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65% samples test positive for Delta variant in genome sequencing at Kasturba hospital

Results of genome sequencing of the first batch of 188 samples at Kasturba Gandhi Hospital were declared on Monday. The hospital requires to undertake further tests to identify Delta Plus variants.
Kasturba Gandhi Hospital. (HT PHOTO)
Published on Aug 23, 2021 11:28 PM IST
ByRupsa Chakraborty, Mumbai

In the first cycle of genome sequencing, Kasturba Gandhi Hospital tested 188 samples of which 128 tested positive for the Delta variant. This is the first time that the Brihanmumbai Municipal Corporation (BMC) got genome sequencing report within a week.

The Delta variant, also known as B.1.617.2 of Sars-Cov-2, the virus that causes Covid-19, was first detected in India in late 2020. This variant, which continues to be the dominant variant across the globe, has now spread to 80 countries.

Genome sequencing is an exercise to study the changes in the structure of the virus over time. A combination of changes in the ribonucleic acid of the virus can give birth to a new variant.

The hospital requires to undertake further tests to identify Delta Plus variants.

“In the first cycle, 65% of the samples tested positive for the Delta variant. Two samples have been identified with Alpha variant and 24 with Kappa,” said Suresh Kakani, additional commissioner, BMC.

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When asked if any sample tested positive for Delta Plus, Dr Jayanti Shastri, in-charge of the molecular diagnostic reference laboratory of the hospital, said, “We need further tests for that.”

Delta Plus (AY.1) is a mutation of the highly transmissible Delta variant and was detected in the state during the second wave. In June, the Union health ministry declared it as the variant of concern.

The 188 samples which were tested were collected from international passengers, Covid-19 hot spots, places with high transmission rate among others.

On August 4, the hospital inaugurated the machines for genome sequencing, making it the first civic-run hospital to conduct the tests in the state. After over two weeks of installation process, the hospital started the procedure of genome sequencing on August 17. The results of the first cycle were declared on Monday.

“We started the first stage on August 17 and boarded the samples for sequencing on August 20. The reports of the analysis came on Monday,” she said.

Whole genome sequencing tests comprise three phases—library presentation which in simple form is called pre-sequencing preparation, which takes two-three days. The researchers sequence the samples in the machine that generally takes 4-5 hours. In the third stage, they analyse the results to understand the variations.

Since genome sequencing is not a diagnostic tool, suspected Covid-19 patients will have to undergo compulsory RT-PCR for the diagnosis.

“Unlike RT-PCR which is a target-based testing, sequencing helps to identify unknown pathogens that will help us to understand the genetic coding of the viruses,” she said.

As HT reported earlier, the machines have been procured through donations that cumulatively cost around 10.5 crore. An US-based biotech company has donated 6.4 crore. Mumbai-based ATE Chandra Foundation has donated 4 crore for the machine.

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