Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

Carla Mavian; Sergei Kosakovsky Pond; Simone Marini; Brittany Rife Magalis; Anne Mieke Vandamme; Simon Dellicour; Samuel V. Scarpino; Charlotte Houldcroft; Julian Villabona-Arenas; Taylor K. Paisie; Nídia S. Trovão; Christina Boucher; Yun Zhang; Richard H. Scheuermann; Olivier Gascuel; Tommy Tsan Yuk Lam; Marc A. Suchard; Ana Abecasis; Eduan Wilkinson; Tulio de Oliveira; Ana I. Bento; Heiko A. Schmidt; Darren Martin; James Hadfield; Nuno Faria; Nathan D. Grubaugh; Richard A. Neher; Guy Baele; Philippe Lemey; Tanja Stadler; Jan Albert; Keith A. Crandall; Thomas Leitner; Alexandros Stamatakis; Mattia Prosperi; Marco Salemi

doi:10.1073/pnas.2007295117

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

Carla Mavian
, Sergei Kosakovsky Pond
, Simone Marini
, Brittany Rife Magalis
, Anne Mieke Vandamme
, Simon Dellicour
, Samuel V. Scarpino
, Charlotte Houldcroft
, Julian Villabona-Arenas
, Taylor K. Paisie
, Nídia S. Trovão
, Christina Boucher
, Yun Zhang
, Richard H. Scheuermann
, Olivier Gascuel
, Tommy Tsan Yuk Lam
, Marc A. Suchard
, Ana Abecasis
, Eduan Wilkinson
, Tulio de Oliveira

Ana I. Bento, Heiko A. Schmidt, Darren Martin, James Hadfield, Nuno Faria, Nathan D. Grubaugh, Richard A. Neher, Guy Baele, Philippe Lemey, Tanja Stadler, Jan Albert, Keith A. Crandall, Thomas Leitner, Alexandros Stamatakis, Mattia Prosperi, Marco Salemi

Research output: Contribution to journal › Letter › peer-review

61 Scopus citations

Original language	English
Pages (from-to)	12522-12523
Number of pages	2
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	117
Issue number	23
DOIs	https://doi.org/10.1073/pnas.2007295117
State	Published - 9 Jun 2020
Externally published	Yes

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10.1073/pnas.2007295117

Cite this

Mavian, C., Pond, S. K., Marini, S., Magalis, B. R., Vandamme, A. M., Dellicour, S., Scarpino, S. V., Houldcroft, C., Villabona-Arenas, J., Paisie, T. K., Trovão, N. S., Boucher, C., Zhang, Y., Scheuermann, R. H., Gascuel, O., Lam, T. T. Y., Suchard, M. A., Abecasis, A., Wilkinson, E., ... Salemi, M. (2020). 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, 117(23), 12522-12523. https://doi.org/10.1073/pnas.2007295117

@article{ab7c021196914b9e93bd2a32a9cc5d83,

title = "Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable",

author = "Carla Mavian and Pond, \{Sergei Kosakovsky\} and Simone Marini and Magalis, \{Brittany Rife\} and Vandamme, \{Anne Mieke\} and Simon Dellicour and Scarpino, \{Samuel V.\} and Charlotte Houldcroft and Julian Villabona-Arenas and Paisie, \{Taylor K.\} and Trov{\~a}o, \{N{\'i}dia S.\} and Christina Boucher and Yun Zhang and Scheuermann, \{Richard H.\} and Olivier Gascuel and Lam, \{Tommy Tsan Yuk\} and Suchard, \{Marc A.\} and Ana Abecasis and Eduan Wilkinson and \{de Oliveira\}, Tulio and Bento, \{Ana I.\} and Schmidt, \{Heiko A.\} and Darren Martin and James Hadfield and Nuno Faria and Grubaugh, \{Nathan D.\} and Neher, \{Richard A.\} and Guy Baele and Philippe Lemey and Tanja Stadler and Jan Albert and Crandall, \{Keith A.\} and Thomas Leitner and Alexandros Stamatakis and Mattia Prosperi and Marco Salemi",

note = "Funding Information: We are grateful to Paul Sharp, Andrew Rambaut, and Nicola De Maio for their insightful suggestions and critical reading of our manuscript. C.M., B.R.M., M.P., and M.S. were, in part, supported by NSF Division of Environmental Biology Award 2028221 and NIH National Institute of Allergy and Infectious Diseases Award 1R21AI138815-01. The contents of this article are solely the responsibility of the authors and do not necessarily represent the official views of the National Institutes of Health.",

year = "2020",

month = jun,

day = "9",

doi = "10.1073/pnas.2007295117",

language = "English",

volume = "117",

pages = "12522--12523",

journal = "Proceedings of the National Academy of Sciences of the United States of America",

issn = "0027-8424",

publisher = "National Academy of Sciences",

number = "23",

}

Mavian, C, Pond, SK, Marini, S, Magalis, BR, Vandamme, AM, Dellicour, S, Scarpino, SV, Houldcroft, C, Villabona-Arenas, J, Paisie, TK, Trovão, NS, Boucher, C, Zhang, Y, Scheuermann, RH, Gascuel, O, Lam, TTY, Suchard, MA, Abecasis, A, Wilkinson, E, de Oliveira, T, Bento, AI, Schmidt, HA, Martin, D, Hadfield, J, Faria, N, Grubaugh, ND, Neher, RA, Baele, G, Lemey, P, Stadler, T, Albert, J, Crandall, KA, Leitner, T, Stamatakis, A, Prosperi, M & Salemi, M 2020, '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, vol. 117, no. 23, pp. 12522-12523. https://doi.org/10.1073/pnas.2007295117

TY - JOUR

T1 - Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

AU - Mavian, Carla

AU - Pond, Sergei Kosakovsky

AU - Marini, Simone

AU - Magalis, Brittany Rife

AU - Vandamme, Anne Mieke

AU - Dellicour, Simon

AU - Scarpino, Samuel V.

AU - Houldcroft, Charlotte

AU - Villabona-Arenas, Julian

AU - Paisie, Taylor K.

AU - Trovão, Nídia S.

AU - Boucher, Christina

AU - Zhang, Yun

AU - Scheuermann, Richard H.

AU - Gascuel, Olivier

AU - Lam, Tommy Tsan Yuk

AU - Suchard, Marc A.

AU - Abecasis, Ana

AU - Wilkinson, Eduan

AU - de Oliveira, Tulio

AU - Bento, Ana I.

AU - Schmidt, Heiko A.

AU - Martin, Darren

AU - Hadfield, James

AU - Faria, Nuno

AU - Grubaugh, Nathan D.

AU - Neher, Richard A.

AU - Baele, Guy

AU - Lemey, Philippe

AU - Stadler, Tanja

AU - Albert, Jan

AU - Crandall, Keith A.

AU - Leitner, Thomas

AU - Stamatakis, Alexandros

AU - Prosperi, Mattia

AU - Salemi, Marco

N1 - Funding Information: We are grateful to Paul Sharp, Andrew Rambaut, and Nicola De Maio for their insightful suggestions and critical reading of our manuscript. C.M., B.R.M., M.P., and M.S. were, in part, supported by NSF Division of Environmental Biology Award 2028221 and NIH National Institute of Allergy and Infectious Diseases Award 1R21AI138815-01. The contents of this article are solely the responsibility of the authors and do not necessarily represent the official views of the National Institutes of Health.

PY - 2020/6/9

Y1 - 2020/6/9

UR - https://www.scopus.com/pages/publications/85085037581

U2 - 10.1073/pnas.2007295117

DO - 10.1073/pnas.2007295117

M3 - Letter

C2 - 32381734

AN - SCOPUS:85085037581

SN - 0027-8424

VL - 117

SP - 12522

EP - 12523

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

IS - 23

ER -