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Emerging phylogenetic structure of the SARS-CoV-2 pandemic

View ORCID ProfileNicholas M. Fountain-Jones, Raima Carol Appaw, Scott Carver, Xavier Didelot, Erik Volz, Michael Charleston
doi: https://doi.org/10.1101/2020.05.19.103846
Nicholas M. Fountain-Jones
1School of Natural Sciences, University of Tasmania, Hobart, Australia
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  • For correspondence: Nick.FountainJones@utas.edu.au
Raima Carol Appaw
1School of Natural Sciences, University of Tasmania, Hobart, Australia
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Scott Carver
1School of Natural Sciences, University of Tasmania, Hobart, Australia
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Xavier Didelot
2School of Life Sciences and Department of Statistics, University of Warwick, Coventry, UK
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Erik Volz
3MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Imperial College London, UK
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Michael Charleston
1School of Natural Sciences, University of Tasmania, Hobart, Australia
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Abstract

Since spilling over into humans, SARS-CoV-2 has rapidly spread across the globe, accumulating significant genetic diversity. The structure of this genetic diversity, and whether it reveals epidemiological insights, are fundamental questions for understanding the evolutionary trajectory of this virus. Here we use a recently developed phylodynamic approach to uncover phylogenetic structures underlying the SARS-CoV-2 pandemic. We find support for three SARS-CoV-2 lineages co-circulating, each with significantly different demographic dynamics concordant with known epidemiological factors. For example, Lineage C emerged in Europe with a high growth rate in late February, just prior to the exponential increase in cases in several European countries. Mutations that characterize Lineage C in particular are non-synonymous and occur in functionally important gene regions responsible for viral replication and cell entry. Even though Lineages A and B had distinct demographic patterns, they were much more difficult to distinguish. Continuous application of phylogenetic approaches to track the evolutionary epidemiology of SARS-CoV-2 lineages will be increasingly important to validate the efficacy of control efforts and monitor significant evolutionary events in the future.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/nfj1380/covid19_evolution

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 4.0 International license.
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Posted May 19, 2020.
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Emerging phylogenetic structure of the SARS-CoV-2 pandemic
Nicholas M. Fountain-Jones, Raima Carol Appaw, Scott Carver, Xavier Didelot, Erik Volz, Michael Charleston
bioRxiv 2020.05.19.103846; doi: https://doi.org/10.1101/2020.05.19.103846
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Emerging phylogenetic structure of the SARS-CoV-2 pandemic
Nicholas M. Fountain-Jones, Raima Carol Appaw, Scott Carver, Xavier Didelot, Erik Volz, Michael Charleston
bioRxiv 2020.05.19.103846; doi: https://doi.org/10.1101/2020.05.19.103846

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