New Covid variants can be predicted early for interventions, claims study

Express News Service

BHUBANESWAR: Amid the third wave of the coronavirus pandemic, a recent study has claimed that the future variants of SARS-CoV-2 virus can be predicted early for actionable interventions. In a first-ever study in the country and a much-needed breakthrough, scientists analysing genomes have found out how the virus evolves with new mutations within a host and new lineages are generated.

The researchers from six prominent institutes, including Bhubaneswar-based Institute of Life Sciences (ILS), claimed the new mutated variants can be predicted through the analysis of intra-host single nucleotide variations (iSNVs) in the SARS-CoV-2 genome few months before their actual spread.  

They accessed samples of COVID-19 diagnosed patients sequenced during two different periods of the pandemic. In phase I, they analysed 1,347 samples collected by June 2020 from China, Germany, Malaysia, UK, US and different regions of India to perceive a genome-wide iSNV map in SARS-CoV-2 infected populations. They observed 16,410 iSNV sites spanning the viral genome, including residues that defined the B.1 and B.6 lineages that were prominent in the samples before June 2020. 

In phase II, analysis of another set of 1,774 genomes sequenced in India between November 2020 and May 2021 revealed that majority of the Delta (B.1.617.2) and Kappa (B.1.617.1) lineages appeared as iSNVs before getting fixed as variants of concern (VOCs) in the population.

A senior scientist at ILS, Dr Sunil K Raghav said that when the virus mutates within the same person (host) and generates new mutations, it can be captured in next-generation sequencing called intra-host single nucleotide variations (iSNVs).

If the frequency of some mutations increases in a virus within the same person, it can be identified by iSNV analysis and with time when the frequency increases it could lead to VOC generation like Delta.

“Analysing samples sequenced in India, we found the majority of Delta and Kappa lineages to carry iSNVs before the incidence in the population. This indicates that conjoint analysis of iSNVs will provide some clues on the evolvability and prove to be an important asset in genomic surveillance. Had the analysis been done earlier, Delta could have been predicted,” Raghav said.

Head of Department of Bioscience and Bioengineering at IIT-Jodhpur and former chief scientist at IGIB Prof Mitali Mukerji said the study showed that tracking and analysing iSNVs as part of the ongoing genome surveillance could be important for early identification of potential VOCs and actionable interventions.

“We also observed iSNV sites at 20 out of 23 mutations in the spike protein that have been recently reported to confer antibody resistance. These mutations can have major implications in vaccine response. Conjoint analysis with the intra-host variability would help predict the spread and infectivity of viral strains in the population,” she added.

Researchers from other institutes included Delhi-based Institute of Genomics and Integrative Biology (IGIB), Ghaziabad-based Academy of Scientific and Innovative Research (AcSIR), Centre for Cellular and Hyderabad-based Molecular Biology (CCMB), National Centre for Disease Control (NCDC) and Indian Institute of Technology (IIT), Jodhpur.