Optimal test pooling for efficient PCR testing of SARS-CoV2
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BRIEF REPORT
Optimal test pooling for efficient PCR testing of SARS-CoV2 Edgar D. Klenske1 Received: 31 May 2020 / Accepted: 3 June 2020 © Royal Academy of Medicine in Ireland 2020
Letter to the Editor The new coronavirus SARS-CoV2 is spreading rapidly. Due to its high infectiousness for both pre-symptomatic and asymptomatic cases, it is crucial to test many people quickly. Once infected individuals are identified, they can be quarantined to slow down the spread of the virus. However, the testing capacities are limited and in many regions of the world the demand is already exceeding the existing capacity. Increasing this capacity in normal ways can be difficult due to the availability of test kits and trained laboratory staff. Recently, several research groups have proposed and developed testing protocols based on test pooling to make better use of the existing testing capacity (see, e.g., [1], [2]). With test pooling, the sample swabs of test subjects are used twice: once in an archive tube and once in the pool tube. Several samples are combined in the pool tube, so that they can be tested simultaneously. The content of the pool tube is analyzed with a test based on the polymerase chain reaction (PCR). Due to the high sensitivity of the PCR test, the result will be positive if at least one of the samples is positive for SARS-CoV2. If the sample pool tests positive, each sample has to be re-tested individually. For small prior infection probabilities, such a testing procedure can be highly efficient, because many samples can be tested simultaneously with a small number of test kits. Similar testing strategies have formerly successfully been used in sample screening for human immunodeficiency viruses (HIV) [3], influenza [4], and other diseases. While media outlets report optimistically on the tremendous increase of testing capacity due to pooling methods, it is important to take the prior infection probability into account. If the chosen pool size is too small, more samples
Edgar D. Klenske
[email protected] 1
Bosch Center for Artificial Intelligence, Robert-Bosch-Campus 1, 71272 Renningen, Germany
could be tested with the same number of test kits. If the chosen pool size is too large, testing capacity will be wasted due to the necessary re-testing, because too many pools are tested positive. In order to make the best use of the existing testing capacity, it is important to select a pool size that is optimal, or at least near-optimal, given the circumstances. We focus on testing protocols that do not change the sensitivity of the original test [2], because they are especially easy to carry out in the lab and thus less errorprone than tests where varying sensitivity has to be taken into account. Let p(C) be the prior probability for the samples being positive for SARS-CoV2. This is essentially the prevalence of SARS-CoV2 among the subjects being tested. This probability can be estimated by expert knowledge or field experience, e.g., by analyzing infection numbers of similar cohorts. Since we have to re-test al
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