PT  - JOURNAL ARTICLE
AU  - Sanket Desai
AU  - Aishwarya Rane
AU  - Asim Joshi
AU  - Amit Dutt
TI  - Evolving Insights from <em>SARS-CoV-2</em> Genome from 200K COVID-19 Patients
AID  - 10.1101/2021.01.21.427574
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.01.21.427574
4099  - http://biorxiv.org/content/early/2021/01/21/2021.01.21.427574.short
4100  - http://biorxiv.org/content/early/2021/01/21/2021.01.21.427574.full
AB  - We present an updated version of our automated computational pipeline, Infection Pathogen Detector IPD 2.0 with a SARS-CoV-2 module, to perform genomic analysis to understand the pathogenesis and virulence of the virus. Analysing the currently available 208911 SARS-CoV2 genome sequences (as accessed on 28 Dec 2020), we generate an extensive database of sample- wise variants and clade annotation, which forms the core of the SARS-CoV-2 analysis module of the analysis pipeline. A comparative account of lineage-specific mutations in the newer SARS-CoV-2 strains emerging in the UK, South Africa and Brazil along with data reported from India identify overlapping and lineages specific acquired mutations suggesting a repetitive convergent and adaptive evolution. Thus, the persistence of pandemic may lead to the emergence of newer regional strains with improved fitness. IPD 2.0 also adopts the recent dynamic clade nomenclature and shows improvement in accuracy of clade assignment, processing time and portability, to its predecessor and thus could be a vital tool to help facilitate genomic surveillance in a population to identify variants involved in breakthrough infections.Competing Interest StatementThe authors have declared no competing interest.