Bengaluru, 3 more cities to participate in mega Covid genome sequencing

An ambitious programme to conduct large-scale and in-depth genome sequencing of samples from Covid-19 patients in four cities — Bengaluru, Hyderabad, Pune and Delhi — is set to begin.

Scientists say the project, which will sequence samples independent of the Indian Sars-CoV-2 Genetics Consortium (Insacog), will not only boost India’s genomic efforts, but will deliver near real-time insights to municipal authorities in these four cities about how the novel coronavirus has been evolving.

Professor Rakesh Mishra, former director, Centre for Cellular and Molecular Biology (CCMB), Hyderabad, who is the project advisor, explained that eight national labs will sequence 60,000 samples over the course of the next 12 months. The three-year project has been endowed with Rs 70 crore in funding from the Rockefeller Foundation.

“Out of this, Rs 25 crore will be provided for the initial first year. The project will be extended by an additional two years if the first year is successful,” explained Professor Satyajit Mayor, director for the National Centre for Biological Sciences (NCBS), also an advisor for the project.

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“There was some coordination required to get all eight national labs on board. We are now ready to start,” added Professor Mishra. That the project will boost India’s sequencing efforts is without a doubt. As per authoritative sources, India has only done about 50,295 sequences in total since the start of the Covid-19 pandemic.

“It is also an exercise to build capacity and to make it a model to be replicated in other places,” explained Professor L S Shashidhara of the Pune Knowledge Cluster. “The model can be used for other diseases, such as tracking the new variant of dengue, which was recently reported.”

The 60,000 initial sequences will be split across the four cities.

Professor Shashidhara said the sequencing strategy will be two-pronged. About 35,000 samples will be retrospective, sequencing samples from December to June 2021. The rest will be current samples.

“The retrospective samples are to assess the genomic makeup of the epidemic based on the test positivity rate. We want to determine viral factors that contributed to the dynamics of the pandemic, specifically through the first and second waves,” Professor Shashidhara said.

According to Surabhi Srivastava, Research Coordinator, Genomics and Bioinformatics at CCMB, Hyderabad, between 10 to 15,000 sequences will be done from samples in Bengaluru.

“Local state and city health authorities have been very supportive.

“In Bengaluru, the Bruhat Bengaluru Mahanagara Palike (BBMP) has provided us with the entire line lists of patients, so we can pick and choose whose samples we want to sequence. This gives us the ability to conduct broad-spectrum sequencing, which will give us the necessary data to conduct analysis,” added Mishra.

While this project is outside of Insacog’s existing sequencing efforts, all the results will be aligned with the consortium, Mishra explained.

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