Pooling of coronavirus tests under unknown prevalence

Abstract Diagnostic testing for the novel coronavirus is an important tool to fight the coronavirus disease (Covid-19) pandemic. However, testing capacities are limited. A modified testing protocol, whereby a number of probes are ‘pooled’ (i.e. grouped), is known to increase the capacity for testing. Here, we model pooled testing with a double-average model, which we think to be close to reality for Covid-19 testing. The optimal pool size and the effect of test errors are considered. The results show that the best pool size is three to five, under reasonable assumptions. Pool testing even reduces the number of false positives in the absence of dilution effects.

[1]  X. Lyu,et al.  Sample Pooling as a Strategy of SARS-COV-2 Nucleic Acid Screening Increases the False-negative Rate , 2020, medRxiv.

[2]  A. Meyers,et al.  Recommendations for sample pooling on the Cepheid GeneXpert® system using the Cepheid Xpert® Xpress SARS-CoV-2 assay , 2020, bioRxiv.

[3]  A. Regev,et al.  Using viral load and epidemic dynamics to optimize pooled testing in resource constrained settings , 2020, medRxiv.

[4]  M. Schmidt,et al.  FACT- Frankfurt adjusted COVID-19 testing- a novel method enables high-throughput SARS-CoV-2 screening without loss of sensitivity , 2020, medRxiv.

[5]  Ajit Rajwade,et al.  Tapestry: A Single-Round Smart Pooling Technique for COVID-19 Testing , 2020, medRxiv.

[6]  S. Sarin,et al.  Pooled RNA sample reverse transcriptase real time PCR assay for SARS CoV-2 infection: a reliable, faster and economical method. , 2020, medRxiv.

[7]  S. Lohse,et al.  Pooling of samples for testing for SARS-CoV-2 in asymptomatic people , 2020, The Lancet Infectious Diseases.

[8]  E. Albert,et al.  Pooling of nasopharyngeal swab specimens for SARS‐CoV‐2 detection by RT‐PCR , 2020, medRxiv.

[9]  Moran Yassour,et al.  Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection , 2020, Clinical Microbiology and Infection.

[10]  S. Hinrichs,et al.  Assessment of Specimen Pooling to Conserve SARS CoV-2 Testing Resources , 2020, American journal of clinical pathology.

[11]  Mauricio Olivares,et al.  Optimizing RT-PCR detection of SARS-CoV-2 for developing countries using pool testing , 2020, medRxiv.

[12]  Chengyu Yuan A statistical method of batch screening entrying population from abroad by stages and groups in COVID-19 nucleic acid testing , 2020 .

[13]  B. Pinsky,et al.  Sample Pooling as a Strategy to Detect Community Transmission of SARS-CoV-2. , 2020, JAMA.

[14]  A. Berger,et al.  Ad hoc laboratory-based surveillance of SARS-CoV-2 by real-time RT-PCR using minipools of RNA prepared from routine respiratory samples , 2020, Journal of Clinical Virology.

[15]  Yael Mandel-Gutfreund,et al.  Evaluation of COVID-19 RT-qPCR test in multi-sample pools , 2020, medRxiv.

[16]  R. Dorfman The Detection of Defective Members of Large Populations , 1943 .