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Emerging phylogenetic structure of the SARS-CoV-2 pandemic

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Fountain-Jones, Nicholas M., Appaw, Raima Carol, Carver, Scott, Didelot, Xavier, Volz, Erik and Charleston, Michael (2020) Emerging phylogenetic structure of the SARS-CoV-2 pandemic. Virus Evolution, 6 (2). veaa082. doi:10.1093/ve/veaa082

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Official URL: http://dx.doi.org/10.1093/ve/veaa082

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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. 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: Journal Article
Subjects: R Medicine > RA Public aspects of medicine
Divisions: Faculty of Science > Life Sciences (2010- )
Faculty of Science > Statistics
Library of Congress Subject Headings (LCSH): COVID-19 (Disease), COVID-19 (Disease) -- Epidemiology
Journal or Publication Title: Virus Evolution
Publisher: Oxford University Press
ISSN: 2057-1577
Official Date: July 2020
Dates:
DateEvent
10 November 2020Available
July 2020Published
26 October 2020Accepted
Volume: 6
Number: 2
Article Number: veaa082
DOI: 10.1093/ve/veaa082
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
DP190102020Australian Research Councilhttp://dx.doi.org/10.13039/501100000923

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