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Journal articles
Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable
Carla Mavian 1, * Sergei Kosakovsky Pond 2 Simone Marini 1 Brittany Rife Magalis 1 Anne-Mieke Vandamme 3, 4 Simon Dellicour 3, 5 Samuel V. Scarpino 6 Charlotte Houldcroft 7 Christian Julián Villabona-Arenas 8 Taylor K. Paisie 1 Nídia S. Trovão 9 Christina Boucher 1 Yun Zhang 10 Richard H. Scheuermann 10, 11 Olivier Gascuel 12 Tommy Tsan-Yuk Lam 13 Marc A. Suchard 14 Ana Abecasis 4 Eduan Wilkinson 15 Tulio de Oliveira 15 Ana I. Bento 16 Heiko A. Schmidt 17 Darren Martin 18 James Hadfield 19 Nuno Faria 20 Nathan D. Grubaugh 21 Richard A. Neher 22 Guy Baele 3 Philippe Lemey 3 Tanja Stadler 23 Jan Albert 24 Keith A. Crandall 25 Thomas Leitner 26 Alexandros Stamatakis 27, 28 Mattia Prosperi 1, * Marco Salemi 1, *
*
Corresponding author
Carla Mavian 1
Correspondent author
Sergei Kosakovsky Pond 2
Author
Simone Marini 1
Author
Brittany Rife Magalis 1
Author
Anne-Mieke Vandamme 3, 4
Author
ORCID : 0000-0002-6594-2766IdRef : 076529576
Simon Dellicour 3, 5
Author
ORCID : 0000-0001-9558-1052
Samuel V. Scarpino 6
Author
Charlotte Houldcroft 7
Author
Yun Zhang 10
Author
ORCID : 0000-0003-4045-9046
Richard H. Scheuermann 10, 11
Author
Olivier Gascuel 12
Author
ORCID : 0000-0002-9412-9723
Tommy Tsan-Yuk Lam 13
Author
Nuno Faria 20
Author
Nathan D. Grubaugh 21
Author
Richard A. Neher 22
Author
Guy Baele 3
Author
ORCID : 0000-0002-1915-7732
Philippe Lemey 3
Author
ORCID : 0000-0003-2826-5353
Tanja Stadler 23
Author
ORCID : 0000-0001-6431-535X
Jan Albert 24
Author
Keith A. Crandall 25
Author
Thomas Leitner 26
Author
Alexandros Stamatakis 27, 28
Author
ORCID : 0000-0003-0353-0691
Mattia Prosperi 1
Correspondent author
Marco Salemi 1
Correspondent author
1
UF - University of Florida [Gainesville] (Gainesville, FL 32611 - United States)
2
Temple University [Philadelphia] (Temple University
1801 N. Broad Street
Philadelphia, PA 19122 USA - United States)
- Pennsylvania Commonwealth System of Higher Education (PCSHE) (United States)
3
KU Leuven - Catholic University of Leuven - Katholieke Universiteit Leuven (Oude Markt 13 - bus 5005, 3000 Leuven - Belgium)
4
NOVA - Universidade Nova de Lisboa = NOVA University Lisbon (Campus de Campolide
1099-085 Lisboa - Portugal)
5
ULB - Université libre de Bruxelles (Avenue Franklin Roosevelt 50 - 1050 Bruxelles - Belgium)
6
Northeastern University [Boston] (360 Huntington Ave., Boston, Massachusetts 02115 - United States)
7
CAM - University of Cambridge [UK] (The Old Schools, Trinity Lane, Cambridge CB2 1TN - United Kingdom)
8
LSHTM - London School of Hygiene and Tropical Medicine (Keppel Street
London
WC1E 7HT
- United Kingdom)
9
Fogarty International Center (Bethesda, MD - United States)
- NIH - National Institutes of Health [Bethesda] (9000 Rockville Pike, Bethesda, Maryland 20892 - United States)
10
JCVI - J. Craig Venter Institute [La Jolla, USA] (4120 Capricorn Lane, La Jolla, CA 92037 - United States)
11
UC San Diego - University of California [San Diego] (UCSD, 9500 Gilman Dr., La Jolla, CA 92093 USA - United States)
- UC - University of California (United States)
12
Bioinformatique évolutive - Evolutionary Bioinformatics (Département Biologie Computationnelle, C3BI, 25-28 rue du Docteur Roux 75724 Paris Cedex 15 - France)
- Institut Pasteur [Paris] (25-28, rue du docteur Roux, 75724 Paris cedex 15 - France)
- CNRS - Centre National de la Recherche Scientifique : USR3756 (France)
13
HKU - The University of Hong Kong (Pokfulam, Hong Kong - Hong Kong SAR China)
14
David Geffen School of Medicine [Los Angeles] (United States)
- UCLA - University of California [Los Angeles] ( Los Angeles, Californie 90095 - United States)
- UC - University of California (United States)
15
UKZN - University of KwaZulu-Natal [Durban, Afrique du Sud] (South Africa)
16
Indiana University [Bloomington] (107 S. Indiana Avenue, Bloomington, IN 47405-7000 - United States)
- Indiana University System (United States)
17
University of Vienna [Vienna] (Universitätsring 1, 1010 Wien - Austria)
18
University of Cape Town (Private Bag X3, Rondebosch 7701, South Africa - South Africa)
19
FHCRC - Fred Hutchinson Cancer Research Center [Seattle] (1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 - United States)
20
University of Oxford [Oxford] (Wellington Square, Oxford OX1 2JD - United Kingdom)
21
YSPH - Yale School of Public Health (60 College Street P.O. Box 208034 New Haven - United States)
22
Biozentrum [Basel, Suisse] (Klingelbergstrasse 70, 4056 Basel, Suisse - Switzerland)
- Unibas - University of Basel (Petersplatz 1, P. O. Box 4001 Basel - Switzerland)
23
D-BSSE - Department of Biosystems Science and Engineering [ETH Zürich] (Mattenstrasse 26 4058 Basel, Switzerland - Switzerland)
- ETH Zürich - Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (Hauptgebäude, Rämistrasse 101, 8092 Zürich - Switzerland)
24
Karolinska Institutet [Stockholm] (Solnavägen 1, 171 77 Solna
Stockholm - Sweden)
25
Milken Institute School of Public Health (950 New Hampshire Ave, NW, Washington, DC 20052 - United States)
- GW - The George Washington University (2121 Eye Street, NW , Washington, DC 20052 - United States)
26
LANL - Los Alamos National Laboratory (P.O. Box 1663 Los Alamos, NM 87545 - United States)
27
HITS - Heidelberg Institute for Theoretical Studies (D-69118 Heidelberg Germany - Germany)
28
KIT - Karlsruher Institut für Technologie (P.O.box 3640, 76021 Karlsruhe - Germany)
Document type :
Journal articles
Domain :
Complete list of metadata
https://hal-pasteur.archives-ouvertes.fr/pasteur-03037656
Contributor : Anna Zhukova Connect in order to contact the contributor
Submitted on : Thursday, December 3, 2020 - 10:58:50 AM
Last modification on : Wednesday, November 30, 2022 - 11:22:07 AM
Long-term archiving on: : Thursday, March 4, 2021 - 6:47:07 PM
Contributor : Anna Zhukova Connect in order to contact the contributor
Submitted on : Thursday, December 3, 2020 - 10:58:50 AM
Last modification on : Wednesday, November 30, 2022 - 11:22:07 AM
Long-term archiving on: : Thursday, March 4, 2021 - 6:47:07 PM
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12522.full.pdf
Publication funded by an institution
Licence
Distributed under a Creative Commons Attribution 4.0 International License
Identifiers
- HAL Id : pasteur-03037656, version 1
- DOI : 10.1073/pnas.2007295117
- PUBMED : 32381734
- PUBMEDCENTRAL : PMC7293693
Citation
Carla Mavian, Sergei Kosakovsky Pond, Simone Marini, Brittany Rife Magalis, Anne-Mieke Vandamme, et al.. Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable. Proceedings of the National Academy of Sciences of the United States of America, 2020, 117 (23), pp.12522-12523. ⟨10.1073/pnas.2007295117⟩. ⟨pasteur-03037656⟩
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