Tapestry: A Single-Round Smart Pooling Technique for COVID-19 Testing
Sabyasachi Ghosh, Ajit Rajwade, Srikar Krishna, Nikhil Gopalkrishnan, Thomas E. Schaus, Anirudh Chakravarthy, Sriram Varahan, Vidhya Appu, Raunak Ramakrishnan, Shashank Ch, Mohit Jindal, Vadhir Bhupathi, Aditya Gupta, Abhinav Jain, Rishi Agarwal, Shreya Pathak, Mohammed Ali Rehan, Sarthak Consul, Yash Gupta, Nimay Gupta, Pratyush Agarwal, Ritika Goyal, Vinay Sagar, Uma Ramakrishnan, Sandeep Krishna, Peng Yin, Dasaradhi Palakodeti, and Manoj Gopalkrishnan
medRxiv, 2020
The COVID-19 pandemic has strained testing capabilities worldwide. There is an urgent need to find economical and scalable ways to test more people. We present Tapestry, a novel quantitative nonadaptive pooling scheme to test many samples using only a few tests. The underlying molecular diagnostic test is any real-time RT-PCR diagnostic panel approved for the detection of the SARS-CoV-2 virus. In cases where most samples are negative for the virus, Tapestry accurately identifies the status of each individual sample with a single round of testing in fewer tests than simple two-round pooling. We also present a companion Android application BYOM Smart Testing which guides users through the pipetting steps required to perform the combinatorial pooling. The results of the pooled tests can be fed into the application to recover the status and estimated viral load for each individual sample.NOTE: This protocol has been validated with in vitro experiments that used synthetic RNA and DNA fragments and additionally, its expected behavior has been confirmed using computer simulations. Validation with clinical samples is ongoing. We are looking for clinical collaborators with access to patient samples. Please contact the corresponding author if you wish to validate this protocol on clinical samples.Competing Interest StatementThe authors have declared no competing interest.Clinical TrialNot applicable, we did not work with patient samples, only analytically validated in a wet lab with non-human RNA.Funding StatementMG was supported by SERB grants EMR/2017/004089 and MTR/2018/000817. SK thanks the Simons Foundation for funding. NCBS authors thank the Department of Atomic Energy, Government of India, for funding under project no. 12-R&D-TFR-5.04-0800. SV thanks Wellcome Trust- DBT Alliance Early Career Fellowship (IA/E/16/1/502996) for funding. No external payment, service, or funding was received beyond this.Author DeclarationsAll relevant ethical guidelines have been followed; any necessary IRB and/or ethics committee approvals have been obtained and details of the IRB/oversight body are included in the manuscript.YesAll necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI 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).YesI 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.YesAll the data referred to in the manuscript is available in the manuscript. Installation files for the phone app are made available at the google drive link below. The installer will need to activate “Developer mode” on their Android device before installation. https://play.google.com/store/apps/details?id=com.app.byom