Genome Sequencing Helps Nail Virus Spread and Mutation | India News
YOUspoke with experts to understand what genome surveillance is and how it evaluates the impact of virus mutations.
For genome sequencing, a swab sample collected by RT-PCR is used to amplify the virus and identify if it is different from those previously detected. Genomic surveillance is resource intensive, costing Rs 8,000-10,000 to sequence a sample. Also, it takes around 24 hours to get a result, while testing or comparing with other strains to understand change and impact takes up to two days.
“It’s like the binary language of the computer where there are really only 0’s and 1’s 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 the DNA of an organism is read to interpret the complete genome of a virus ”, said former ICMR chief epidemiologist, the Dr. Raman Gangakhedkar.
“We need to detect all 17 mutations to confirm the UK strain. To do this, we have to map the entire genome of the virus and not just the spike gene. The UK variant has multiple mutations in different genes, ”said scientist Varsha Potdar, director of the National Influenza Center (NIC) at the Indian Council for Medical Research-National Institute of Virology (ICMR-NIV).
If differences are found, data analysis 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 which helps to assess virus spread quickly and robustly.
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 address its future spread.
Studying accumulated mutations in viral genomes allows comparison of virus samples and viral lineages to understand whether local outbreaks are caused by transmission of single or multiple viral lineages, experts said.
For example, genome sequencing of the samples during the first months of the outbreak showed that there were viruses from different countries due to global mobility that no Indian lineage allowed, Dr. Gangakhedkar said.