TOIspoke to experts to understand what genome surveillance is and how it assesses impact of virus mutations.
For genome sequencing, a swab sample collected through RT-PCR is used to amplify the virus to identify whether it is different from the previously detected ones. Genomic surveillance is resource intensive as it costs around Rs 8,000-10,000 to sequence one sample. Besides, it takes around 24 hours for a result, whereas analysing or comparing with other strains to understand the change and impact takes up to two days.
“It is like the computer binary language where actually there is only 0 and 1 and depending on how they are coded, they can be read. Similarly, in genome sequencing, the order or sequence of As, Cs, Gs, and Ts that make up an organism’s DNA is read to interpret the whole genome of a virus,” former chief epidemiologist of ICMR Dr Raman Gangakhedkar said.
“We need to detect all the 17 mutations to confirm the UK strain. For this, we have to map the whole genome of the virus and not just the spike gene. The UK variant has multiple mutations in different genes,” scientist Varsha Potdar, head of National Influenza Centre (NIC) at the Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), said.
If dissimilarities are detected, data analytics is used to determine the changes and their impact. India has designated 10 regional genome sequencing laboratories to examine 5% of positive samples for genome sequencing that helps assess the spread of the virus in a rapid and robust manner.
Even before the UK strain was discovered, India was sequencing genomic data to fully understand the spread and evolution of the SARS CoV-2 virus, and to tackle its future spread.
The study of accumulated mutations in the viral genomes enables comparison of virus samples and viral lineages in order to understand if local outbreaks are caused by transmission of single or multiple viral lineages, experts said.
For instance, genome sequencing of samples during the early months of the outbreak showed that there were viruses from different countries because of global mobility which was not allowing any Indian lineage, Dr Gangakhedkar said.