COVID Fight: Why’s India Still Not Focussing On Genome Sequencing?

We are still not sequencing coronavirus samples in India. This shows our approach is still reactive, not proactive.

Coronavirus variants: New corona mutations and variants are being reported from Japan, Brazil, UK and South Africa. India needs to focus on genome sequencing.

(Photo: iStock) 

The uptick in the number of COVID-19 cases is a cause of worry. Even the prime minister expressed his concern to all states in a recent meeting. He stressed the importance of following protocols, scaling up RT-PCR testing and vaccinations.

Yet, there is an important point he did not touch upon — the sequencing of the COVID-19 virus samples in the country. This shows that India’s approach to the pandemic is still reactive and not proactive.

It is well-known by now that the novel coronavirus is mutating with time. If the mutations make it more virulent but less deadly, we need to prepare for more sick people. If it makes it less virulent but more deadly, we must prepare for more social distancing and expedite contact-tracing.

The government’s focus is to reduce the test positivity to 5 percent. This is like saying, ‘we do not care if the virus kills or hurts more. We only have a problem if it infects more than a given number of people every day’.

To understand which way the virus is mutating, we need to sequence its genome. This must be done thoroughly and regularly.

Coronavirus is Mutating in India Rapidly — What Are We Doing About It?

The United Kingdom set up the COVID-19 Genomics Consortium (COG-UK) for this purpose. Established with a £20 million grant, the program tied-up with major universities and research institutes. It leverages its facilities to carry out genome sequencing of the COVID-19 virus.

Since its establishment in April 2020, the Consortium has sequenced over 3.5 lakh virus samples. It has contributed over 45 percent of the viral sequences in the public databases globally.

It is the thorough sequencing that enabled the recognition of the ‘UK variant’ of COVID-19. Without sequencing data, the rise in cases would be attributed to poor public behaviour.

After much delay, India too launched its own sequencing initiative in December 2020. Called INSACOG — Indian SARS CoV-2 Genomics Consortia — the program was first tasked to find if the UK variant had made inroads into India.

After analysing a few positive samples and testing travellers from the UK, the Consortium concluded that it hadn’t.

News that foreign variants are not behind the recent rise in cases is actually a matter of concern. Samples tested by the Indian Institute of Science in Bangalore (not part of INSACOG) revealed a higher number of mutations than the national and global average. This means the virus is mutating rapidly in India as well.

COVID Surge Can’t Only Be Due to People’s Behaviour — Something About the Virus Has Also Changed

The INSACOG program has suffered sample sourcing issues from all states. That it found no mention in a meeting with all chief ministers is quite shocking. Instead, the blame for the surge in cases is being shifted on the public.

Public behaviour has not changed much since the festive season last year. We saw this public behaviour as COVID-19 cases began their surprising downward trajectory. We have held mass gatherings and conducted elections during this time.

The surge cannot be because of people’s behaviour alone. Something has changed about the virus and we do not know what that is.

To understand the change, the INSACOG program must run on all cylinders. Yet, little work has happened on the ground. The amount allocated to the project is Rs. 100 crores or £ 9 million. That’s lesser than half the budget of COG-UK for a population that’s 20 times larger. More importantly, that funding hasn’t arrived. Earlier this month, the Consortium that could have sequenced over 80,000 viral samples had managed just over 3500, with participants' own funds.

Why Our Health Ministry Is Unable to ‘Pin the Blame’ On New Corona Variants

During its inception, INSACOG planned to sequence five percent of reported positive cases. This is what the COG-UK program is also doing, and it is commendable. In a press conference on 17 March, NITI Aayog member VK Paul said that sequencing was sophisticated and it could not be done in lakhs. This realisation within months of INSACOG’s launch, questions the seriousness with which it was set up.

With the recent rise in cases, we need to process samples on war-footing and continuously. Comments from the NITI Aayog member signal that it will not be pushing the agenda further.

This is not only tragic but also irresponsible.

The latest update from INSACOG reported a virus variant with two mutations in 15-20 percent of the samples tested across the country. The total number of samples sequenced still stood at 10,787. With such abysmally low numbers, the Health Ministry could not attribute the recent spike in the cases to this new variant either, leaving us equally clueless like before.

What’s the Way Forward in COVID Fight?

One could argue that deploying vaccines would be a cost-effective alternative to sequencing. With just over 2.3 percent of the population vaccinated, we are far away from reaping its benefits. Rather, sequencing efforts must continue even after vaccinations.

Studies about the Brazilian variant show that it can reinfect people. Pfizer and AstraZeneca vaccines are less effective against new variants. An increase in vaccination numbers will result in more mutations in the virus. Only sequencing can provide the answers that we need to proactively determine our policy for future surges.

(A molecular biologist by day and a blogger by night, Ameya Paleja writes about genetics, microbes and the future of technology at Coffee Table Science.  Scientific research and policy making are also areas of his interest. You can tweet to him at @ameyapaleja. This is an opinion piece and the views expressed are the author’s own. The Quint neither endorses nor is responsible for them.)