A health worker takes a swab sample from a passenger at KSRTC bus station, Bangalore on December 14, 2020. Photo: PTI/Shailendra Bhojak

It is now expected that in every major outbreak of the novel coronavirus, genome sequencing will be a crucial part of epidemic surveillance. But even as India’s third wave is underway, driven by the omicron variant, at least five facilities part of the country’s genome sequencing consortium have reportedly halted work.

NDTV reported on Thursday that the cause was a shortage of reagents. All of these facilities are part of the Indian SARS-CoV-2 Genomics Consortium (INSACOG). The central government oversees this consortium, which currently includes 38 laboratories. According to the report, the five institutions ran out of funds to purchase the compounds needed to sequence positive patient samples.

The Center usually refutes reports it claims to be wrong through the Press Information Office – but this time it did not. That said, Friday times now quoted unnamed Health Ministry officials as saying there was no shortage of reagents.

Also on Friday, National COVID Task Force Chairman Vinod K. Paul said all was well with India’s genome sequencing effort and the consortium had sequenced around 16,000 viral genomes from samples. in December.

He, however, said nothing about a shortage of reagents. (He also said that India has sequenced the second highest number of samples in the world; a fact check by The science of yarn found this entirely false.)

At a review meeting that Prime Minister Narendra Modi chaired on December 23, he stressed the importance of genome sequencing. He had made the same remark during a COVID-19 response review meeting the previous month.

Even Union Health Minister Mansukh Mandaviya had instructed state officials to ensure that the minimum number of positive samples were sent for sequencing each month. The science of yarn revealed in November that states were stumbling.

Now, however, it appears that a shortage of reagents is limiting genome sequencing efforts at the other end of the pipeline — the end the Center directly oversees.

The governments of Maharashtra, Kerala and Delhi have launched their own genome efforts in addition to INSACOG. Of all the samples that have been sequenced so far in the country, 27.1% are from Maharashtra, 8.9% from Kerala and 7.9% from Delhi.

When the Center created the consortium in December 2020, it said 5% of all positive samples would be sequenced. But India has never been able to sequence even 1% of all those samples. Four months later, the Center revised the strategy to say that all states should send 30 samples per month from each of their sentinel sites (a site where large numbers of people are tested for COVID-19).

But even at the beginning of 2021, there was a problem related to reagents: as The science of yarn reported, the Ministry of Finance had passed an order in May 2020 restricting the importation of goods worth less than Rs 200 crore. This immediately pinched the supply of reagents and some plastic lab equipment for which no Indian manufacturer existed. And genome sequencing efforts have slowed.

January 21, Economic period reported that genome sequencing uncovered the omicron variant in 90-95% of all positive samples, compared to 50% of samples through the last week of 2021.

Anurag Agarwal, director of the Institute of Genomics and Integrative Biology in New Delhi, told the paper that even if the omicron variant becomes more dominant, the delta variant is likely to persist in some small population groups because it is more virulent. .

For this reason, genome sequencing is an important tool from a public health perspective: to understand which variant is spreading where and how fast, and to adjust our policy response accordingly.