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An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic

View ORCID ProfileSudhir Kumar, View ORCID ProfileQiqing Tao, Steven Weaver, Maxwell Sanderford, View ORCID ProfileMarcos A. Caraballo-Ortiz, Sudip Sharma, Sergei L. K. Pond, Sayaka Miura
doi: https://doi.org/10.1101/2020.09.24.311845
Sudhir Kumar
1Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
2Department of Biology, Temple University, Philadelphia, PA
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  • ORCID record for Sudhir Kumar
  • For correspondence: s.kumar@temple.edu spond@temple.edu sayaka.miura@temple.edu
Qiqing Tao
1Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
2Department of Biology, Temple University, Philadelphia, PA
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Steven Weaver
1Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
2Department of Biology, Temple University, Philadelphia, PA
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Maxwell Sanderford
1Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
2Department of Biology, Temple University, Philadelphia, PA
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Marcos A. Caraballo-Ortiz
1Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
2Department of Biology, Temple University, Philadelphia, PA
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  • ORCID record for Marcos A. Caraballo-Ortiz
Sudip Sharma
1Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
2Department of Biology, Temple University, Philadelphia, PA
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Sergei L. K. Pond
1Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
2Department of Biology, Temple University, Philadelphia, PA
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  • For correspondence: s.kumar@temple.edu spond@temple.edu sayaka.miura@temple.edu
Sayaka Miura
1Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
2Department of Biology, Temple University, Philadelphia, PA
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  • For correspondence: s.kumar@temple.edu spond@temple.edu sayaka.miura@temple.edu
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Abstract

We report the likely most recent common ancestor of SARS-CoV-2 – the coronavirus that causes COVID-19. This progenitor SARS-CoV-2 genome was recovered through a novel application and advancement of computational methods initially developed to reconstruct the mutational history of tumor cells in a patient. The progenitor differs from the earliest coronaviruses sampled in China by three variants, implying that none of the earliest patients represent the index case or gave rise to all the human infections. However, multiple coronavirus infections in China and the USA harbored the progenitor genetic fingerprint in January 2020 and later, suggesting that the progenitor was spreading worldwide as soon as weeks after the first reported cases of COVID-19. Mutations of the progenitor and its offshoots have produced many dominant coronavirus strains, which have spread episodically over time. Fingerprinting based on common mutations reveals that the same coronavirus lineage has dominated North America for most of the pandemic. There have been multiple replacements of predominant coronavirus strains in Europe and Asia and the continued presence of multiple high-frequency strains in Asia and North America. We provide a continually updating dashboard of global evolution and spatiotemporal trends of SARS-CoV-2 spread (http://sars2evo.datamonkey.org/).

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Updated to include a much larger collection of genomes (as many as 174,000 genomes)

  • http://igem.temple.edu/COVID-19

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-ND 4.0 International license.
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Posted January 19, 2021.
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An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic
Sudhir Kumar, Qiqing Tao, Steven Weaver, Maxwell Sanderford, Marcos A. Caraballo-Ortiz, Sudip Sharma, Sergei L. K. Pond, Sayaka Miura
bioRxiv 2020.09.24.311845; doi: https://doi.org/10.1101/2020.09.24.311845
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An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic
Sudhir Kumar, Qiqing Tao, Steven Weaver, Maxwell Sanderford, Marcos A. Caraballo-Ortiz, Sudip Sharma, Sergei L. K. Pond, Sayaka Miura
bioRxiv 2020.09.24.311845; doi: https://doi.org/10.1101/2020.09.24.311845

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