Corona Daily 108: India’s Virus Surveillance: An Unfunded Story

Earlier, in the UK context, I wrote about the criticality of genomic surveillance. Identifying and quantifying each virus avatar is a key weapon in the coronavirus war. Without the virus gene sequences, vaccines were not possible.

India has a human talent pool that is among the best in the world. At least ten major labs can conduct genome detective work. On 12 May 2020, during the national lockdown, PM Modi appealed to Indians to become self reliant. In this age of globalization, talking about self-reliance is illiteracy; displayed time and again by the likes of Trump and Modi. Talking about self-reliance during a pandemic is lunacy.

Within three days, the order issued by India’s Finance Ministry referred to that speech. “In  pursuance of the Prime Minister’s address to the nation… in order to prove self-reliance…it has been decided no tender up to Rs 200 crore ($27 million) will be allowed.” The order became effective immediately, with no notice period.

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Labs analysing positive samples use specialised plastic containers and reagents, both imported from American companies such as Illumina. There are no Indian substitutes. The order banning tenders below Rs 200 crore brought to a halt most sequencing by September 2020. All labs ran out of reagents. The labs complained to the Ministry of Finance. The ministry finally exempted the labs in January 2021. Eight valuable months were wasted by a single piece of thoughtless paper.

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In December 2020, a welcome initiative brought India’s ten major labs together in a consortium with an unwieldy name INSACOG (Indian SARS-CoV-2 Genomics consortium). Detailed 18-page guidelines were issued.

The consortium had three ambitious goals: (a) Mapping the spread of the UK variant across India (b) Investigating regional outbreaks for early detection of new variants. (c) Continuous surveillance program to sequence 5% of all positive samples across India+100% of all positive samples of international arrivals.  

The analysis on positive samples would be conducted with retrospective effect. Rs 115 crore ($16 million) funding was promised. It was a well-conceived initiative.  

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Positive samples must be sent by the testing labs to one of the consortium labs. The samples need to be preserved at temperatures between -80 and -20. Many labs had destroyed the past samples. The consortium would accept only RT-PCR tests. Many states had conducted large scale antigen tests that didn’t qualify. By February, the consortium should have investigated 45,000 samples, it managed 3,500.

Sanctioned money doesn’t mean real money. Part of the money, Rs 80 crore was finally released on 31 March, the last day of the Indian financial year.

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The maximum capacity of the ten labs is 1,000 samples a day. In reality, they analysed about 100 a day. Today, India has 380,000 new cases. To keep the 5% mission of the consortium, it should analyse 19,000 samples today. But the maximum capacity is 1000 samples a day. In effect, the mission works only if the number of cases is low. India produces 2 million vaccines a day, but aims to vaccinate 4 million people daily. The case of the genomic surveillance is similar.

There has been talk about the Indian variant, a double mutant, a triple mutant. Data based on small samples is not reliable. And detective work must be accompanied by police action. The double mutant variant was detected in October 2020. It was found again in November and December. That discovery needed urgent action. By February, that variant exploded, causing a surge in Maharashtra state.

Competent genomic surveillance can track the effects of superspreader events. Wide-ranging genomic analysis could have verified and quantified the impact of the Kumbh Mela and election rallies. Instead, Indians are left with anecdotal evidence of obituaries of people returning from such events.

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Within less than a year of its self-reliance resolve, India is now looking in all directions for oxygen and other help. If the rich nations want to offer help, they should consider funding India’s genomic surveillance labs to ramp up their capacity. A large scale genome analysis in India is a global, not local, necessity.  

Ravi