Author:
Ghosh Sabyasachi,Rajwade Ajit,Krishna Srikar,Gopalkrishnan Nikhil,Schaus Thomas E.,Chakravarthy Anirudh,Varahan Sriram,Appu Vidhya,Ramakrishnan Raunak,Ch Shashank,Jindal Mohit,Bhupathi Vadhir,Gupta Aditya,Jain Abhinav,Agarwal Rishi,Pathak Shreya,Rehan Mohammed Ali,Consul Sarthak,Gupta Yash,Gupta Nimay,Agarwal Pratyush,Goyal Ritika,Sagar Vinay,Ramakrishnan Uma,Krishna Sandeep,Yin Peng,Palakodeti Dasaradhi,Gopalkrishnan Manoj
Abstract
AbstractThe COVID-19 pandemic has strained testing capabilities worldwide. There is an urgent need to find economical and scalable ways to test more people. We presentTapestry, 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 applicationBYOM Smart Testingwhich 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.
Publisher
Cold Spring Harbor Laboratory
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