Why are genome sequencing and constant monitoring still important? Expert explains

Dr Chitra Pattabiraman of the Infectious Disease Research Foundation speaks about the Covid-19 scenario and what scientists are doing.

ByChetana Belagere

Published Dec 28, 2022 | 1:35 PMUpdatedDec 28, 2022 | 3:57 PM

Dr Chitra Pattabiraman has been researching on novel and emerging viruses, how they mutate or diversify, impacting their ability to infect humans. (Supplied)

Two sub-lineages of the Omicron variant — BF.7 and XBB — of the Covid-causing SARS-CoV-2 were detected in India in July.

Though the latter is the dominant variant spreading in the country, it has not created yet another Covid-19 wave, said Dr Chitra Pattabiraman, Chief Scientific Officer, of the Infectious Disease Research Foundation.

Dr Pattabiraman has been researching new and emerging viruses, and how they mutate or diversify, impacting their ability to infect humans.

In an exclusive interview with South First, Dr Pattabiraman explained the importance of genome sequencing of Covid positive samples, collected particularly from hospitals, clusters and international travellers.

“The data gives an idea of a possible outbreak — providing the key signals we are looking for,” she said.

What is genome sequencing?

Dr Pattabiraman explained the process by citing the example of a string of beads of different colours.

Dr Chitra Pattabiraman. (Supplied)

Dr Chitra Pattabiraman. (Supplied)

“Consider DNA or any genomic material as a string of beads. Any genome material is made up of beads of four different colours. Imagine SARS-CoV-2 as a long string of around 30,000 beads.

“For instance, a pink bead is followed by two greens and a blue. This is a sequence. While conducting genomic sequencing, we try to identify those four chemicals, and in what sequence.

When a virus mutates, you get a different sequence. This change will alter the virus itself.

“We are tracking these kinds of changes. The change could then result in a higher transmission, greater severity of the disease or no change at all,” she explained.

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Dominant variants in India

After analysing the publicly available sequencing data from GISAID, Dr Pattabiraman said India now has only the Omicron variant post a wave in January 2022.

Mutation and case prevalence in India. (Supplied)

Mutation and case prevalence in India. (Supplied)

GISAID (Global Initiative on Sharing Avian Influenza Data) is a global initiative and primary source providing open access to genomic data of influenza viruses and the coronavirus.

“Until the last week, there have been no other viral lineages in the country. Omicron has several sub-lineages. The XBB and BF.7 are sub-lineages of Omicron. Studies conducted across the world have that they are not more virulent.”

She added that the BF.7 was detected in India in July itself but did not spread rapidly. It did not show an increasing trend in environmental surveillance.

Also read: What is wastewater surveillance? 

The South Indian scene

In South India, the sub-variant XBB and its sub-lineages are seen. However, Dr Pattabiraman added that the variants showed no changes in environmental and wastewater surveillance, which tests sewage samples for the virus.

Mutation and case prevalence in Karnataka. (Supplied)

Mutation and case prevalence in Karnataka. (Supplied)

The researcher is working closely with other virus-tracking groups in Karnataka

“Data available in the public domain, and genome and waste-water surveillance we have taken up in Karnataka, revealed that the Omicron wave early in the year was mostly dominated by BA.1 and BA.2 lineages,” she said.

By mid-2022, we had BA.2.75 and in between, there were several Omicron sub-lineages. From around September onwards, we also found BA.4 and BA.5. After that it has been XBB,” Dr Pattabiraman revealed. “There was a slight spike when XBB was detected.”

Researchers resorted to environmental surveillance since the number of cases and active circulation of the virus among the population was less. Multiple groups, including the IDRF, took up environmental surveillance.
“In Karnataka, we are doing hyperlocal environmental surveillance,” she explained.

“We found with supporting data that there was a minor spike in cases (lesser than the initial Omicron wave). The data showed spikes in July, August, September and October, dominated by XBB. The spikes correlated with our genome data too,” the scientific officer revealed.

She attributed the minor spurt to the immune landscape. The majority of the population has been inoculated against the virus with two doses of the preventive vaccine, a booster dose and at least one natural infection.
“The immune landscape is set up in such a way that we don’t expect a significant increase in cases,” Dr Pattabiraman added.

She recalled that BF.7, detected around July, did not infect many people compared to other sub-variants then spreading.

“Based on the available evidence, we don’t think BF.7 would spread rapidly. However, there is a need for monitoring any possible change like this sub-lineage,” she said.

Also read: No need for panic over BF.7 variant in India

The importance of screening travellers

Screening international travellers will provide an idea of what is circulating globally.

“As long as the virus is circulating among the population or people are infected with the virus for a longer period, there is a possibility of the virus undergoing further mutation. Hence, we should continue monitoring,” Dr Pattabiraman explained the need for continued surveillance

One way to keep a tab on the virus is to screen international travellers or monitor the affected patients. “We have seen several variants of SARS-CoV-2, spreading rapidly over the past three years. Screening travellers will help in detecting the variants,” she said.

The scientists are also looking for any increase in hospital admissions, correlating with changes in the virus.

Dr Pattabiraman said if the genomic mutation is drastic, the virus will also undergo a similar change that the immune system will fail to recognise it. It leads to immune escape and severe infection.

Surveillance methods in Karnataka

Dr Pattabiraman’s team and other groups under the Bengaluru corporation are doing wastewater surveillance.

“We are going hyperlocal. It means that we are looking at apartment complexes, institutions, airports and hospitals. We are testing wastewater in all these places to detect the virus’s nucleic acid, its genetic material. This helps in estimating the extent of virus present in the population,” she added.

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Chances of missing a variant

Dr Pattabiraman is confident that the country’s surveillance system has improved and is better positioned than in 2019.

“Baseline genomic surveillance in the country has been going on. Since multiple groups are involved, we are in a position to better understand what (variant) is circulating. We do need more samples but it is highly unlikely that we will miss any changes.” she said.

“While it is important to track variants when the cases increase. But you need to continuously monitor. We are in a position to identify things by tracking them over time.”