IIT Bombay researchers have developed an algorithm which can be used to help conduct pooled testing of samples for COVID-19. In order to validate this protocol – known as Tapestry Pooling – in vitro experiments using synthetic RNA and DNA fragments have been carried out by NCBS and InSTEM, Bengaluru, and Wyss Institute of Biologically Inspired Engineering, U.S. Further validation using clinical samples is under way.
An important part of managing the COVID-19 pandemic is aggressive testing of people and quarantining those who test positive, to contain the spread. Until now, in India tests have been carried out only on people with travel history and their contacts, and on clusters that have known to be infected. This is due to the lack of sufficient testing kits to test a larger population. In this context, pooling of samples is one way of reducing the number of test kits used and increases testing capacity.
Pooled tests
Pooling of samples involves testing them in batches, and when pooled sample tests positive, then individual samples are assessed. Using combinatorics, an algorithm is found that unscrambles the test results and tells you which of the individuals in the pool are positive.
In effect, the number of tests that need to be carried out is less than if there had to be test done for each individual.
The Android application named BYOM Smart Testing, which was developed by Shop 101, guides the user on how to perform the test. The technician enters how many samples they want to test, and the prevalence rate. They are given a pooling matrix.
“Samples are pooled according to this pooling matrix. Pools are tested and the quantitative reading from the tests is entered into our algorithm, which reconstructs the list of positives, negatives, and their viral loads,” says Manoj Gopalkrishnan, from IIT Bombay and corresponding author of the preprint posted in MedRxiv server. Preprints are yet to be peer-reviewed.
The present version of the protocol has fixed numbers of samples. That is, for instance, 40 samples can be tested in 16 RT-PCR tests (up to 3 positives). This can go up to 961 samples that can be tested in 93 RT-PCR tests (up to 10 positives).
“In version 2, the user will be able to tell how many samples they want tested, and we will give corresponding pooling instructions,” explains Dr Gopalkrishnan. Being a non-adaptive test, all the RT-PCR tests in Tapestry pooling are conducted at one go. This could take four hours to perform typically. An adaptive test which has two rounds of testing, can take twice the amount of time.
Graceful failure mode
The protocol also has a so-called graceful failure mode. “It estimates actual prevalence rate in the batch and if this is much higher than the projected prevalence so that the algorithm is not able to identify all positives exactly, it returns a list of suspected positives which includes all the positives, and possibly a few false positives which can be eliminated in round two of testing,” explains Dr Gopalkrishnan.
The group is in the process of drafting and obtaining permissions for a clinical trial in collaboration with Tata Memorial Hospital, Kasturba Hospital and P.D. Hinduja Hospital, in Mumbai, Malabar Cancer Centre, in Thalassery, Kerala, and NCBS, Bengaluru.
