India boosting genome testing in search for Omicron

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India is bolstering its Covid-19 genome sequencing efforts as it hopes that early detection of the newly-emerged Omicron variant will help avoid a repeat of the Delta-fuelled wave of infections that brought its health system close to collapse earlier this year.

Public health officials aim to analyse positive tests from airports within 48 hours and more than a dozen state-funded laboratories could be included in the current 38 that are part of the Indian SARs-COV-2 Genomics Consortium, or INSACOG, according to Priya Abraham, director of India’s National Institute of Virology.

“We learnt a lot from the second wave,” Mr Abraham, whose state-funded institution has been instrumental in detecting and mapping Covid in India, said. “The country as a whole and the government of India realizes this capacity has to be exponentially expanded.”

However, concerns remain about gaps in India’s overall Covid-19 surveillance, especially given its past track record of lax imposition of testing and isolation protocols ahead of the emergence of the newest variant.

After opening up its borders to foreign tourists in recent weeks, following dwindling infection rates, India on Wednesday will re-impose airport testing and home quarantine for fully vaccinated arrivals from countries that have registered omicron cases.

The variant, which was first identified in southern Africa last week, is feared to be more transmissible and able to evade vaccine barriers than the predominant Delta strain that emerged in India.

Despite the moves to ramp up both testing and sequencing, some government officials and experts speculate that Omicron may already be circulating in the nation that’s home to about 1.4 billion people, but which along with other large countries like China and the US has yet to detect a single case.

Abraham’s NIV, which holds a library of about 300 Covid-19 strains and is headquartered in the western city of Pune, will also seek to isolate Omicron to allow Indian vaccine makers, including Bharat Biotech International and the Serum Institute of India, to potentially calibrate their shots to the new variant. Spokespeople from both companies weren’t able to immediately comment.

The moves follow criticism that Prime Minister Narendra Modi’s government for months downplayed the early warning signs of Delta’s existence before it was designated a variant of concern in May, allowing mass public gatherings to continue during state elections and religious events despite soaring infection rates.

Efforts by a number of Indian laboratories to map the progress of the virus were also severely hampered last year by an inadvertent import ban on the chemical reagents needed by sequencing machines.

While it was eventually overturned in January, the 10 original institutions that formed INSACOG in December last year took a number of months to gear up – just as delta began its spread across the country.

“There’s definitely more preparedness compared to last time,” said Mr Abraham. “We’ve got that structure in place — if anything we’ve expanded, we are also networking with some of the major medical schools, that network is much stronger and wider.”

INSACOG’s target to analyse 5 per cent of all positive Covid-19 samples was largely abandoned during India’s second wave as infection rates peaked at more than 400,000 a day in May, leading to widespread oxygen, hospital bed and drug shortages.

Since then, infections in the country have plateaued to below 10,000 a day, attributed in part to increased vaccine uptake along with high levels of exposure to the disease.

Mr Abraham said there was scope to do more sequencing in light of the new variant, but pointed to wider improvements in India’s health care system, with oxygen plants created and a vaccination campaign that gained momentum in recent months after a stuttered start thanks to an early shortage of shots.

“The experience of the second wave in India was a profound shock and that has helped to shape public opinion and government policy towards ensuring that India should never go through this again,” said Gautam Menon, a professor of physics and biology at Ashoka University who has worked on modelling outbreaks.

“Caseloads are low in India at the moment and that will help to divert sequencing and surveillance to this effort, at least initially,” he said. “I am more concerned right now about lags in reporting, which is certainly not happening in real-time.”