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Phylodynamics of SARS-CoV-2 in France, Europe, and the world in 2020

Although France was one of the most affected European countries by the COVID-19 pandemic in 2020, the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) movement within France, but also involving France in Europe and in the world, remain only partially characterized in this tim...

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Autores principales: Coppée, Romain, Blanquart, François, Jary, Aude, Leducq, Valentin, Ferré, Valentine Marie, Franco Yusti, Anna Maria, Daniel, Léna, Charpentier, Charlotte, Lebourgeois, Samuel, Zafilaza, Karen, Calvez, Vincent, Descamps, Diane, Marcelin, Anne-Geneviève, Visseaux, Benoit, Bridier-Nahmias, Antoine
Formato: Online Artículo Texto
Lenguaje:English
Publicado: eLife Sciences Publications, Ltd 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10179682/
https://www.ncbi.nlm.nih.gov/pubmed/37159510
http://dx.doi.org/10.7554/eLife.82538
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author Coppée, Romain
Blanquart, François
Jary, Aude
Leducq, Valentin
Ferré, Valentine Marie
Franco Yusti, Anna Maria
Daniel, Léna
Charpentier, Charlotte
Lebourgeois, Samuel
Zafilaza, Karen
Calvez, Vincent
Descamps, Diane
Marcelin, Anne-Geneviève
Visseaux, Benoit
Bridier-Nahmias, Antoine
author_facet Coppée, Romain
Blanquart, François
Jary, Aude
Leducq, Valentin
Ferré, Valentine Marie
Franco Yusti, Anna Maria
Daniel, Léna
Charpentier, Charlotte
Lebourgeois, Samuel
Zafilaza, Karen
Calvez, Vincent
Descamps, Diane
Marcelin, Anne-Geneviève
Visseaux, Benoit
Bridier-Nahmias, Antoine
author_sort Coppée, Romain
collection PubMed
description Although France was one of the most affected European countries by the COVID-19 pandemic in 2020, the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) movement within France, but also involving France in Europe and in the world, remain only partially characterized in this timeframe. Here, we analyzed GISAID deposited sequences from January 1 to December 31, 2020 (n = 638,706 sequences at the time of writing). To tackle the challenging number of sequences without the bias of analyzing a single subsample of sequences, we produced 100 subsamples of sequences and related phylogenetic trees from the whole dataset for different geographic scales (worldwide, European countries, and French administrative regions) and time periods (from January 1 to July 25, 2020, and from July 26 to December 31, 2020). We applied a maximum likelihood discrete trait phylogeographic method to date exchange events (i.e., a transition from one location to another one), to estimate the geographic spread of SARS-CoV-2 transmissions and lineages into, from and within France, Europe, and the world. The results unraveled two different patterns of exchange events between the first and second half of 2020. Throughout the year, Europe was systematically associated with most of the intercontinental exchanges. SARS-CoV-2 was mainly introduced into France from North America and Europe (mostly by Italy, Spain, the United Kingdom, Belgium, and Germany) during the first European epidemic wave. During the second wave, exchange events were limited to neighboring countries without strong intercontinental movement, but Russia widely exported the virus into Europe during the summer of 2020. France mostly exported B.1 and B.1.160 lineages, respectively, during the first and second European epidemic waves. At the level of French administrative regions, the Paris area was the main exporter during the first wave. But, for the second epidemic wave, it equally contributed to virus spread with Lyon area, the second most populated urban area after Paris in France. The main circulating lineages were similarly distributed among the French regions. To conclude, by enabling the inclusion of tens of thousands of viral sequences, this original phylodynamic method enabled us to robustly describe SARS-CoV-2 geographic spread through France, Europe, and worldwide in 2020.
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spelling pubmed-101796822023-05-13 Phylodynamics of SARS-CoV-2 in France, Europe, and the world in 2020 Coppée, Romain Blanquart, François Jary, Aude Leducq, Valentin Ferré, Valentine Marie Franco Yusti, Anna Maria Daniel, Léna Charpentier, Charlotte Lebourgeois, Samuel Zafilaza, Karen Calvez, Vincent Descamps, Diane Marcelin, Anne-Geneviève Visseaux, Benoit Bridier-Nahmias, Antoine eLife Epidemiology and Global Health Although France was one of the most affected European countries by the COVID-19 pandemic in 2020, the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) movement within France, but also involving France in Europe and in the world, remain only partially characterized in this timeframe. Here, we analyzed GISAID deposited sequences from January 1 to December 31, 2020 (n = 638,706 sequences at the time of writing). To tackle the challenging number of sequences without the bias of analyzing a single subsample of sequences, we produced 100 subsamples of sequences and related phylogenetic trees from the whole dataset for different geographic scales (worldwide, European countries, and French administrative regions) and time periods (from January 1 to July 25, 2020, and from July 26 to December 31, 2020). We applied a maximum likelihood discrete trait phylogeographic method to date exchange events (i.e., a transition from one location to another one), to estimate the geographic spread of SARS-CoV-2 transmissions and lineages into, from and within France, Europe, and the world. The results unraveled two different patterns of exchange events between the first and second half of 2020. Throughout the year, Europe was systematically associated with most of the intercontinental exchanges. SARS-CoV-2 was mainly introduced into France from North America and Europe (mostly by Italy, Spain, the United Kingdom, Belgium, and Germany) during the first European epidemic wave. During the second wave, exchange events were limited to neighboring countries without strong intercontinental movement, but Russia widely exported the virus into Europe during the summer of 2020. France mostly exported B.1 and B.1.160 lineages, respectively, during the first and second European epidemic waves. At the level of French administrative regions, the Paris area was the main exporter during the first wave. But, for the second epidemic wave, it equally contributed to virus spread with Lyon area, the second most populated urban area after Paris in France. The main circulating lineages were similarly distributed among the French regions. To conclude, by enabling the inclusion of tens of thousands of viral sequences, this original phylodynamic method enabled us to robustly describe SARS-CoV-2 geographic spread through France, Europe, and worldwide in 2020. eLife Sciences Publications, Ltd 2023-04-26 /pmc/articles/PMC10179682/ /pubmed/37159510 http://dx.doi.org/10.7554/eLife.82538 Text en © 2023, Coppée et al https://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Epidemiology and Global Health
Coppée, Romain
Blanquart, François
Jary, Aude
Leducq, Valentin
Ferré, Valentine Marie
Franco Yusti, Anna Maria
Daniel, Léna
Charpentier, Charlotte
Lebourgeois, Samuel
Zafilaza, Karen
Calvez, Vincent
Descamps, Diane
Marcelin, Anne-Geneviève
Visseaux, Benoit
Bridier-Nahmias, Antoine
Phylodynamics of SARS-CoV-2 in France, Europe, and the world in 2020
title Phylodynamics of SARS-CoV-2 in France, Europe, and the world in 2020
title_full Phylodynamics of SARS-CoV-2 in France, Europe, and the world in 2020
title_fullStr Phylodynamics of SARS-CoV-2 in France, Europe, and the world in 2020
title_full_unstemmed Phylodynamics of SARS-CoV-2 in France, Europe, and the world in 2020
title_short Phylodynamics of SARS-CoV-2 in France, Europe, and the world in 2020
title_sort phylodynamics of sars-cov-2 in france, europe, and the world in 2020
topic Epidemiology and Global Health
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10179682/
https://www.ncbi.nlm.nih.gov/pubmed/37159510
http://dx.doi.org/10.7554/eLife.82538
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