Genome sequencing dashboard to understand variants of virus

In a first, a start-up incubated at the Indian Institute of Technology (IIT), Bombay, has developed a genome sequencing dashboard for the Brihanmumbai Municipal Corporation (BMC) to understand and manage the Covid-19 pandemic better, as part of the pilot with Kasturba Hospital

In a first, a start-up incubated at the Indian Institute of Technology (IIT), Bombay, has developed a genome sequencing dashboard for the Brihanmumbai Municipal Corporation (BMC) to understand and manage the Covid-19 pandemic better, as part of the pilot with Kasturba Hospital.

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A genome is the genetic data of any organism. By sequencing the genome, one can get around 30,000 data points about the organism’s genome. Therefore, genome sequencing of the Covid-19 virus helps better understand the virus transmission.

This dashboard, created by HaystackAnalytics—a healthcare startup incubated under the Society for Innovation and Entrepreneurship (SINE) at IIT-B —is an analytical tool that helps epidemiologists and public health officials understand data retrieved from genome sequencing of ribonucleic acid (RNA) samples from Covid-19 patients.

Genome sequencing has four key steps – sample processing, creating a DNA library, sequencing the data from the genomes and analysing the data. Getting results from genome sequencing can take between 72 hours and 15 days. Haystack has also been able to reduce the time taken for processing and sequencing data from genomes to less than 36 hours.

“In each of the four steps, we made changes to get a final reduction in turnaround time. For the first three steps, we needed high-end infrastructure for next-generation sequencing work. This was setup at the BioNEST facility at SINE, IIT-B, with support from the Biotechnology Industry Research Assistance Council of the union department of biotechnology. Analysis is one of the biggest bottlenecks that requires huge cloud-computing or high-performance computing clusters. We had already developed a low-compute genomic analysis platform for tuberculosis. We used that platform for Covid sequencing. This reduced the analysis time from 12-24 hrs to 15-20 minutes,” said Anirvan Chatterjee, founder of Haystack.

Ashwini Bhide, additional municipal commissioner (east suburbs), BMC, said the dashboard was created as a pilot project by the health department in association with the civic-run Kasturba Hospital. Suresh Kakani, additional municipal commissioner for the BMC’s health department, said it was part of the BMC’s plan to set up its own genome sequencing lab at the hospital, for which the BMC has tied up with various agencies.

Starting mid-March, Chatterjee’s team of scientists, led by Amrutraj Zade (PhD in biosciences and bioengineering from IIT-B) collected RNA samples from international passengers, atypical clinical presentations, children with Covid-19 infection, and patients who contracted the infection in clusters with high positivity rate. The samples were sequenced using nanopore technology and analysed at the BioNEST. The analysed data is then reflected in a simpler format for health officials.

“Currently, Covid-19 analysis is primarily based on RT-PCR tests, which only gives us a yes or no response of whether the patient is positive. RT-PCR gives us the number of cases, but says nothing about the virus variant. To better understand the virus, we need to know what kind of virus strains we are dealing with,” said Chatterjee. The dashboard created by Haystack can reference the sample with over 30 billion data points, which can indicate the strain of the variants of the virus, what kind of variants and what age groups are more likely to be affected, among others.

Dr Jayanthi Shastri, professor and head of the microbiology department of Kasturba Hospital, said, “Interpretation of genome sequencing data is a tough task for which we require trained bio informationists. This dashboard breaks down the data and makes it ready to use by health professionals. This is going to be of great help to public health officials in understanding how different variants behave, and how much the new strain varies from the Wuhan one.”

The genome sequencing data can be amalgamated into a patient report. “The setup that we have created can be imagined like a ‘COVID Genomics Pop-up’ which can be easily integrated into any current day hospital/lab,” said Chatterjee. The dashboard works similar to any e-commerce shopping portals, where products can be compared and cross-referenced against various parameters.

The project is funded by the Centre for Augmenting WAR with Covid-19 Health Crisis (CAWACH) initiative of the Department of Science and Technology (DST), Government of India. “We are confident in the next few months, genome sequencing for Covid is going to be as popular as today’s RT-PCR. And Haystack now has the solution to provide this entire thing at a cost which is already affordable. The beta version of the dashboard is up and running. We are closely working with health officials to further develop the product,” Chatterjee added.