149659 - Emerging phylogenetic structure of the SARS-CoV-2 pandemic.pdf (498.24 kB)
Emerging phylogenetic structure of the SARS-CoV-2 pandemic
journal contribution
posted on 2023-05-21, 07:02 authored by Nicholas Fountain-JonesNicholas Fountain-Jones, Raima AppawRaima Appaw, Scott CarverScott Carver, Didelot, X, Volz, E, Michael CharlestonMichael CharlestonSince 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.
Funding
Australian Research Council
History
Publication title
Virus EvolutionVolume
6Article number
veaa082Number
veaa082Pagination
1-6ISSN
2057-1577Department/School
School of Natural SciencesPublisher
Oxford University PressPlace of publication
United KingdomRights 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.Repository Status
- Open