The Dutt Lab at ACTREC- Tata Memorial Centre developed an automated computational tool, Infectious Pathogen Detector (IPD), to identify the presence of 1,060 different pathogens in any genome sequence, along with SARS-CoV-2 sequecne. The tool generates an automated report with information about the abundance of SARS-CoV-2 sequence in the sample, mutations present and to ascribe a phylogenetic clade assignment to the sample. A researcher can either upload sequence to the server hosted at ACTREC or download the tool and perform bulk analysis to generate automated reports frorm here: http://www.actrec.gov.in/pi-webpages/AmitDutt/IPD/IPD.html. The findings from the study were published in Briefings in Bioinformatics.

Using the tool, Dr. Dutt and group further performed a comprehensive analysis of 2.58M mutations from more than 200K samples. They report for the first time that mutations in the SARS-CoV-2 genome occur at the rate of 6.6 non-silent and 5 silent mutations per sample. The study further reveals 13 hotspot residues that occur at least in 40,000 or more samples, including the D614G mutation. Furthermore, the analysis of 3,361 Indian COVID-19 patient samples revealed a comparable mutation rate with 5.17 non-silent and 4.39 silent mutations per sample with four common hotspot mutations with the emergent UK, SA and Brazil strains, including D416G. No significant occurrence of N439K, E484K, or N501Y mutations among the Indian samples except for 2 samples with S477Y spike protein mutation.