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Tapestry: A Single-Round Smart Pooling Technique for COVID-19 Testing

2020; Cold Spring Harbor Laboratory; Linguagem: Inglês

10.1101/2020.04.23.20077727

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, Manoj Gopalkrishnan,

Advanced biosensing and bioanalysis techniques

Abstract 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.