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Evolving Insights from SARS-CoV-2 Genome from 200K COVID-19 Patients

View ORCID ProfileSanket Desai, Aishwarya Rane, Asim Joshi, View ORCID ProfileAmit Dutt
doi: https://doi.org/10.1101/2021.01.21.427574
Sanket Desai
1Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
2Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
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Aishwarya Rane
1Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
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Asim Joshi
1Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
2Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
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Amit Dutt
1Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra, 410210, India
2Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Maharashtra, 400094, India
3Adjunct Faculty, Institute of Advanced Virology, Kerala State Council for Science, Technology and Environment, Govt. of Kerala, Thonnakkal, Kerala, 695317, India
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  • For correspondence: adutt@actrec.gov.in
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Abstract

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 Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 21, 2021.
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Evolving Insights from SARS-CoV-2 Genome from 200K COVID-19 Patients
Sanket Desai, Aishwarya Rane, Asim Joshi, Amit Dutt
bioRxiv 2021.01.21.427574; doi: https://doi.org/10.1101/2021.01.21.427574
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Evolving Insights from SARS-CoV-2 Genome from 200K COVID-19 Patients
Sanket Desai, Aishwarya Rane, Asim Joshi, Amit Dutt
bioRxiv 2021.01.21.427574; doi: https://doi.org/10.1101/2021.01.21.427574

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