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India will want to scale up genome sequencing: Sharon Peacock, Genomics UK


India should scale up genome sequencing to find out if the coronavirus variant is mutating and whether a shift in mutation is behind decline in the country’s Covid-19 cases, chair of Covid-19 Genomics UK (COG-UK) Sharon Peacock told ET in an exclusive interview.

“Genome sequencing could define whether or not a fall in prevalence of Covid-19 in India is due, at least in part, to a shift in variants causing the disease,” said Peacock in her first interview to an Indian newspaper. “Regardless of rates of infection, if there is ongoing variant replacement, I would want to know what it is being replaced by, because one variant tends to be replaced by another variant that is fitter,” she said.

The British microbiologist’s comments come days after world leaders at the G7 Carbis Bay summit decided to scale up genome sequencing to 10% of all new positives and boost global surveillance amid the pandemic. While the UK is sequencing 50-60% of all positive samples, India is sequencing less than 1% against a target of 5% it had set for itself.

Peacock heads COG-UK, a group of public health agencies and academic institutions in the UK created in March 2020 to sequence and analyse genomes, which has sequenced 500,000 samples — or half the coronavirus genomes mapped globally — so far, making it the world leader in the field.

In contrast, India sequenced 30,000 samples till the first week of June. India began genome sequencing in December 2020, after it established INSACOG, a consortium of 10 laboratories, which has grown to 28 now.

“India will want to scale up genome sequencing. The country has challenges of scale based on size and population,” said Peacock. “It will be important to consider sampling strategy, with a proportion of sequencing capacity used for randomly selected samples as well as sequencing in areas where an increase in cases is occurring.”

Genome sequencing can better inform India’s vaccine policy, according to Peacock. “It is a key tool in assisting with vaccine rollout and maintaining efficacy,” she said.

Detecting Variants

Peacock said, “There is every reason to continue genome sequencing in the longer term to detect emergence of future variants that have immune escape.”

COG-UK has evolved over the past year from a consortium that generated data to an agency guiding the UK’s public health policy steps on Covid-19. Tracing the journey of COG-UK from when it discovered the Alpha variant, Peacock said, “With the Alpha variant, there were two observations that came together. The first was a surge in cases during lockdown in Kent in the UK in November 2020. At that stage, it was difficult to be sure whether this was due to the virus or human behaviour.”

The second observation was genetic, said the microbiologist. “Alpha variant had 23 different mutations, which set it apart. The two observations came together, and a period of intensive investigation led to evidence that showed a cause and effect – a link between the increasing cases and a variant that was more transmissible,” she said.

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