Omicron Variant Surge | Can India’s Genome Sequencing System Keep Up?

Why is genome sequencing important in the fight against COVID-19? Is India sequencing enough positive samples?

5 min read
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With the Omicron variant surging across the world, there has been a renewed interest among scientists, health authorities, as well as the regular public in keeping abreast with the latest developments when it comes to the COVID-19 virus.

On 30 December, Delhi Health Minister Satyendar Jain, in a press conference, spoke about how 46 percent of COVID-19 cases in Delhi were of the Omicron variant, as per the latest genome sequencing report.

In another news report, Dr Dipu T.S., Associate Professor, Division of Infectious Diseases, Amrita Hospital, Kochi, told IANS, "according to statistics from Global Initiative on sharing all Influenza Data (GIS AID) - an open-access resource for viral genomic data - Omicron has surpassed all other variants as the most common in India. The Omicron variant was discovered in almost 60 per cent of the samples sequenced in India during the last few days of December."


Where does this data come from?

How many samples of positive cases are really sequenced for variants in India?

How much of the 'third wave' in India is driven by the new variant of concern really?

The answers to these questions do not come easy.

Genome Sequencing in India

Genome sequencing is the process through which the DNA of a virus is studies to identify mutations and gauge its spread and behaviour.

In fact, in late 2021, it was thanks to their robust genome sequencing program that South Africa was able to detect and report the Omicron variant as early on as they did.

The vital role of genome sequencing in the fight against COVID-19 was recognised by countries as the world emerged out of the first wave and geared up to more infectious variants.

But apart from some countries like South Africa, Israel, the UK, and other countries in Europe, there has been a noticeable and consistent void in the virus surveillance systems of countries across of the world, including India.

To begin with, getting any information about COVID-19 genome sequencing in India requires one to jump through several hoops. One reason for this could be that genome sequencing in India is carried out centrally.

In India, "the INSACOG's network of laboratories is responsible for sequencing, and INSACOG is the nodal agency for all COVID-19 sequencing, so these results must ultimately emanate from them, even though states also have access to these results," explains Dr Gautam I. Menon, Professor, Departments of Physics and Biology, Ashoka University.

This data though, is all very hush-hush and not available in the public domain.


In a previous article, experts spoke to The Quint, about the lack of access to centrally collected COVID-19 data in India, and how it comes in the way of making effective science based interventions.

But why is this data important? Does one even need to know what COVID variant they are infected with?

What Variant Have I Caught?

The thing is, as an individual, there is not much to gain from knowing what variant of COVID you have been infected with considering the symptoms and treatment don't vary by variants.

Dr Anurag Agarwal, director of the Institute of Genomics and Integrative Biology, an institute of the Council of Scientific and Industrial Research (CSIR-IGIB) reiterates this, saying,

“At an individual level, once Omicron has rapidly spread, there is only a small clinical value for knowing Omicron vs Delta. The treatment, except for monoclonal antibodies, will be identical at this time. Severe disease can occur with either, although frequency is lower with Omicron.”

And yet, genome sequencing has been at the core of the fight against the COVID-19 pandemic the world over.

What makes genome sequencing a critical tool to have?

For one, Dr Anurag Agarwal explains, “As always, sequencing will help identify further changes to the virus, which cannot be done in any other way.”

"Genome sequencing will help guide the degree of penetration of Omicron into communities," adds Dr Agarwal.

"Genome sequencing is also being encouraged in situations such as use of monoclonal antibodies, which work against Delta but not Omicron. Health ministry is validating and introducing such tests."
Dr Anurag Agarwal, Director, CSIR-IGIB

So, a robust virus surveillance system with efficient genome sequencing can help us stay toe to toe, if not a step ahead of the virus as it mutates, and can help us identify community transmission to implement targetted intervention.

This brings us to the question, why is India's genome sequencing rate still so low?

Two Little, Too Late?

Low number of sample sequencing was a concern that was raised by experts even during the devastating second wave with the Delta variant. And yet, not much seemed to have changed.

India has, so far sequenced and shared only 0.3 percent of its total positive samples according to a report in Bloomberg.

As per official reports shared with PTI, 468 samples from Delhi were analysed between 21-28, 38 percent were classified as that of the Omicron variant. To put this into perceptive, in the same week, Delhi recorded 2,814 positive COVID-19 cases.

But, according to Dr Agarwal, sequencing is done of select samples with good reason.

“Genomic sequencing is on the samples received, which is not all samples. High-risk samples such as travellers, contacts are prioritised for sequencing.”
Dr Anurag Agarwal, Director, CSIR-IGIB

Moreover, he explains, only a fraction of positive cases needs to be sequenced to study community spread of a variant.

According to Dr Agrawal, state data about the percentage of omicron cases are projections from the small number of samples sequenced, but this works because, he says, "it is a projection with reasonable accuracy - since percentages would be roughly the same in a reasonably sized group drawn from all cases."


Even so, the question arises, what's stopping India from ramping up sequencing, if it could help better understand a third COVID wave?

One reason for this could be the high centralised nature of the process.

Apart from Maharashtra and Kerala, all states send their COVID positive samples to a handful of centrally run labs under the Indian SARS-CoV-2 Genomics Consortium (INSACOG), creating a severe bottle neck.

In fact, experts in India have been lobbying for allowing more private hospitals, and even states to conduct these tests.

Although some effort has been put to expanding the testing capacity—Rajasthan has also developed state run facilities for genome sequencing— the number remains low this time around as well.

According to Dr Gautam Menon, ramping up genome sequencing in a country like India is such a short period of time is not an easy feat.

"The difference is largely capacity and manpower and not so much technology. In smaller countries with much better sequencing capabilities, it is possible to sequence every positive case or at least a good fraction of them."
Dr Gautam Menon, Professor of Physics and Biology, Ashoka University

"It isn't easy to ramp up sequencing all of a sudden. It needs trained manpower, for one, as well as suitable capacity. The government should open up testing to private laboratories as well - this would help to address the testing shortfall."

But, according to Dr Agrawal, efforts are being made to widen India's scope of sequencing capabilities.

"Since there are two lineages of Omicron in India (BA.1 and BA.2) and S-gene dropout tests from abroad only identify BA.1, India is developing better indigenous tests that can identify both."

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Topics:  Genome   COVID-19   Omicron 

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