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HaystackAnalytics, a Mumbai-based biotech startup, is using genomics to trace the transmission of coronavirus in India. Incubated at the Indian Institute of Technology, Bombay (IIT-B), HaystackAnalytics aims to understand the transmission patterns of the virus to help the government plan a better strategy to fight the Covid-19 pandemic.
HaystackAnalytics is sequencing the genome of the coronavirus to understand virus transmission. In layman language, a genome contains genetic data of an organism and sequencing the genome helps researchers to get around 30K data points per sample.
Founder of HaystackAnalytics Anirvan Chatterjee said that the startup is using DNA fingerprinting to trace the recent common ancestor who spread the virus. “Theoretically, we can draw the entire trace of the virus back to Wuhan. This means that the transmission chain can be drawn out,” Chatterjee told the Hindustan Times.
Globally, many studies have shown that transmission of the virus is different in every country. For instance, every Covid-19 patient in Washington can be traced back to a single individual while multiple transmission points are reported in Italy.
Chatterjee said that the need to understand the transmission in India has arrived. According to him, understanding the Covid-19 spread between states will help the government to strategise 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,” he added.
As of now, HaystackAnalytics has been able to differentiate four distinct Covid-19 transmission patterns in the data. This helped the startup to enable four different containment strategies. “These four are community transmission, local transmission, cluster transmission and travel transmission,” Chatterjee said.
HaystackAnalytics has also developed a platform to trace the transmission. The open-source platform demonstrates contact-tracing and epidemiology of coronavirus and is accessible at https://haystackanalytics.in. Based on the data provided by HaystackAnalytics, one can map the contacts of Covid-19 positive cases without physically mapping hundreds of households.
Chatterjee said that contact tracing has emerged as the backbone of all efforts to prevent the transmission of Covid-19 in India. However, he said that the current mechanism of tracing the cases physically is increasing the risk of transmission more.
Explaining further, he said, “Current Covid-19 epidemiology, which uses community healthcare workers for undertaking extended interrogation of Covid-19 patients and extensive on-foot contact, is significantly increasing the risk of disease for health workers. The mechanism can also make them carriers of the virus.”
For the global genomics data, HaystackAnalytics used an open-source platform to build their analytics platform for contactless contact tracing of Covid-19 cases.
As of now, HaystackAnalytics is in talks with law enforcement agencies to use their platform to track Covid-19 patients. The startup has kept its platform as open-source to encourage more people to use it and improvise it with data.