Journal article

Temporal signal and the phylodynamic threshold of SARS-CoV-2

Sebastian Duchene, Leo Featherstone, Melina Haritopoulou-Sinanidou, Andrew Rambaut, Philippe Lemey, Guy Baele

Virus Evolution | OXFORD UNIV PRESS | Published : 2020

Abstract

The ongoing SARS-CoV-2 outbreak marks the first time that large amounts of genome sequence data have been generated and made publicly available in near real time. Early analyses of these data revealed low sequence variation, a finding that is consistent with a recently emerging outbreak, but which raises the question of whether such data are sufficiently informative for phylogenetic inferences of evolutionary rates and time scales. The phylodynamic threshold is a key concept that refers to the point in time at which sufficient molecular evolutionary change has accumulated in available genome samples to obtain robust phylodynamic estimates. For example, before the phylodynamic threshold is re..

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Grants

Awarded by Australian Research Council


Awarded by Australian National Health and Medical Research Council


Awarded by Wellcome Trust


Awarded by European Research Council under the European Union's Horizon 2020 research and innovation programme


Awarded by Research Foundation-Flanders ('Fonds voor Wetenschappelijk Onderzoek-Vlaanderen')


Awarded by Interne Fondsen KU Leuven/Internal Funds KU Leuven


Awarded by Research Foundation-Flanders ('Fonds voor Wetenschappelijk Onderzoek - Vlaanderen')


Funding Acknowledgements

S.D. was supported by an Australian Research Council Discovery Early Career Researcher Award (DE190100805) and an Australian National Health and Medical Research Council (APP1157586). A.R. was supported by the Wellcome Trust (Collaborators Award 206298/Z/17/Z-ARTIC network). P.L. acknowledges funding from the European Research Council under the European Union's Horizon 2020 research and innovation programme (725422-ReservoirDOCS) and the Research Foundation-Flanders (`Fonds voor Wetenschappelijk Onderzoek-Vlaanderen', G066215N, G0D5117N, and G0B9317N). G.B. acknowledges support from the Interne Fondsen KU Leuven/Internal Funds KU Leuven (C14/18/094)), and the Research Foundation-Flanders ('Fonds voor Wetenschappelijk Onderzoek - Vlaanderen', G0E1420N).