Omicron in India: Here's how genomic surveillance can help in tackling new COVID-19 variant

India has joined a growing list of countries where Omicron has arrived after two infections linked to the newest WHO-designated Variant of Concern (VoC) were reported in Karnataka. While the world waits for more details to emerge on how much of a worry Omicron really is, health experts, including the WHO, are stressing the need for countries to step up on genomic surveillance to identify variants of the novel coronavirus that may display an ability to evade public and social health counter-measures. Towards that end, the Centre has urged states to ramp up testing and increase the submission of samples for genomic sequencing. Here’s how it’ll help.

How can genomic surveillance help?

Unusual symptoms of a viral infection that she began observing in patients sometime around the middle of November led a South African doctor to apprehend that a new variant of the novel coronavirus may have emerged.

She wasted no time in alerting South Africa’s National Institute of Communicable Diseases (NICD), which on November 25 announced to the world the emergence of the B.1.1.529 variant of the novel coronavirus that has now been named Omicron and designated as a Variant of Concern (VoC) by the World Health Organisation (WHO).

Preliminary findings have made the WHO state that this variant may pose an “increased risk of reinfection… as compared to other VOCs" and that it “may have a growth advantage", that is, Omicron may be able to spread faster from one person to another. Samples from which the variant was isolated, reports say, were collected by South African authorities between November 14 and 16, the actions coinciding with a sudden surge in cases in the country. This variant was also flagged by officials in neighbouring Botswana.

Thus, within two weeks of health experts first observing unusual symptoms and amid a rise in case count, the country managed to identify a whole new variant that has triggered widespread worries over its impact on the pandemic’s trajectory.

While South Africa has been unhappy with restrictions imposed on travel from the country, the fact remains that quick identification of the new variant allows governments to roll out what they anticipate to be the requisite steps to control the spread of this new variant. On the other hand, some vaccine manufacturers have already said they are looking at tweaking existing vaccines to attack the mutations on Omicron.

Now, think of a situation where South Africa did not have any mechanism to undertake genomic surveillance and, hence, failed to catch the rise of Omicron. It may have been too late, in such a scenario, before anybody realised that a new variant has broken through, seeding breakthrough cases and reinfections and putting health systems under increased pressure.

What is genome surveillance?

A gene, at the basic level, is a unit of heredity. It helps determine the characteristics and physical properties that one generation inherits from its parents. For a virus-like Sars-CoV-2, the genetic information dictates how it infects human cells and makes copies of itself. But while human genes are made of DNA, Sars-CoV-2 is an RNA virus. And, given that it is a microscopic entity, the Sars-CoV-2 has a genome — which is the complete set of genes or genetic material present in a cell or organism — built of around 30,000 nucleotides, which in turn are the building blocks of DNA or RNA.

Sound confusing? Well, to cut a long story short, genomic surveillance involves tracking changes in this genetic make-up of the virus to see how changes in the order of the nucleotides are bringing about changes in how the virus behaves. That is, whether it’s able to spread faster, evade antibodies gained through prior infection or vaccination, escape detection in tests, etc.

As the WHO notes, Sars-CoV-2 “like all viruses, accumulates nucleotide mutations over time [and] these mutations result in the formation of distinct viral lineages". The emergence of new variants is expected, WHO says, pointing out that while “most have no impact on viral behaviour, some mutations may produce changes" in its structure, which may be far-reaching enough to merit close attention and an upgrade in counter-measures.

Thus, as the US CDC points out, “genomic sequencing allows scientists to identify Sars-CoV-2 and monitor how it changes over time into new variants, understand how these changes affect the characteristics of the virus, and use this information to better understand how it might impact health".

How is genomic surveillance done?

As experts from the University of Pittsburgh note in an article in The Conversation, while a Covid-19 diagnostic test is concerned with confirming whether an individual has contracted the disease, “genetic sequencing decodes the genome of Sars-CoV-2 virus in samples from patients".

“Before the Covid-19 pandemic, this kind of genomic surveillance was reserved mainly for conducting small studies of antibiotic-resistant bacteria, investigating outbreaks and monitoring influenza strains," the researchers write. However, as a report in the journal Nature says, “the pandemic has ushered in an era of genomic surveillance in which scientists are tracking genomic changes to a virus at a speed and scale never seen before".

Genomic surveillance involves undertaking sequencing of positive samples of Sars-CoV-2 to determine its entire genetic makeup, which would reveal changes in areas of the genome that in turn would allow scientists to gauge how the changes impact the virus’s behaviour.

WHO says that tracking of variants “can be done through genomic surveillance as well as through detection of epidemiological signals and unexpected trends". But such sequencing requires advanced labs and highly-trained researchers, something that most countries across the world lack, which prompted WHO to note that countries with low capacity to perform sequencing “are strongly encouraged to take steps to facilitate access to existing regional and international sequencing networks and partnerships".

Even though sequencing capacity varies “significantly within and between countries", the UN health agency says that “capacities for Sars-CoV-2 sequencing activities have expanded considerably as the pandemic has evolved".

How is India conducting genomic surveillance?

In guidelines for genomic surveillance released in July this year, the Indian Sars-CoV-2 Genomics Consortium (INSACOG) says it was established to expand genomic sequencing of Sars-CoV-2 across the nation and, after initially starting with a network of 10 regional laboratories across the country, has expanded to include 28 centres mapped to the states and UTs to ensure smooth flow of samples.

INSACOG says that its “overall aim… is to monitor the genomic variations in the Sars-CoV-2 on a regular basis through a multi-laboratory network". The objective through such surveillance is to achieve early detection of variants, determine the genomic variants in cases like breakthrough infections, superspreader events, etc., correlate the surveillance data with epidemiological data and suggest public health actions based on such analysis.

For this, INSACOG has identified “sentinel sites", which are designated RT-PCR labs and secondary and tertiary care hospitals in states and UTs. Such sentinel sites were envisaged to cover at least 80 per cent of the districts of a state with labs required to send at least 15 samples every 15 days to the designated INSACOG genome sequencing laboratory (IGSL).

One key requirement spelt out by WHO regarding genomic surveillance is for submitting genome sequences to an international, publicly available database, such as the one maintained by GISAID. Amid a global health crisis like the Covid-19 pandemic, close collaboration between countries and health experts can result in swift response to the rise of new variants and public databases are an important aid towards that end.

GISAID, among the most prominent of the global genomic databases that are maintaining a repository of Sars-CoV-2 variants, has so far had more than 5.5 million samples submitted to it. At 523, Iceland leads the list of countries in terms of sequences submitted for every 1,000 cases. India has so far submitted 1.66 sequences for every 1,000 cases with the figures for the US, which has the world’s highest case count, and Brazil, with the third-highest caseload, at 29.1 and 3.05, respectively.

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