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

New Delhi: After over a year, SARS-CoV-2, the virus behind the COVID-19 pandemic continues to multiply, mutate and spread. Since the outbreak, researchers across the world have found multiple variants of coronavirus that differ from the one found in Wuhan, China in December 2019 which is considered to be the ‘original’ strain. In order to identify and know about the new strains that coronavirus mutates into, scientists are scanning samples from infected persons through a process called ‘genome sequencing’. While this method has been used for years to study organisms like virus, bacteria, plants, animal and humans, NDTV spoke to experts to understand how it can help in combating the COVID-19 pandemic.

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What Is Genome Sequencing And How Does It Work?

According to Dr Chandrakant Lahariya, epidemiologist and public health specialist based in Delhi, genome is the complete genetic material of an organism. It is like an instruction manual which contains information about the make-up of the organism, he said. While human genomes are made of DNA (Deoxyribonucleic acid), a virus genome can be made of either DNA or RNA (Ribonucleic acid). DNA and RNA provide genetic instructions for growth and functioning of organisms. Coronavirus is made of RNA. Genome sequencing is a technique that reads and interprets genetic information found within DNA or RNA, said Dr Preeti Kumar, Vice President- Public Health System Support at the Public Health Foundation of India (PHFI).

Dr. Kumar further explained that genome sequencing or Whole Genome Sequencing (WGS) involves analysing the genetic code of an organism and is done with the help of powerful computers. While talking about the need for sequencing, she said,

As we know well that virus undergoes mutation, as they replicate. Mutation are tiny errors in the genetic code that occur during the duplication process. While some are harmless, others can bring about such changes in the virus that can make it more transmissible or deadly. So, it is important to keep a track of the genomic sequencing in order to check the virulence of the virus. As the number of differences between viral strains increase, it’s likely that the resulting viruses will also behave differently in terms of how fast it spreads, the kind of symptoms and the intensity of the disease it causes. The differences can be beneficial, harmful or inconsequential. Different variants can have different tendencies and may need new containment and treatment strategies.

Explaining the process of genome sequencing, Dr Rakesh Mishra, director of the Council of Scientific and Industrial Research- Centre for Cellular and Molecular Biology (CSIR- CCMB), Hyderabad said that after a sample in the form of the swab is tested positive through RT-PCR (Reverse transcription-polymerase chain reaction) test, it can be sent to sequencing labs. He further said that researchers break open the virus’s cells, isolate the genetic material in the form of RNA from it, convert it into DNA and analyse it using technology. The RNA of SARS-CoV-2 contains almost 30,000 molecules with distinct physical and chemical properties. So, by looking at these molecules, scientists can determine the sequence of the genome for that virus. Then, they compare the final sequence with that of previous strains to check whether it is a new or an existing strain.

According to Dr Lahariya, genome sequencing help scientists find the exact location in the virus where a mutation has taken place. If the mutation happens in significant proteins of the virus like the spike proteins which helps it to infect the human cell, then the virus is likely to spread at a faster speed, he said.

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How Can Genome Sequencing Help Fight The Pandemic?

By analysing differences in the genetic code of viruses from different patients, scientists aim to identify the transmission of the virus in real-time and see if different strains are emerging and which strains are more dominating in a particular country or area, said Dr Lahariya. He further explained that the information on the genetic makeup of the virus can help build strategies for public health and clinical care as well as devising containment measures.

According to Dr Lahariya, genome sequencing is useful for identifying hotspots or superspreaders (individuals who transmit the infection to a larger number of people than expected). This information provides insights to the policymakers for planning targeted public health interventions.

An understanding of the viral genomic sequence can assist researchers in designing treatments and vaccines that target specific function of the virus and also helps in preparing for further changes in the virus as it mutates and evolves, said Dr Lahariya.

According to the Global Initiative on Sharing All Influenza Data (GISAID), the open genome repository for viruses that cause influenza and COVID-19, there have been almost 5.25 lakh SARS-CoV-2 genomes sequence studies till February 12. Dr Lahariya said that while there is no set standard for optimal number of samples that should be sequenced, there is a need to ramp up sequencing in almost every country including India as much as possible. He said that currently, the United Kingdom has been leading the world’s sequencing which is roughly 5 per cent of the positive samples while India is doing way less than 1 per cent.

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Genomic Surveillance for Coronavirus (SARS-CoV-2) In India

India started sequencing genomes of COVID-19 positive samples in the beginning of the pandemic itself. According to the Ministry of Health and Family Welfare (MoHFW), in order to further enhance the genome surveillance, the Government of India formed Indian SARS-CoV-2 Genomics Consortium (INSACOG) in December 2020 for centralised genome surveillance of the novel coronavirus in the country. Coordinated by Department of Biotechnology (DBT) along with MoHFW, Indian Council of Medical Research (ICMR), and Council of Scientific and Industrial Research (CSIR), the consortium brings together 10 labs from around the country with a cumulative sequencing infrastructural capacity of more than 25,000 samples a month.

According to the Genome Evolution Analysis Resource for COVID-19 (GEAR-19), a dashboard built by CSIR- CCMB, India has submitted 5,898 genome sequences till date which is only 0.05 per cent of the total number of cases in the country. The INSACOG, according to Dr Mishra, aims to increase the sequencing to 5 per cent in the coming months. For this, it has asked the labs to ensure that genome sequences are coming from all parts of the country and samples from all the people arriving in India who test positive will be sent for genome sequencing to know about mutations.

The World Health Organsiation has urged countries to expand sequencing studies to address the unknown strains of coronavirus. It explained that coronavirus mutation first found in the United Kingdom had spread to over 50 countries while the one found in South Africa has spread in over 20 nations. Another strain, from Brazil, is being analysed and could impact immune response, WHO said. Dr Matshidiso Moeti, Regional Director for Africa, WHO said while addressing a press conference,

Even if the new variant is not more virulent, a virus that can spread more easily will put further strain on hospitals and health workers who are in many cases already overstretched. This is a stark reminder that the virus is relentless, that it still presents a manifest threat.

Even if the new variant is not more virulent, a virus that can spread more easily will put further strain on hospitals & health workers who are in many cases already overstretched. This is a stark reminder that the virus is relentless, that it still presents a manifest threat. https://t.co/TL7neDudhG

— Dr Matshidiso Moeti (@MoetiTshidi) January 15, 2021

This is a defining moment in the pandemic. #HealthWorkers are exhausted, health systems are stretched & we’re seeing supplies of oxygen run dangerously low in some countries. We must #ACTogether as common humanity & rollout vaccines to health workers & those at highest risk. pic.twitter.com/UCVERZWxg7

— Tedros Adhanom Ghebreyesus (@DrTedros) January 15, 2021

WHO asserted that more the virus spreads, higher are chances of mutations and new strains to come up, so it is important to vaccinate a critical mass of people to break the chain of transmission at soon as possible and till then it is essential to follow preventive measures like social distancing, hand hygiene, wearing masks and taking the vaccine to avoid infections.

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