eCite Digital Repository

Emerging phylogenetic structure of the SARS-CoV-2 pandemic


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]

PDF (Published version)

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 (, 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


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

Repository Staff Only: item control page