BENGALURU: As the number of cases continues to rise, health professionals say genome sequencing should be part of India’s strategy to track the spread and evolution of SARS-CoV-2.A proper genetic surveillance system is the “need of the hour”, but India does not yet have one, said Dr Vishal Rao, dean of academics at HCG Cancer Care Centre and a member of the state’s expert committee on Covid.
“Whole viral genome sequencing allows for better understanding of the transmission of the virus, including whether it is mutating and becoming a larger threat,” Dr Rao said.
While governments across the world have been on their toes since the outbreak, the detection of the “double mutant” - a combination of two mutations not seen anywhere else in the world except in India - have only added to the urgency.
“It won’t take much time for the variant to be found in other states too. If we do not sample enough, we will not be able to establish whether the variant has any role to play in increased infectivity or in making Covid-19 more severe,” said Dr Satyanarayana Mysore, renowned pulmonologist, Manipal Hospital, Bengaluru.
Genome sequencing of a section of virus samples by the Indian SARS-CoV-2 Consortium on Genomics (INSACOG), a consortium of 10 labs across the country, has so far revealed the presence of two mutations, E484Q and L452R together, in at least 200 samples from Maharashtra, and a handful in New Delhi, Punjab and Gujarat. INSACOG is testing about 2,400 samples per day across the country but it is not enough, doctors say.
“While the two mutations have been individually identified in other variants of SARS-CoV-2 globally, and have been associated with a reduction in vaccine efficacy and infectivity, their combined effect and biological implication has not yet been understood,” Dr Rao said.
Researchers are also irked that INSACOG has not made the data of these genomes public, which includes the kind of variants that have shown up in different populations and their rates among new infections following the surge.
Dr Rao said that there is a great need for real-time genome sequencing data which the public health system can use to respond faster to outbreaks as they emerge.
While the UK has been doing well on the this front, virologists in India say INSACOG faces a severe shortage of funds and staff.
Covid-19 Genomics UK (COG-UK) Consortium and the Wellcome Sanger Institute have raised £12.2m in funding from the UK’s Department of Health and Social Care Testing Innovation Fund to create a real-time surveillance system of emerging outbreaks, supported by new software being developed by the Sanger Institute and researchers from the consortium’s network.
But in India, INSACOG has only just started, and its labs are arranging funding on their own, said Dr V Ravi, the nodal officer of INSACOG’s lab at NIMHANS in Bengaluru.
“Real-time genome sequencing is a myth. Genome sequencing takes time. It is resource intensive,” he said.
The process itself is simple enough, and takes between 18-24 hours.
“But the volume of data it generates is so large that the system will take a long time to analyse it. After this, it has to be manually checked and matched with existing genomes and if there is a change, it can be concluded that there is a new variant. So, this process cannot be compressed into a couple of days. With the kind of resources we have now, it is impossible. One sample at present takes a minimum of a week,” Dr Ravi said, adding that with more resources, it can be compressed into three days.
A sophisticated system needs to be put in place to use genome sequencing to tackle the pandemic: From collection of proper Covid positive samples with Ct value less than 25 (Ct value indicates viral load; lower the value, higher the viral load and vice versa), and prioritising clusters, travellers, and geographical representation, to genome sequencing,” Dr Ravi said.