April 1, 2021 1:21:48 am
By mid-April, Kasturba hospital will become the first government hospital in Mumbai to conduct genome sequencing on Covid-19 test samples to assess mutations in cases surfacing locally and among international passengers arriving in the city.
Genome sequencing involves analysis of the genetic code of the virus, which helps scientists find the exact location where a mutation has taken place. Mutations in specific proteins of the virus tend to make it more virulent. The sequencing will help in analysing its virulence as well as its spreading pattern. Genome sequencing is both time consuming and expensive, costing Rs 7,000 to Rs 12,000 per sample.
Additional Municipal Commissioner Suresh Kakani said that until now, Mumbai was sending its samples to the National Institute of Virology in Pune for genome sequencing, which would take several days to come up with results. Over the last three months, Mumbai has sent at least 223 samples to various government laboratories and found UK variants of the virus in 22 of them. No additional information on other mutations has been released to BMC, Kakani added.
To do away with transportation issues and delay in results, BMC’s Kasturba molecular diagnostic lab is tying up with Haystack Analytics, a start-up of IIT-Bombay, to perform in-house sequencing. So far, 40 samples have been sequenced under the collaboration. IIT has received 200 samples for the purpose.
Dr Jayanthi Shastri, in charge of the Kasturba laboratory, said they will undertake genome sequencing to answer specific research questions. “Earlier, transmission of the virus in the entire family was not uniform. Women in a family were not getting as infected as men. Now, all are getting infected. Though transmission has increased, the severity of the virus has decreased. Sequencing can help answer all these questions,” she added.
BMC plans to look at samples taken from one neighbourhood or family clusters to see if a specific mutation is driving the transmission pattern.
BMC Commissioner Iqbal Singh Chahal has told the media that all members of a family are testing positive now within a few hours of one another, a pattern he attributed to a mutant virus. Officials said a city-based genome sequencing lab will ensure that BMC is able to detect mutations faster, helping drive policy decisions.
Shastri said samples can deteriorate while being transported to another city or get exposed to varying temperatures. “We have limited resources that we need to judiciously use. We will use a strict criteria for selecting samples for sequencing.”
The laboratory will procure a Nanopore sequencing technology, which does not need huge investment and is cost effective if more samples are processed in one go. Other two common sequencing technologies are Illumina and Ion Torrent.
Across Maharashtra, 1,600 Covid-19 positive samples have been sequenced so far. In 206 samples, a double mutation of E484Q and L452R was detected. Civic officials said they need to sequence more samples to check if either of these two mutations are responsible for Mumbai’s surge.
The Kasturba lab, which is saving all test samples of positive patients, has a deep freezer that currently stores over a lakh samples. Shastri said preserving samples is essential to test in case of reinfection or if older samples need sequencing.
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