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)

1 UF - University of Florida [Gainesville]
2 Temple University [Philadelphia]
3 KU Leuven - Catholic University of Leuven - Katholieke Universiteit Leuven
4 NOVA - Universidade Nova de Lisboa = NOVA University Lisbon
5 ULB - Université libre de Bruxelles
6 Northeastern University [Boston]
7 CAM - University of Cambridge [UK]
8 LSHTM - London School of Hygiene and Tropical Medicine
9 Fogarty International Center
10 JCVI - J. Craig Venter Institute [La Jolla, USA]
11 UC San Diego - University of California [San Diego]
12 Bioinformatique évolutive - Evolutionary Bioinformatics
13 HKU - The University of Hong Kong
14 David Geffen School of Medicine [Los Angeles]
15 UKZN - University of KwaZulu-Natal [Durban, Afrique du Sud]
16 Indiana University [Bloomington]
17 University of Vienna [Vienna]
18 University of Cape Town
19 FHCRC - Fred Hutchinson Cancer Research Center [Seattle]
20 University of Oxford
21 YSPH - Yale School of Public Health
22 Biozentrum [Basel, Suisse]
23 D-BSSE - Department of Biosystems Science and Engineering [ETH Zürich]
24 Karolinska Institutet [Stockholm]
25 Milken Institute School of Public Health
26 LANL - Los Alamos National Laboratory
27 HITS - Heidelberg Institute for Theoretical Studies
28 KIT - Karlsruher Institut für Technologie

Domains: Computer Science [cs]; Bioinformatics [q-bio.QM]

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⟩