Software that helps analyse coronavirus genome for mutations
doi:10.1038/nindia.2021.32 Published online 17 February 2021
Researchers have developed a computational tool that can help a user identify various mutations across the genome of the novel coronavirus1.
The tool, named ‘Infectious Pathogen Detector’ (IPD), can also detect and analyse genome sequences of various strains of viruses and bacteria in any kind of data, the researchers, from the Tata Memorial Centre in Mumbai, found.
The tool, they say, will help understand the genome variability and evolution of the coronavirus within various populations, paving the development of therapies for COVID-19.
The IPD could detect mutations present in the coronavirus genome, using the Wuhan coronavirus strain as reference, with an option to download its source code to perform bulk analysis offline. It then presents the data in a statistically disciplined manner, allowing comparison of pathogen genomes across various samples.
To keep track of novel mutations in emerging coronavirus strains, the researchers, led by Amit Dutt and Sanket Desai, developed IPD 2, an upgraded version of the IPD that they applied on more than 200,000 samples of the coronavirus genome isolated from COVID-19 patients from 155 countries, including India2.
Scanning almost 2.58 million mutations in all these samples, they identified more than 4000 unique mutations in the coronavirus genome of the Indian samples. They found mutations in genes that encode specific proteins, allowing the entry of the virus into host cells.
A higher inherent mutation rate in these proteins could make it easier for the virus to spread, Dutt says.
1. Desai, S. et al. An integrated approach to determine the abundance, mutation rate and phylogeny of the SARS-CoV-2 genome. Briefings. Bioinformatics. (2021) doi:10.1093/bib/bbaa437
2. Desai, S. et al. Evolving insights from SARS-CoV-2 genome from 200K COVID-19 patients. BioRXiv (2021) doi: 10.1101/2021.01.21.427574