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Genome sequencing finds B.1.617 becoming dominant variant of concern in India: INSACOG scientists

Over 20,000 samples of SARS-CoV-2 have been sequenced from across states, and the consortium has identified variants of concern in 8,000 samples with B.1.617 variant being the dominant one.

Written by Anuradha Mascarenhas | Pune |
Updated: May 21, 2021 7:12:56 am
Over 20,000 samples of SARS-CoV-2 have been sequenced from across states, and the consortium has identified variants of concern in 8,000 samples with B.1.617 variant being the dominant one.

Scientists across various institutions under Indian SARS-CoV-2 Genomics Consortium (INSACOG) have said the B.1.617.2 variant was beginning to take over as the dominant variant of concern in the country.

INSACOG is the leading national consortium of top scientific institutions in the country involved in genome sequencing of the virus. Over 20,000 samples of SARS-CoV-2 have been sequenced from across states, and the consortium has identified variants of concern in 8,000 samples with B.1.617 variant being the dominant one.

“The picture is still not uniform across states,” Dr Sujit Singh, chief of National Centre for Disease Control told The Indian Express.

“Somewhere it is B.1.617 and somewhere it is B.1.1.7. (UK variant). There are sub-lineages of B.1.617 and we are finding maximum of B.1.617.2,” Dr Singh said. B.1.617 is the technical name of the variant first reported in India. It has three sub-lineages 1, 2 and 3 and B.1.617.2 has been designated a variant of concern in UK. World Health Organization (WHO) has also declared it to be a variant of global concern with chief scientist Dr Soumya Swaminathan stating that it might may be “dodging vaccine protections”. At INSACOG, scientists are also studying whether the variants that are emerging are leading to severity of disease and trying to understand the reason behind breakthrough infections.

“Is it that the variants are not being actually protected? We need to keep checking with more vaccines coming in now,” said Dr Saumitra Das, director of National Institute of Biomedical Genomics, who is coordinating genome sequencing at INSACOG.

Dr Das said longitudinal studies were being planned to address concerns on how long the antibody titre lasted after vaccination. At present, effort was on clinical correlation with mutants, he added.

He also said a final list was being prepared that will include more centres to monitor genomic variations in SARS-CoV-2 on a regular basis. There were 10 regional genome sequencing laboratories and more applied centres had been shortlisted, he added.

“There is a need for more such centres as people are also getting infected at some of the institutes and workforce can be limited at some. Also, there are some places where we could not reach and could not get enough samples for genome sequencing. Transportation of samples is a challenge as the medium of dry ice has to be used. Hence, with all these issues, we also decided to expand to more districts so as to increase the number of the samples that can be sequenced,” he said.

Dr Das further said while the private sector had not yet been tapped, those with genome sequencing machines at different institutions could be involved in the process. “This is a process and we have to see whether they have reagents and adequate manpower. Some have been shortlisted,” he added.

While INSACOG scientists were looking at a proper representation of different states apart from routine genomic surveillance of samples, they will also keep a watch for any super spreader event or surge in any particular district, Dr Das said.

“Every country is doing that and, hence, the strategy in India is along similar lines,” Dr Das said, adding that it was important to primarily establish epidemiological and clinical correlation with the mutants.

“This is an RNA virus, which is bound to mutate, and subsequent waves would be partly because of the virus and our attitude towards it. Vaccines will be rolled out and there will be a challenge for the virus to escape the protection the vaccine offers. However, we can prevent future waves if we restrict gatherings and stick to appropriate behaviour,” he said.

BJ Medical College to be part of INSACOG, take up genome sequencing

In Pune, BJ Medical College will be included in INSACOG for genomic surveillance of samples, Dr Rajesh Karyakarte, head of the microbiology department at BJMC, said.

The lab had first observed mutations at sites E484 and L452 in the spike protein of SARS-CoV-2. The BJMC lab had tied up with National Centre for Cell Science, which had first identified this variant from samples received from Maharashtra in March. Consequently, the potential importance of this variant happened when it was correlated with international data on L452R and outbreaks in Maharashtra, according to a statement from Department of Biotechnology.

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