What Is Genome Sequencing And How Is It Helping Fight The COVID-19 Pandemic?

New Delhi: The world is into the third year of the COVID-19 pandemic but the new variants of SARS-CoV-2 are still emerging as the virus continues to infect people, multiply, mutate and spread further. According to the World Health Organization (WHO) which has been keeping a track of these variants, Genome Sequencing is an important tool for identifying and understanding the characteristics of the new strains. Genome sequencing has been used for years to study organisms like viruses, bacteria, plants, animals and humans. NDTV spoke with Dr Rakesh Mishra, Director, Tata Institute For Genetics and Society and former director of Council Of Scientific And Industrial Research–Centre For Cellular And Molecular Biology (CCMB), about how India has scaled up its genome sequencing capability and how crucial will this be in not just fighting COVID-19 but also other disease outbreaks.

Also Read: Genome Sequencing Is Important To Track, Identify Variants And Control COVID-19 Pandemic: Epidemiologist Aditi Hazra

NDTV: Is it something unique of SARS-Cov-2 that it is mutating so much and we have so many variants?

Dr Rakesh Mishra: There are several such viruses already known that mutate. There is nothing unusual about SARS-CoV-2. Mutation in these viruses is a very crucial component of their survival strategy. So, this is how they acquire new characteristics and evade the immune system because they have to find a host again and again. If they don’t do that then they will be eliminated. So, new variants will keep coming. This is because once we get infected or vaccinated, we develop immunity, but for reinfecting us, the virus will have to fight the immunity developed in the body. The virus is always aiming to infect as many people as possible. Coronavirus has now acquired this characteristic and has become very infectious. The future variants will be even more infectious in order to survive. So, mutation is a very natural process that is expected from such viruses.

NDTV: Coronavirus outbreaks have happened in the past, be it the SARS outbreak in 2002 or the MERS outbreak in 2012. How is this pandemic different from these earlier outbreaks?

Dr Rakesh Mishra: There are a couple of factors that make the SARS-CoV-2 unique. The first is that our behaviour has changed. Compared to 20 years ago, the planet has become much smaller in terms of the mobility of the people. When we travel, we also carry viruses and infections. The second factor is that this virus is far more infectious than the earlier SARS (Severe Acute Respiratory Syndrome) and MERS (Middle East Respiratory Syndrome). Luckily, SARS-CoV-2 is not as lethal as SARS and MERS. Because SARS-CoV-2 spreads so fast that it became a pandemic. In November last year, it was found that there is a new variant called ‘Omicron’ in the African countries and within 4-5 weeks, the virus had spread all over the world.

NDTV: How were the past coronavirus outbreaks curtailed and why are we struggling to put an end to the COVID-19 pandemic, this is when we have numerous vaccines that have been developed in record time, which was not the case with the earlier outbreaks?

Dr Rakesh Mishra: When a virus becomes infectious, it has many advantages because it is able to present new variants faster. Variants come only when the virus infects an individual and creates new mutations. Most of the mutations are not useful for the virus and would disappear but the few that are more infectious, survive and start to dominate in the population. While a person infected with the earlier SARS or MERS could infect only one or two people, a person infected by SARS-CoV-2 can infect 10 or even more people. There is a chain reaction in this case.

Thankfully, we have vaccines to keep the mortality in control. Vaccines have saved millions of lives. While vaccines are not able to prevent the infection but they are able to prevent the seriousness of the disease. Also, since this virus spreads faster and new variants come soon before our bodies get prepared for the fight, new variants attack us. Take the case of Omicron, this variant spread so fast that although a lot of people had prior immunity or- through infection or vaccine- but the virus was able to breakthrough that immunity.

Also Read: Coronavirus Outbreak Explained: What Is Genome Sequencing And How Can It Help Combat COVID-19 Pandemic

NDTV: What is genome sequencing and what role does is it play in disease outbreaks or its prevention?

Dr Rakesh Mishra: Genome is the genetic material of all living beings. The genome of coronavirus is in the form of RNA while most of the others have DNA as their genetic material. Complete sequencing is reading the complete detail of the genetic material of the genome is called genome sequencing. For genome sequencing, we decipher the chemical unit that makes a genome with help of technology and machines. So, we know exactly what those 30,000 letters in this virus are. Now, as the virus is changing, those changes get added in the sequence so we can plot the relationship between one infection to another, the way we can plot the relationship among individuals by just reading their DNA sequence.

By reading the genome of the virus, we can find out how it is spreading, which was the path it followed – whether it was first found in Mumbai, then in Delhi and so on. Also, it is to be noted that some variants are more harmful and some less harmful so if we see somewhere people start falling sick suddenly, we must check whether a new variant has come or is the number rising because people are becoming complacent. When we see that there is a new variant, then we know that we have to take additional precautions.

Another important thing that genome sequencing does is that the data collected through it can help in the development of medicines and vaccines. The vaccines against COVID-19 could be developed in a very short span of time because as soon as the virus was identified, its sequence was made available and within weeks, people started working on vaccines.

NDTV: In terms of genome sequencing how big are India’s capabilities vis-a-vis other countries in the world? What kind of infrastructure does India have for genome sequencing?

Dr Rakesh Mishra: Genome sequencing capability is reasonable in our country, particularly for sequencing the genome of SARS-CoV-2. We have developed tremendous capacity for it. So for genome sequencing of SARS-CoV-2, capacity is not an issue. There are almost 12 places in the country where thousands of genomes can be sequenced per day and there are hundreds of other centres, where small scale sequencing is being done. The only logistical challenge is we have to import the chemicals that are used for running genome sequencing machines which cost a lot. If we could make our own chemicals required for genome sequencing, it will become cheaper. Currently, each sequencing costs, Rs. 3,000-5,000.

NDTV: Prior to the pandemic what was India using genome sequencing for and how was it driving policy decisions?

Dr Rakesh Mishra: We have been using genome sequencing for studying people for years. For example, studies done by the Council Of Scientific And Industrial Research–Centre For Cellular And Molecular Biology show that 70,000 years ago, people of Andaman came from Africa using waterways to reach the Andaman and Nicobar. So, this was established because of genome sequencing. This way we could also figure out how the Indian sub-continent was populated. Also, India has a rich variety of ethnic groups with as many as over 5,000 ethnic groups. We can distinguish them not only by their features but also by their genes. Genome sequencing has now become extremely useful in deciding what kind of diseases we might get and what kind of treatment should we take particularly for cancer and psychiatric disease. It is important to note that over 50 per cent of the time medicines do not work on individuals with certain genetic makeup. So, if we carefully study the genetic information, we can tell which drug will be useful for which person and we can avoid unnecessary treatment and also the toxicity that a person goes through without getting any benefit from those treatments. Genome sequencing is also used for improving the variety of cattle and crops.

Also Read: Nearly 48 Per Cent Rise In Home Isolation Cases Of Covid In A Week In Delhi: Report

NDTV: In the case of India how has genome sequencing evolved since the COIVD-19 outbreak?

Dr Rakesh Mishra: We do not need to develop genome sequencing; the technology is already in place. It is just that more and more laboratories have started using it as now smaller machines are also available for it that cost up to Rs. 2 lakh. The big machines may cost up to Rs. 9 crore. The smaller machines can be used in remote places and do not require much infrastructure to set up. This is has helped in building capacities for genome sequencing locally. Never before in history we have used genome sequencing so much for surveillance purposes.

NDTV: What percentage of the samples being tested for COVID-19 are being genome sequenced and is it as per any established international benchmarks?

Dr Rakesh Mishra: Earlier we were not sequencing enough. But during the second wave, we started doing it in a more organised manner with the setting up of the multi-laboratory, multi-agency, pan-India network to monitor genomic variations INSACOG (Indian SARS-CoV-2 Genomics Consortium). During the third wave, we were sequencing enough. The one criteria that we can say we have sequenced enough is that we have not been caught off guard that a new variant came and could not pick it up early on.

We must not relax sequencing. When the cases are low, we tend to become a little bit relaxed. But this is the time we should actually be sequencing more because now wherever we find new variants, we should focus there and choke the virus wherever it is emerging rather than when it spreads at many places because then it gets out of control. If we see somewhere people are falling sick more, every person who comes to the hospital must be sequenced. Planning and implementation of genome sequencing strategy should not be relaxed.

NDTV: What are some of the big learnings from this pandemic?

Dr Rakesh Mishra: The pandemic has made us realise how important infectious diseases are. We have seen that maximum damage has happened in developed countries. We can no longer ignore infectious diseases. Another learning is that although we say that we are a civilized world, look how one country has more vaccines whereas an entire continent has none. It is a matter of shame for all of us. Also, it is not even safe for the world. So, vaccine equity is extremely important. To me, another important thing is that now we should realise that this planet belongs to all creatures and not just human beings. All pandemics come from the wild because we encroach their space, we disturb them. We have to learn to live within the scope of limited resources. We also need to look at our present healthcare system and strengthen it.

Also Read: COVID-19: These Cities Make Masks Mandatory Yet Again As Cases Rise In India

You can listen to the full Banega Swasth India podcast discussion by hitting the play button on the Spotify player embedded above.

Follow us on Apple Podcasts and Google Podcasts. Please also rate us and leave a review.

NDTV – Dettol have been working towards a clean and healthy India since 2014 via the Banega Swachh India initiative, which is helmed by Campaign Ambassador Amitabh Bachchan. The campaign aims to highlight the inter-dependency of humans and the environment, and of humans on one another with the focus on One Health, One Planet, One Future – Leaving No One Behind. It stresses on the need to take care of, and consider, everyone’s health in India – especially vulnerable communities – the LGBTQ population, indigenous people, India’s different tribes, ethnic and linguistic minorities, people with disabilities, migrants, geographically remote populations, gender and sexual minorities. In wake of the current COVID-19 pandemic, the need for WASH (Water, Sanitation and Hygiene) is reaffirmed as handwashing is one of the ways to prevent Coronavirus infection and other diseases. The campaign will continue to raise awareness on the same along with focussing on the importance of nutrition and healthcare for women and children, fight malnutrition, mental wellbeing, self care, science and health, adolescent health & gender awareness. Along with the health of people, the campaign has realised the need to also take care of the health of the eco-system. Our environment is fragile due to human activity, which is not only over-exploiting available resources, but also generating immense pollution as a result of using and extracting those resources. The imbalance has also led to immense biodiversity loss that has caused one of the biggest threats to human survival – climate change. It has now been described as a “code red for humanity.” The campaign will continue to cover issues like air pollution, waste management, plastic ban, manual scavenging and sanitation workers and menstrual hygiene. Banega Swasth India will also be taking forward the dream of Swasth Bharat, the campaign feels that only a Swachh or clean India where toilets are used and open defecation free (ODF) status achieved as part of the Swachh Bharat Abhiyan launched by Prime Minister Narendra Modi in 2014, can eradicate diseases like diahorrea and the country can become a Swasth or healthy India.