IIT Jodhpur researchers identify COVID-19 RNA variations and their implications

Researchers at the Indian Institute of Technology (IIT), Jodhpur have identified variations in the RNA of COVID-19 virus using state-of-the-art genomic sequencing methods, according to officials. The scientists have also studied the fixation of these intra-host variations into extra-host variations and mutations that lead to variants. The results of the two-phase study have been published in the journal Nucleic Acid Research.

“The RNA structure of the COVID-19 virus frequently undergoes minor modifications within the host cells (intra-host variations). These modifications occur at the nucleotide level – nucleotide being the building block of the RNA molecule. Many of these intra-host variations are caused by enzymes present in the host cell as an immune response,” said Mitali Mukerji, Head, Department of Bioscience and Bioengineering, IIT Jodhpur.

“Thus, many of these variations are harmless or even destructive to the virus itself. However, some variations can enhance the survivability of the virus, and become fixed as extra-host variations that could potentially lead to variants-of-concern,” she added.

The research team studied intra-host Single Nucleotide Variations (iSNV) using a sequencing platform called Illumina.

According to the theme, during the first phase of the project in 2020, they 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 30th June, 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-II 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,” Mukherjee said.