The night of 29 January 2020 was one of the most strenuous of Pragya Yadav’s life. Yadav, a scientist at the National institute of Virology, had already spent a few days and nights ensuring that her laboratory was prepared to test samples of the first two Indians thought to have COVID-19. Earlier that day, Yadav had conducted two rounds of tests in two different laboratories to confirm that the samples were indeed positive for the alarming new disease spreading across the world. By the evening, she was back in her laboratory to sequence the viral samples and to understand the genetic constitution of the virus.
“I remember that night very clearly,” Yadav said. She is a bespectacled, soft-spoken woman who patiently answered my barrage of questions, pausing to explain the jargon of genomic sequencing. “Me and my team had just wrapped up the testing work by 7 pm and went home, but were back on campus by 10:30 pm to discuss our sequencing strategy,” she recalled. Yadav and Priya Abraham, the director of the NIV, decided that the team would work through the night to complete sequencing. This was arduous work, and also harrowing. They had to handle samples of a highly contagious new pathogen that they knew little about apart from the fact that it was making people very ill and rapidly claiming lives. They also had to wear suffocating protective gear that made physical conditions inside the laboratory next to unbearable. Yadav and her team summoned all their strength to work through the night and the next day while ignoring anxious calls from their families. They finished sequencing by the morning of 30 January. “We finally had a whole genome sequence, a blueprint of the virus,” Yadav said.
What Yadav had decoded was a structure and constitution of the virus from the sample she was sent, one of many similar sequences from similar samples around the world that could help unlock its mechanisms, which in turn could indicate how the disease could be controlled. The SARS-CoV-2 virus that causes COVID-19 is made up of a single RNA strand which contains all the information it needs to evolve and multiply in a host body. “Basically, we look at this strand of RNA and we see the pattern used to produce protein, replicate itself and infect a potential host,” Saket Choudhary, a postdoctoral student at the New York Genome Centre, said. “So we can then use this information to build drugs and develop new vaccines that can break these patterns of the virus. The more you know about how it functions, the more likely it is that you will be able to incapacitate it.”
India’s genomic sequencing efforts have advanced significantly since the time Yadav and her colleagues sequenced that first sample. Yadav’s team had to do this work at the only laboratory in the country equipped for testing and sequencing. By mid-2020, a few Indian scientists associated with the department of biotechnology, which falls under the union ministry of science and technology, had begun collecting a representative pool of blood samples from infected individuals across the country. They found that different mutations of the virus had already started emerging locally, especially in states that had witnessed surges in infections. “This is an RNA virus and we knew it is likely to mutate quickly but not at this scale and this fast,” Dr Saumitra Das, the former director of the National institute of Biomedical Genomics, said. “By the latter half of 2020, it was more evident that there was a correlation between the surge in cases and variations in the virus. So an important question emerged: what is the exact link between variants and these surges?”
This link was one reason why the government of India decided to form a consortium of laboratories for COVID-19 genome sequencing. The other was to join the global effort to fight the pandemic, for which many other countries had already initiated concerted sequencing efforts. In December 2020, the department of biotechnology officially set up the Indian SARS-CoV2 Consortium on Genomics or INSACOG, which was an unprecedented nationwide effort initiated to sequence COVID-19 samples. “When the UK variant emerged [in December 2020] and cases rose rapidly over there, that is when it was decided to concretise this plan and formally establish INSACOG,” Das, who also worked as a coordinator for the consortium, said.