Maharashtra Chief Minister Uddhav Thackeray on Wednesday inaugurated Mumbai’s first genome sequencing laboratory in Kasturba Hospital. The laboratory would enable the government to detect new variants of Sars-CoV-2 – the virus that causes the coronavirus disease.

Till now, Maharashtra relied on the Indian SARS-CoV-2 Genomic Consortia, or INSACOG, a network of 10 laboratories established by the Union health ministry in December, for genome sequencing.

Thackeray said the need to be self-sufficient in genome sequencing first arose at the beginning of the second wave, when Amravati district reported a spike in Covid-19 numbers. “In February, the cases began rising there [Amravati] and they could not be controlled,” the chief minister said. “Later, we were informed that the spike was due to the Delta variant. We realised we need to do something to ensure faster sequencing.”

In January and February, samples from Amravati and other districts were collected by the National Institute of Virology in Pune. The institute shared detailed results with the Maharashtra government and district authorities after a prolonged delay in April. By then, the second wave had rolled across Maharashtra.

The genome sequencing equipment in Kasturba Hospital. Credit: Kasturba Hospital

The Brihanmumbai Municipal Corporation’s lab can run 384 samples in one round. Each sequencing test would cost around Rs 10,000 to Rs 12,000. The cost could be further brought down if the kits are purchased in bulk, said Dr Jayanthi Shastri, who heads the Department of Microbiology at the BYL Nair Hospital. The Kasturba Hospital’s molecular lab works under the microbiology department of Nair Hospital.

Besides the 10 laboratories identified by the Centre to conduct genome sequencing for all states, Maharashtra has signed an MoU with the Council of Scientific and Industrial Research Institute of Genomics and Integrative Biology to carry out genome sequencing of around 3,600 Covid-19 samples per month. The turn-around time for results ranges between a few weeks to a few months. The Mumbai lab hopes to shorten this gap to four to five days.

Shastri said that owing to the high sequencing cost, they plan to select Covid-19 samples of foreign travellers, reinfected cases and from hotspots. “Since we will be able to get results within 4-5 days, this can aid in policy planning, early identification of possible hotspots and pandemic preparedness,” she said.

The Maharashtra health department on Wednesday also discussed the possibility of setting up two new genome sequencing labs in Nanded and Aurangabad. “We have discussed the proposal, it is yet to be approved,” a state official said.

Sequencing the coronavirus genome and detecting new variants is important, scientists say, because it could provide a whole range of information that could help countries with their pandemic response. Among other things, it could tell us how the virus is mutating, possibly adapting to vaccines, and the way new variants are travelling across geographies. This is most effective when data is generated in bulk and fast and shared in real-time.

Currently, besides Mumbai, Pune has two genome sequencing labs under the National Institute of Virology and the Council of Scientific and Industrial Research.

The CSIR-IGIB has identified 23 Delta plus variants in Maharashtra till date but found no evidence of faster transmissibility. The Kasturba lab will also focus on identification of the delta plus variant. The lab has tied up with Haystack Analytics, a start up in IIT Bombay, for sequencing.

The Kasturba lab was set up in 2007 for molecular diagnostics after a deluge led to widespread leptospirosis cases and samples had to be sent to the Andaman and Nicobar Islands for testing.

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