Early in March, India became the fifth country in the world to sequence the genome of the novel Coronavirus, or Covid-19, and share its data with the international community. Pune-based National Institute of Virology, an institution under the Indian Council of Medical Research, the country’s nodal health research body, sent the first two data sets to an open database shared by researchers globally.
Labs, largely from China, the United States and the Netherlands, have so far contributed just over 1,100 samples to the database, which researchers across the world can use to analyse and work on tests, vaccines and drugs to combat the pandemic. In India, the first set of genome data — detailing the complete DNA of the virus – came from individuals in Kerala who had contracted the virus.
“The volume of the sample and the concentration of the virus play a crucial role during the sequencing of the virus genome. In some samples that we received, there was less virus concentration and in case of clinical samples, sometimes the volume was less. These were some of the challenges,” says Professor Priya Abraham, Director of the National Institute of Virology.
The SARS-CoV2 genome, as it is formally known, has about 30,000 base pairs, somewhat like a long string with 30,000 places where each one of these occupy one of four chemicals called nucleotides. This long string, with its unique combination of nucleotides, is what uniquely identifies the virus and is called its genomic sequence. To put that in context, a human genome, which is more complex, has 3 billion base pairs.
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Genome data is essential to build tests, find drugs and vaccines. It is also needed to figure out if there has been a mutation of the virus and how that will affect different populations. It is also key to finding measures to deal with its spread.
“We need to know how the virus mutates, correlate sequence variation and its severity on patients,” says Professor S Vijaya of the Department of Microbiology and Cell Biology at the Indian Institute of Science who has done extensive research on tuberculosis and the Japanese Encephalitis virus. Scientists are of the view that India needs to sequence more strains as the virus mutates.
“It is important to understand whether there are new variants, why is a cluster seeing more serious patients and some milder?” Vijaya says. “In Italy, the fatality rate is in 10% of the infected patients, in China it was 2%. We need to isolate strains that have a sequence variation that are more pathogenic,” she adds. The novel Coronavirus, whose initial host is suspected to be a bat, originated in Hubei province of China last December.
China was initially slow to realise the magnitude of the virus, which affects the respiratory organs. Since then, the contagious disease that spreads through droplets, either through saliva or when a person coughs or sneezes, has turned into a global pandemic. There is no vaccine or drug yet for the outbreak that has killed thousands, largely people with underlying medical conditions such as cardiac, diabetes and respiratory problems.
So far, the most effective measure has been to isolate people who have tested positive, quarantine them and increase social distancing to contain its spread. India has seen the disease enter the third phase of community spread — people who have not had any contact with those infected, testing positive for the virus. The World Health Organisation warned that the pandemic was accelerating.
It took 67 days for cases to reach the 100,000 mark globally, 11 days to hit 200,000 and just four days to touch 300,000 cases. So far, more than 6,000 people in Italy have died from the virus, surpassing even that of China. More than 16,500 people have died across the world. Given the severity of the problem and the global lockdowns in place, India needs to do more sequencing of the virus before it spreads, researchers say.
Since reporting its first positive case on January 30, the country has seen that number swell to more than 500, and nine people dead so far. “If we do more sequencing, we can identify what is the rate of change in the virus, how it is spreading and the how much of the virus (based on its variations) is there in the population,” says Chitra Pattabiraman, India Alliance Early Career Fellow at the Department of Neurovirology of the Bengaluru-based National Institute of Mental Health and Neurosciences (Nimhans).
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Pattabiraman, a virologist who has done genome sequencing to identify pathogens in brain infections, says sequencing in the earliest phases of an outbreak is valuable because it helps in faster decision making on how to tackle its spread. India should sequence more strains so that it can contribute to research globally, she says.
“We need to develop more capacity and share more strains with the global network. We have forever used other people’s databases for our research, this provides us the opportunity to contribute to the world community,” she says. The country has around 40 labs, including at the Indian Institute of Science and Manipal University, that have the required bio-safety limits (BSL-3) for sequencing the virus, yet it has not opened up the samples to labs outside of the ICMR network.
“If more labs are allowed to get into studying the strains, I think we can get more understanding of the virus,” says Professor Vijay Chandru, cofounder of Strand Genomics, which was among the first private labs to receive permission to test samples of Covid-19 infections. ICMR is cautious about opening up more labs for genome sequencing because of the stringent standards required to extract the strains, Chandru says.
“Lots of people have capabilities, doing this right is important.” Availability of the Indian sequences will help in understanding the diversity of the viral sequences circulating in the country and its similarities with global strains, Abraham of NIV says. “This would further help in designing specific primers, develop vaccines and drugs that would work better, and local companies would benefit,” she says.
