CCMB, IGIB start sequencing novel coronavirus genome

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With CSIR labs now permitted to test samples of novel coronavirus, Hyderabad-based CCMB and Delhi-based IGIB have started sequencing the genome. CCMB has already sequenced the genome of five isolates.

As on April 7, India has shared nine whole genome sequences of novel coronavirus (SRAS-CoV-2) with the Global Initiative on Sharing All Influenza Data (GISAID) — a public platform started by the WHO in 2008 for countries to share genome sequences. All the nine sequences have been shared by the Pune-based National Institute of Virology. Till recently, NIV had shared only two sequences. The first two were shared on March 5.

So far, 3,086 sequences of the virus isolated from humans have been shared by 57 countries. With 621, the U.S. has shared the most number of sequences, followed by UK (350), Belgium (253) and China (242).

Sequencing the genome of SARS-CoV-2 will help understand where the virus came from, if there are different strains of the virus circulating in India, and how the virus has spread in the country.

On April 2, Indian Council of Medical Research (ICMR) allowed all national research laboratories including those under the Council of Scientific and Industrial Research (CSIR) to conduct testing for novel coronavirus. Since the CSIR labs will now have access to virus samples, they will be in a position to sequence the genome too.

According to the CSIR Director-General Dr. Shekhar C. Mande both Hyderabad-based Centre for Cellular and Molecular Biology (CSIR-CCMB) and the Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi have already started sequencing the virus.

Dr. Rakesh K. Mishra, Director of CSIR-CCMB told me that they began sequencing the genome a few days ago. “We have sequenced the genome of five virus isolates. In three-four weeks, both CCMB and IGIB want to sequence about 200 isolates,” he says.

“Getting the virus in sufficient numbers in a sample is the challenge. If more isolates are available then we can sequence more numbers,” Dr. Mishra says. According to him, CCMB is capable of sequencing around 40 isolates in three-four days.

“The genome of novel coronavirus is small. So sequencing and analysis are simple,” Dr. Mishra says. “We have sequenced the virus that we have tested. So these are from patients in and around Hyderabad. We should be sequencing the virus from across the country to get a picture of the diversity of the virus, if there is any.”

CCMB has both biosafety level (BSL)-2 and BSL-3 labs. The virus is isolated and deactivated in BSL-3 facility and sequenced in BSL-2 facility. “Besides sequencing, we will also be culturing the virus. This will help us study the virus and will be useful while testing vaccines and drugs,” Dr. Mishra says.

Published in The Hindu on April 7, 2020