings Lohse and colleagues report do not seem to be consistent with other research results2,3 nor our experiences. Full-Text PDF Challenges and issues of SARS-CoV-2 pool testingStefan Lohse and colleagues1 described a sample pooling strategy for testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) via RT-PCR to meet the unprecedented demand for laboratory testing. Lohse and colleagues evaluated a range of pool sizes (four to 30 samples per pool) in asymptomatic people. The additional time to deconvolute the larger pools yielding a positive result into sub-pools precludes the use of this strategy in patients with severe acute respiratory illness and high-risk contacts. Full-Text PDF