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Emerging phylogenetic structure of the SARS-CoV-2 pandemic
Citation
Fountain-Jones, NM and Appaw, RC and Carver, S and Didelot, X and Volz, E and Charleston, M, Emerging phylogenetic structure of the SARS-CoV-2 pandemic, Virus Evolution, 6, (2) Article veaa082. ISSN 2057-1577 (2020) [Refereed Article]
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Copyright Statement
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 (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
DOI: doi:10.1186/s12985-021-01633-w
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 Details
| Item Type: | Refereed Article |
|---|---|
| Keywords: | COVID-19, virus demography, phylodynamics, spread, epidemiology |
| Research Division: | Agricultural, Veterinary and Food Sciences |
| Research Group: | Veterinary sciences |
| Research Field: | Veterinary parasitology |
| Objective Division: | Environmental Management |
| Objective Group: | Terrestrial systems and management |
| Objective Field: | Control of pests, diseases and exotic species in terrestrial environments |
| UTAS Author: | Fountain-Jones, NM (Dr Nicholas Fountain-Jones) |
| UTAS Author: | Appaw, RC (Mr Raima Appaw) |
| UTAS Author: | Carver, S (Associate Professor Scott Carver) |
| UTAS Author: | Charleston, M (Professor Michael Charleston) |
| ID Code: | 149659 |
| Year Published: | 2020 |
| Funding Support: | Australian Research Council (DP190102020) |
| Web of Science® Times Cited: | 11 |
| Deposited By: | Zoology |
| Deposited On: | 2022-04-05 |
| Last Modified: | 2022-07-21 |
| Downloads: | 4 View Download Statistics |
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