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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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WRAP-emerging-phylogenetic-structure-SARS-CoV-2-pandemic-Didelot-2020.pdf - Published Version - Requires a PDF viewer. Available under License Creative Commons Attribution 4.0. Download (1260Kb) | Preview |
Official URL: http://dx.doi.org/10.1093/ve/veaa082
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 | ||||||||
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| Subjects: | R Medicine > RA Public aspects of medicine | ||||||||
| Divisions: | Faculty of Science > Life Sciences (2010- ) Faculty of Science > Statistics |
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| 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: |
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| 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: |
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