Large-scale Testing for SARS-CoV-2 using Tapestry Pooling

We have previously described Tapestry Pooling, a scheme to enhance the capacity of RT-qPCR testing, and provided experimental evidence with spiked synthetic RNA to show that it can help to scale testing and restart the economy. Here we report on validation studies with Covid19 patient samples for the Tapestry Pooling scheme with prevalence in the range of 1% to 2%. We pooled RNA extracted from patient samples that were previously tested for Covid19, sending each sample to three pools. Following three different pooling schemes, we pipetted 320 samples into 48 pools with pool size of 20 at prevalence rate of 1.6%, 500 samples into 60 pools with pool size of 25 at prevalence rate of 2%, and 961 samples into 93 pools with pool size of 31 at prevalence rate of 1%. Of the 191 RT-qPCR experiments that we performed, only one pool was incorrect (false negative). Our recovery algorithm correctly called results for the individual samples, with a 100% sensitivity and a 99.9% specificity, with only one false positive across all the 1,781 blinded results required to be called. We show up to 10X savings in number of tests required at a range of prevalence rates and pool sizes. These experiments establish that Tapestry Pooling is robust enough to handle the diversity of sample constitutions and viral loads seen in real-world samples. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement Sandeep Krishna thanks the Simons Foundation for funding as well as the Department of Atomic Energy, Government of India under project no. 12-R\&D-TFR-5.04-0800. AR, MG thank SERB MATRICS grants MTR/2019/0006, EMR/2017/004089, MTR/2018/000817, IITB WRCB grant 10013976, and DST-Rakshak grant 10013980. DP acknowledges support by CSR funding from Azim Premji philanthropy, Standard Chartered Bank, and Punjab National Bank. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: inStem/IEC-18/01 from Institute for Stem Cell and Regenerative Medicine, Institute Human Ethics Committee dated May 18th 2020. All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data, appropriately anonymized, is available as a supplementary file to this submission. Our software implementation of the Tapestry Pooling algorithm is being made available as a web app at .