Using state-of-art genomic sequencing methods, researchers at the Indian Institute of Technology (IIT), Jodhpur, have been successful in identifying variations in the RNA of COVID-19 virus. The fixation of these intra-host variations into extra-host variations and mutations, which is what leads to variants, has been studied by scientists. 

It was in the journal Nucleic Acid Research that the result of their two-phase study was published, stated PTI in a report.

"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, as quoted in a report by PTI.

Mukerji added that this is why these variations are mostly harmless or destructive to the virus. But there are certain variations that can go on to enhance virus' survivability and become extra-host variations. These have the potential to lead to "variants-of-concern".

Using Illumina, which is a sequencing platform, the research team studied intra-host Single Nucleotide Variations (iSNV).

During the project's first phase in the year 2020, the RNA structure of virus samples was analysed. These samples were collected from India's different subpopulations as well as from the UK, the USA, China, Malaysia and Germany to map the iSNV across the virus' RNA structure. It was observed that similar patterns existed across populations and pandemic waves. Over time, the iSNVs were tracked to check if the variants produced inside the host cells can persist outside, thereby becoming fixed as SNVs.

By June 30, 2021, it was found that about 80 per cent of the identified iSNV sites in 2020 became fixed as SNVs. In phase two of the study, the conversion of iSNVs to SNVs was substantiated that showed iSNVs were found in most of the Delta and Kappa variants before their fixation as SNVs by February 2021.

The vaccine response can be affected by the evolution of SNVs from iSNVs. This can happen by altering the antibody generation in infected individuals, mentioned Mukherjee.