Tardy hunt for UK variant of virus

Centre not actively looking for community spread of strain, says scientists

Though the Union Health Ministry has confirmed the presence of 96 instances of the ‘UK variant’ — a form of the Sars-Cov2 associated with high infections — in India, it is yet to significantly begin looking for the variant in those without such history. So far these variants have only been identified in those with international travel history after November.

The new strain, B.1.1.7, has been reported to have several mutations that likely make it more infectious and is said to be responsible for a spike of coronavirus infections in the UK.

Local spread

Scientists associated with the sequencing exercise, on condition of anonymity, told The Hindu that it was “highly unlikely” the variant wasn’t locally present in India in those without travel history and that not enough was being done to actively look for it.

On December 22, the government announced it had set up a consortium of 10 labs across the country to sequence about 45,000 (or 5% of positive cases) from November 23 to December 22.

This is in addition to all of those who’ve come into India from overseas since November 23 and tested positive, as well as those with a travel history in September and October. So far, efforts have been focussed on sampling 3,000-odd genomes with such history.

Identifying such variants is important because in the event of a rapid spike in cases, it can be analysed if certain variants are responsible. It would also be necessary to grow these viruses in the lab so that scientists can then design appropriate tools to make diagnostic devices or even improve vaccine development efforts. Whole genome sequencing involves bigger machines, more expertise and is the only way to quickly and accurately detect emerging variants of the coronavirus.

‘Just a handful’

“So far we’ve only processed only a handful samples in the general population (of the 5% lot). That’s too little and given that the variant has been around since September and many have come in since, there’s a good chance that the variant has spread locally in India,” said a scientist closely associated with the exercise but is anonymous due to restrictions on discussing these with the media.

Another scientist in another lab involved with the sequencing activity said reagents that are necessary for whole genome sequencing were scarce and restrictions imposed by the government since July prohibited sourcing them.

“Some reagents are only available abroad. No Indian company makes them and yet, we’ve been asked to procure locally. This greatly hindered sequencing even though the machines were available.”

Last week, however a notification from the government has eased this and has clarified a “process” to acquire them, the person — again who couldn’t be identified for reasons cited earlier — added, saying, “It will take some time however to catch up on lost time.”

According to a detailed proposal unveiled by the government on December 22, a consortium of 10 labs with the capacity to sequence about 30,000 genomes a month — called INSACOG (Indian Sars-cov2 Genomics Consortium) — was created particularly in the wake of reports of infectious variants in the United Kingdom and South Africa.

This plan, however, indicates that the government would prioritise sequencing genomes of those with travel history before moving on the general population.

Renu Swarup, Secretary, Department of Biotechnology,, which coordinates INSACOG, said problems with procurement had been sorted. “We are constantly on the watch for not only the UK variant but others of interest reported from other countries. The sequencing from the population has begun and so far there seems to be no evidence of a wider spread.”

“We’ve cultured viruses from some of the samples at the National Institute of Virology. The sequencing activity is in progress and so far we can confirm that none of these variants have been identified in those without international travel history,” Dr Balram Bhargava, Director-General, Indian Council of Medical Research, told The Hindu on the sidelines of a press briefing.

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