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Startup uses genomics to trace Covid-19 transmission

By Priyanka Sahoo, Mumbai
PUBLISHED ON APR 28, 2020 07:32 PM IST

A healthcare startup incubated at the Indian Institute of Technology, Bombay (IIT-B), is using genomics (the study of genomes) to trace the transmission of Covid-19 in the country.

A platform launched by HaystackAnalytics demonstrates contactless contact-tracing and epidemiology of the Sars-Cov-2 virus (coronavirus).

In simple terms, a genome is the genetic data of any organism. By sequencing the genome, one can get around 30,000 data points per sample about the organism’s genome. Therefore, a genome sequencing of the virus helps better understand the virus transmission.

The opensource platform available on the website ( helps understand the epidemiology of the virus in different places within the country.

This will help map the contacts of those affected by the virus without having to physically canvas a large number of households.

“Contact tracing has emerged as the backbone of all efforts to prevent the transmission of Covid-19 in India. But, current Covid-19 epidemiology, using community healthcare workers for undertaking extended interrogation of Covid-19 patients and extensive on-foot contact, significantly increases the risk of disease for health workers, and can also make them as carriers of the disease,” said Anirvan Chatterjee, founder of HaystackAnalytics.

The startup incubated by the Society of Innovation and Entrepreneurship (SINE) has proposed prevention of Covid-19 transmission, based on genomics and geospatial mapping.

They have used the Covid-19 global genomics data ( to build analytics for performing contactless contact racing.

“We are using the DNA fingerprinting most recent common ancestor analysis. Theoretically, we can draw the entire trace of the virus back to Wuhan. This means that the transmission chain can be drawn out,” said Chatterjee.

For instance, a global analysis of the data shows that the transmission patterns in say Washington state (in the United States) is different from that in Italy. While Washington State witnessed a clonal outbreak — every patient can be traced back to a single patient in the state, Italy reported multiple transmission events where a high number of cases were found in particular areas.

“Now that the virus is in India, we need to understand how it spreads between states. This will help us strategise our actions against Covid-19. For example, if there is a cluster transmission in a place, a complete lockdown may not be necessary and containing the virus in the cluster will do,” said Chatterjee.

“We were able to clearly differentiate four distinct Covid-19 transmission patterns in the data, which enable four different containment strategies. These four are — community transmission, local transmission, cluster transmission and travel transmission.

Chatterjee said that they are in talks with government bodies to use the platform in their fight against Covid-19. “We have kept the platform open source. We are encouraging more people to use the platform and populate it with more data,” he added.

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