The number of Covid-19 cases in India has just crossed the 25-million or the 2.5 crore mark. That is a 16 million (1.6 crore) increase from November 23 — the date from which the government said it would do the genome sequencing of five per cent of positive cases.

Which means that by now, the Indian SARS-CoV-2 Genomic Consortium (INSACOG) should have sequenced 800,000 (or 8 lakh) genomes of the virus. A May 6 press statement of the Department of Biotechnology said that, so far, about 20,000 samples had been sequenced.

Clearly, the SARS-CoV-2 genome sequencing programme is not going as per planned.

INSACOG is a consortium of 10 laboratories. Quantum wrote to all ten, seeking information. Two replied, saying they were not authorised to speak; Saumitra Das, director of NIBMG, Kalyani, the coordinating institute, said the information was available on the INSACOG website. It isn’t.

Sequencing of the genomes of viral strains is important from a ‘know-thy-enemy' point of view. A genome is the complete set of genetic instructions that is present in an organism, in the form of its DNA. Sequencing refers to knowing the exact sequence of occurrence of the four nucleotide bases—A, C, G and T, which are the first letters of the names of four bio-molecules.

Since each mutation is caused by a change in the genome sequence, knowing the sequences helps keep track of the mutations. In other words, genome sequencing can provide information on mutations or genetic variants that cause the disease or can increase the risk of disease in a person.

On December 22, the government noted in a statement that “the overall aim of the proposed Indian SARS-CoV-2 Genomics Consortium is to monitor the genomic variations in the SARS-CoV-2 on a regular basis through a multi-laboratory network.” It added: “This vital research consortium will also assist in developing potential vaccines in the future.”

The pandemic hit the country so severely in March 2020 that the government had to declare a national lockdown. Yet, it was not until December that the government announced the consortium for genetic sequencing. INSACOG was launched on December 30 last year, a good 11 months after the first case occurred in India.

Even then, things do not appear to have gone on smoothly. For example, INSACOG asked for Rs 100 crore; but it was not until March that any funding arrived and it received Rs 70 crore. But it is not clear whether the programme has been cash-strapped from the start. There have been reports indicating so: Dr Rakesh Mishra, who recently retired as the Director of the Centre for Cellular and Molecular Biology (CCMB), Hyderabad, one of the ten INSACOG institutions, said funding was not a deal breaker because the institutes could manage with their own funds, and with the assurance of more funds coming.

It is clear now that the 5 per cent target is highly unlikely to be achieved ever, because of the rising number of cases. The ‘5 per cent’ was not randomly chosen; it is the minimum .required to keep track of the virus variants. Today, the active cases are rising at about 1.2 lakh a day. Five per cent of it is 6,000 samples. Going by the data provided by the government in its December 22 note, the ten laboratories together have a capacity to sequence about 30,000 samples a month, or 1,000 a day—six times less than what is needed to meet the target.

Only now has the Union Health Minister, Harsh Vardhan, announced that 17 more laboratories would be added to the ten.

It is not that genome sequencing of the SARS-CoV-2 virus began only after INSACOG was formed —laboratories had started the work in April 2020. Initially, about 4,000 samples were sequenced randomly across the country. However, at that time, none thought it necessary to generate detailed reports of the variants.

The work was hampered by the unintended consequence of the government’s ‘AatmaNirbhar Bharat’ order of May 2020, which banned imports of goods worth less than Rs 200 crore to promote local procurement. Genome sequencing requires some imported material and, so, the entire effort of genome sequencing slowed down. Even after the government exempted items needed for genome sequencing from the ambit of the scheme, some special plastics inadvertently remained within the import ban.

So, for several precious months, the effort of genome sequencing was happening in a sporadic and un-coordinated way and it was not until the first report of a UK ‘variant of concern’ was published in December that the government sat up. “The government immediately initiated the network of large-scale sequencing of viral genome,” says the INSACOG note of May 6.

There has been some difficulty in sample collection. The samples have to be provided by hospitals that do RT-PCR tests. "The healthcare system is already over stretched and this is one additional task for them to sort and package samples and RNA preparations regularly for shipping in a cold chain to sequencing centres along with recording extensive metadata to make sequence information useful," Mishra tells Quantum. They have to randomly select 5 per cent of the positive cases. Some people close to the labs say that sample collection has not been happening in a truly scientific way, because of the fatigue among healthcare workers.

All this tell upon identifying variants. Identifying mutants early is important. “We are picking up the variants, but which ones are ‘variants of concern’ would be known only later when they start to show an increasing footprint or any other clinical distinction,” Mishra says.

The poor progress in genome sequencing also affects India’s image abroad, as all countries are required to upload data into a common global repository, called the ‘Global Initiative on Sharing all Influenza data’, or GISAID. This is to alert the world about new mutants. The world is watching apprehensively at India’s massive sweep of the second wave and would be expecting India to capture variants and put the data into the common database.

How much of India’s data has been put into the pool is not known, but the May 6 note said “50 per cent of the data has been uploaded in GISAID”. Since the samples sequenced were “about 20,000”, only about 10,000 have been put into GISAID. As a percentage of the total number of cases in India so far—25 million—this is a miniscule 0.004 per cent.

The world is moving towards ‘next generation sequencing’, or NGS. There are several NGS platforms, but the common feature is that they analyse thousands of bits of DNA chains simultaneously. The process is faster by orders of magnitude. NGS is an important tool in disease control and origin tracing. At such a time, India seems to be a laggard.

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