Genomic sampling in India still adrift, sample collection less than 5%

While most developed countries had started genomic sequencing of samples — to study changes or mutations in virus structures over time — at the start of the pandemic, India took concerted efforts only in December 2020.

The Union health ministry announced the Indian SARS-CoV-2 Genomics Consortium (INSACOG) to ramp up its sequencing efforts. The objective was to collect 5 per cent of all positive Covid samples in every state. However, it has not been able to achieve the 5-per cent mark.

The data analysed by Business Standard from INSACOG’s weekly report shows the government’s record of sample collection has been less than 5 per cent, despite falling cases. Analysing the data from weekly INSACOG reports and pairing it with weekly case data from the Ministry of Health and Family Welfare shows the government could only collate samples of 1.3 per cent, or 2,530 of total positive cases (81,173) during the week in the country.

The highest ratio achieved by India was between October 25 and November 1, when INSACOG collected samples of 3.6 per cent of total cases. Overall, for the 14 weeks for which the data is available, the government’s average sample collection was 1.6 per cent. Since the government announced the formation of INSACOG, only 0.48 per cent of total samples have been collected.

“Every time a new variant is mentioned, or a new variant is detected, the interest in genomic surveillance increases overnight,” said Professor K Srinath Reddy, president, Public Health Foundation of India.

An analysis of samples was picked up in October. Of the total samples processed and sequenced, 96 per cent were analysed on November 8. Until a month ago, only 72 per cent of the samples processed had been analysed. 

The pace of sequencing has also been sluggish. At its peak, the government had sequenced over 16,000 samples in a month; only 10,799 samples were processed in October. 

Albeit somewhat higher than September’s average of 9,584 samples, it was still lower than August’s collection of 12,180 samples.

A comparison with other countries shows how far behind India stands in genomic sequencing. COG-UK, the UK’s consortium of genomic sampling, has sequenced 1.5 million samples, or 14.6 per cent of its total cases.

“South Africa has had an excellent programme of genomic surveillance, far better than the UK in terms of the reporting systems. Britain took from September to November to detect the Alpha variant and it was only in December, it shared the information with the world. South Africa did it within a few days. India also needs to ensure its capacity is built up — both in the public and private sectors. It is kept active not only for this particular virus, but for other viruses as well,” added Reddy.