Research co-led by IIT Jodhpur professor identifies COVID-19 RNA variations, implications

A multi-institutional team co-led by a professor at Indian Institute of Technology (IIT) Jodhpur has used state-of-the-art genomic sequencing methods to identify variations in the RNA (Ribonucleic acid) molecule of the COVID-19 virus.

Mitali Mukerji, professor and head of the Bioscience and Bioengineering department at IIT Jodhpur, who co-led the study, said, “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 signs. 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.”

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. 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.

The research team studied intra-host Single Nucleotide Variations (iSNV) using a sequencing platform called Illumina. During Phase 1 of the project in 2020, scientists analysed the RNA structure of virus samples collected from China, Germany, Malaysia, the United Kingdom, the United States, and different subpopulations of India to map the iSNV across the RNA structure of the virus.

The scientists have also studied the fixation of these intra-host variations into extra-host variations and mutations that lead to variants. Tracking and understanding the fate of iSNVs can help predict the variants of concern and accordingly plan actionable interventions. It can also reveal the differences in individual and population responses to the infection, apart from helping in the design of therapeutic protocols to treat COVID infections.

The results of the two-phase study have been published in the journal, Nucleic Acid Research. This research study was conducted primarily by a team of computational graduates from across distant locations, proving that the pandemic has generated novel cooperation, sharing, and resource-sharing modes for innovative research.

The research was initiated at the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR – IGIB), New Delhi, and was led by IIT Jodhpur and Institute of Life Sciences, Bhubaneswar. The multi-institutional team — led by Mukerji from IIT Jodhpur and Sunil Raghav, a senior scientist at the Institute of Life Sciences — plans to combine iSNV identification protocols with whole-genome sequencing in the future to enable more accurate models for viral epidemiology.

The team includes Ankit Pathak, a B Tech in Computational Sciences, and Gyan Prakash Mishra, a Masters degree holder in Pharmaco-Informatics. Other collaborating institutes are the Academy of Scientific and Innovative Research, Ghaziabad; Council of Scientific and Industrial Research-Center for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad; and National Center for Disease Control (NCDC), New Delhi.

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% 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 on the implications of their findings. 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.