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Emerging phylogenetic structure of the SARS-CoV-2 pandemic.
Fountain-Jones, Nicholas M; Appaw, Raima Carol; Carver, Scott; Didelot, Xavier; Volz, Erik; Charleston, Michael.
  • Fountain-Jones NM; School of Natural Sciences, University of Tasmania, Hobart, 7001, Australia.
  • Appaw RC; School of Natural Sciences, University of Tasmania, Hobart, 7001, Australia.
  • Carver S; School of Natural Sciences, University of Tasmania, Hobart, 7001, Australia.
  • Didelot X; School of Life Sciences and Department of Statistics, University of Warwick, Coventry CV47AL, UK.
  • Volz E; Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, Imperial College London, London W2 1PG, UK.
  • Charleston M; School of Natural Sciences, University of Tasmania, Hobart, 7001, Australia.
Virus Evol ; 6(2): veaa082, 2020 Jul.
Article in English | MEDLINE | ID: covidwho-1388023
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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.
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Full text: Available Collection: International databases Database: MEDLINE Type of study: Observational study / Prognostic study Language: English Journal: Virus Evol Year: 2020 Document Type: Article Affiliation country: VE

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Observational study / Prognostic study Language: English Journal: Virus Evol Year: 2020 Document Type: Article Affiliation country: VE