Coronavirus: Less than 1% samples in India were genome sequenced in three months, says report

Less than 1% or 7,664 of the total coronavirus positive samples tested in the country between January and March 18 were genome sequenced, Down to Earth reported on Wednesday.

Genome sequencing is a technique that reads and interprets genetic information found in the structure of the virus over time. The scientific method is an important tool in gauging the impact of mutant strains of the coronavirus, and in identifying the variants that lead to a rise in the number of cases or deaths.

The Union health ministry had announced that the Indian SARS-COV-2 Genomics Consortium, or INSACOG, would ramp up its sequencing efforts on December 30. The country had planned to do the genome sequencing of 5% of positive Covid-19 samples from every state, and 100% of all positive samples from international travellers. The purpose of this was to identify “potential outbreaks and related strains as part of continuous surveillance”, the Centre told Parliament on March 19.

But the pace of this sequencing has been slow.

India registered 10,22,335 new positive cases between December and March. At 5%, the total number of sampled cases collected for sequencing should be 51,117 for the period, according to Down to Earth.

However, health ministry officials, including Union Health Secretary Rajesh Bhushan and NITI Aayog member (health) Vinod Paul, have refused to specify any number of the samples sequenced during this period, the website reported.

The Centre’s INSACOG comprises 10 prominent research labs. This includes the National Institute of Biomedical Genomics in Kolkata, Institute of Life Sciences in Bhubaneswar, the National Institute of Virology in Pune, along with Delhi’s Institute of Genomics and Integrative Biology, and National Centre for Disease Control.

As per the INSACOG’s guidance document released in December, these institutes have a capacity to sequence more than 30,000 samples a month.

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The Institute of Genomics and Integrative Biology alone has the capacity to sequence more than 10,000 samples a month. But till March 18, it had received only 3,186 samples, of which 1,586 had been sequenced and the rest were under process, according to Down to Earth.

Why is genome sequencing important?

While human genomes are made of DNA (Deoxyribonucleic acid), a virus genome can be made of either DNA or RNA (Ribonucleic acid). Coronavirus is made of RNA. A combination of changes, or mutations in the ribonucleic acid of the virus can give birth to a new variant.

This vast bank of genome sequences is an important resource, particularly as viruses such as the novel coronavirus have a high mutation rate. Since the coronavirus pandemic began, several new variants of the virus have shown up globally.

Renewed outbreaks in states like Maharashtra have raised the question of whether genetic changes in the virus could be driving them. The Union health ministry had on Wednesday said that a new “double mutant variant” of the coronavirus and “variants of concern” have been detected in 18 states in India so far.

But researchers and expert say that it is difficult to understand the extent to which the new variants of Covid-19 play a role in the surge in cases, unless extensive genomic testing is done at a substantial pace.

“We urgently need deeper dives into the data on Covid-19 cases, hospitalisations, deaths, and genome sequencing data, to understand why there is a spike in cases in India,” Gagandeep Kang, professor at the Christian Medical College in Vellore, had told IndiaSpend.

The hurdles

There are several reasons why the pace of genome sequencing in India has been dismal, despite its benefits.

For one, INSACOG still faces bureaucratic hurdles, Down to Earth reported. Even after three months of its launch, it has not received funds despite having asked for more than Rs 90 crore from the Union government, a scientist in one of the consortium’s 10 institutes told the website. As a result, the institutes are forced to divert funds from other sources and grants to this exercise, the scientist claimed.

There are also logistical hurdles. According to the Union health ministry guidelines, samples from only RT-PCR tests and not rapid antigen tests are eligible for sequencing as the latter is known to sometimes result in false negatives.

“The samples have to be sent within three-four days of coming out positive,” Centre for Cellular and Molecular Biology Director General Rakesh Mishra told the website. “Otherwise the purpose is defeated.”

Additionally, the samples are to be stored in these institutes at -80 degrees Celsius. “However, the problem is with logistics that pertain to samples coming from the states,” he said, adding that finding services that would transport a coronavirus positive sample is difficult because of the health risks involved.