IIT-J team identifies Covid RNA variations

IIT Jodhpur has identified variations in the RNA of the Covid-19 virus, using genomic sequencing methods. The RNA structure of the Covid-19 virus frequently undergoes minor modifications within the host cells (aintra-host variations').

In the study, published in the journal Nucleic Acid Research, the team studied intra-host Single Nucleotide Variations (iSNV) using a sequencing platform called Illumina.

"One of the most important aspects to manage the Covid-19 pandemic is to unravel the genetic structure of the virus and pick up early warning signatures, said Dr. Mitali Mukerji, Professor and Head, Department of Bioscience & Bioengineering, IIT Jodhpur.

"We observed 16,410 iSNV sites spanning the viral genome, and a high density of alterations were present in critical areas that could alter or override the body's ability to trigger an immune response," she added.

During Phase 1 of the project in 2020, the IIT scientists analysed the RNA structure of virus samples collected from China, Germany, Malaysia, the UK, the US, and different subpopulations of India to map the iSNV across the RNA structure of the virus. The team has observed similar patterns across populations and waves of the pandemic. It also tracked the iSNVs over time to see if the variants produced inside the host cells can persist outside, thereby becoming fixed as SNVs.

They found that by June 30, 2021 about 80 per cent of the iSNV sites they had identified in 2020 became fixed as SNVs. The conversion of iSNVs to SNVs was substantiated in Phase 2 studies that showed iSNVs were found in most of the Delta and Kappa variants before their fixation as SNVs by February 2021.

"The evolution of SNVs from iSNVs can affect vaccine response by altering the antibody generation in infected individuals," said Mukerji. Tracking and understanding the fate of iSNV can help predict the variants-of-concern and planning actionable interventions.

It also helps to know the differences in individual and population responses to the infection and helps in the design of therapeutic protocols to treat Covid infections. The identification of iSNVs can also help in the identification of key sites in the viral RNA that are important for its survival and spread, the researchers explained.