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Emerging phylogenetic structure of the SARS-CoV-2 pandemic

Fountain-Jones, NM ORCID: 0000-0001-9248-8493, Appaw, RC, Carver, S ORCID: 0000-0002-3579-7588, Didelot, X, Volz, E and Charleston, M ORCID: 0000-0001-8385-341X 2020 , 'Emerging phylogenetic structure of the SARS-CoV-2 pandemic' , Virus Evolution, vol. 6, no. 2 , pp. 1-6 , doi:

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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. Non-synonymous mutations that characterize Lineage C 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.

Item Type: Article
Authors/Creators:Fountain-Jones, NM and Appaw, RC and Carver, S and Didelot, X and Volz, E and Charleston, M
Keywords: COVID-19, virus demography, phylodynamics, spread, epidemiology
Journal or Publication Title: Virus Evolution
Publisher: Oxford University Press
ISSN: 2057-1577
DOI / ID Number:
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Copyright The Author(s) 2020. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) License (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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