IIT-B develops way to detect asymptomatic Covid patients

A multi-institute research team led by the Indian Institute of Technology Bombay (IIT-B) has developed a new testing protocol that could help identify asymptomatic carriers of the Sars-Cov-2 virus that causes Covid-19.

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The 28-member team comprises researchers from IIT-B, National Centre for Biological Sciences, InStem, Harvard University, Harvard Medical School, SASTRA University and the Mumbai-based start-up, Shop101. Tapestry, the new testing method, is described as “a single-round smart pooling technique for Covid-19 testing”.

With Tapestry, one swab sample is sent to three pools. If a sample tests positive, samples in the remaining two pools will also test positive. Tapestry has been validated through laboratory experiments with synthetic RNA and DNA fragments. Results have been confirmed using computer simulation.

“The algorithm describes a novel way to pool samples and test in a single step, thereby conserving resources and increasing testing capacity by increasing throughput,” said Dr Lancelot Pinto, who was not involved in the study and is a pulmonologist at PD Hinduja Hospital in Mahim.

The researchers believe Tapestry could help identify asymptomatic carriers of the virus. “The peculiarity we are seeing with Covid-19 is asymptomatic individuals are carriers and can spread the virus. The only way to combat this is either you put everyone under lockdown or test everyone; neither of which are desirable options. One option is to test as many as possible in a cost-effective way, and one way to do it is by pooling samples,” said Manoj Gopalkrishnan, principal investigator and associate professor, department of electrical engineering, IIT-B.

Tapestry’s method is unlike the technique of pooling samples approved by the Indian Council for Medical Research (ICMR), which requires at least multiple rounds of testing if a sample from a pool tests positive. Each round of testing takes four hours.

Pooling test samples based on ICMR norms involves placing a mixture of five different swab samples in a pool, extracting the virus ribonucleic acid (RNA) and conducting a reverse transcription-polymerase chain reaction (RT-PCR) test that spans four hours at one go. A positive pool indicates that at least one person is infected but the individual’s identity is not known. What follows is retesting and separately extracting virus RNA from each of the five samples from the pool.

“Pooling is a good method and should be deployed more widely. But two rounds of pooling takes eight hours. Our protocol can test 1,000 people in 100 tests and recover up to 10 positives,” said Gopalkrishnan, adding that the single-round pooling technique allows for more extensive testing, which would help identify asymptomatic carriers. “For instance, medical staff, police personnel, delivery personnel, residents in high-density locations or organisations that want to bring employees back can undergo pool testing every day or at least once in two or three days,” said Gopalkrishnan.

The team has also developed an app where laboratory technicians can enter the viral load seen in the test. The algorithm, deployed on the cloud, will then make the calculations and give the test results.

Once permissions come through and clinical trials are successful, the team will approach the ICMR to consider deploying Tapestry in testing centres as well as other institutions such as hospitals and airports.

“Tapestry needs to be validated on clinical specimens, in which the quantum of RNA extracted from each nasopharyngeal swab, pre-test probability, prevalence will all vary across different states/cities,” said Pinto.

In the second phase, the team plans to undertake clinical trials at five testing centres across the country.