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

Carla Mavian; Sergei Kosakovsky Pond; Simone Marini; Magalis, Brittany Rife; AM Vandamme; Dellicoure, Simon; Scarpino, Samuel V.; Houldcroft, Charlotte; Villabona-Arenas, Julian; Paisie, Taylor K.; Nídia Sequeira Trovão; Boucher, Christina; Zhangn, Yun; Scheuermann, Richard H.; Gascuel, Olivier; Lam, Tommy Tsan-Yuk; Marc A. Suchard; AB Abecasis; Wilkinson, Eduan; Túlio de Oliveira; Bentow, Ana I.; Schmidt, Heiko A.; Martin, Darren; Hadfield, James; Nuno Faria; Grubaugh, Nathan D.; Neherc, Richard A.; Guy Baele; Lemeye, Philippe; Stadler,  Tanja; Jan Albert; Crandall, Keith A.; Thomas Leitner; Stamatakis, Alexandros; Prosperi, Mattia; 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, Magalis, Brittany Rife , AM Vandamme, Dellicoure, Simon , Scarpino, Samuel V. , Houldcroft, Charlotte , Villabona-Arenas, Julian , Paisie, Taylor K. , Nídia Sequeira Trovão, Boucher, Christina , Zhangn, Yun , Scheuermann, Richard H. , Gascuel, Olivier , Lam, Tommy Tsan-Yuk , Marc A. Suchard, AB Abecasis, Wilkinson, Eduan, Túlio de OliveiraBentow, Ana I. , Schmidt, Heiko A. , Martin, Darren , Hadfield, James , Nuno Faria, Grubaugh, Nathan D. , Neherc, Richard A. , Guy Baele, Lemeye, Philippe , Stadler, Tanja, Jan Albert, Crandall, Keith A. , Thomas Leitner, Stamatakis, Alexandros , Prosperi, Mattia , Marco Salemi

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

42 Citations (Scopus)

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
Publication status	Published - 7 May 2020

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Mavian, C., Pond, S. K., Marini, S., Brittany Rife , M., Vandamme, AM., Simon , D., Samuel V. , S., Charlotte , H., Julian , V-A., Taylor K. , P., Trovão, N. S., Christina , B., Yun , Z., Richard H. , S., Olivier , G., Tommy Tsan-Yuk , L., Suchard, M. A., Abecasis, AB., Eduan, W., ... 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

Mavian, Carla ; Pond, Sergei Kosakovsky ; Marini, Simone ; Brittany Rife , Magalis, ; Vandamme, AM ; Simon , Dellicoure, ; Samuel V. , Scarpino, ; Charlotte , Houldcroft, ; Julian , Villabona-Arenas, ; Taylor K. , Paisie, ; Trovão, Nídia Sequeira ; Christina , Boucher, ; Yun , Zhangn, ; Richard H. , Scheuermann, ; Olivier , Gascuel, ; Tommy Tsan-Yuk , Lam, ; Suchard, Marc A. ; Abecasis, AB ; Eduan, Wilkinson, ; de Oliveira, Túlio ; Ana I. , Bentow, ; Heiko A. , Schmidt, ; Darren , Martin, ; James , Hadfield, ; Faria, Nuno ; Nathan D. , Grubaugh, ; Richard A. , Neherc, ; Baele, Guy ; Philippe , Lemeye, ; Tanja, Stadler, ; Albert, Jan ; Keith A. , Crandall, ; Leitner, Thomas ; Alexandros , Stamatakis, ; Mattia , Prosperi, ; Salemi, Marco. / Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable. In: Proceedings of the National Academy of Sciences of the United States of America. 2020 ; Vol. 117, No. 23. pp. 12522-12523.

@article{2cf5b2f0a329445b86c388fcd81da9b8,

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 {Brittany Rife}, Magalis, and AM Vandamme and Dellicoure, Simon and {Samuel V.}, Scarpino, and Houldcroft, Charlotte and Villabona-Arenas, Julian and {Taylor K.}, Paisie, and Trov{\~a}o, {N{\'i}dia Sequeira} and Boucher, Christina and Zhangn, Yun and {Richard H.}, Scheuermann, and Gascuel, Olivier and {Tommy Tsan-Yuk}, Lam, and Suchard, {Marc A.} and AB Abecasis and Wilkinson, Eduan and {de Oliveira}, T{\'u}lio and {Ana I.}, Bentow, and {Heiko A.}, Schmidt, and Martin, Darren and Hadfield, James and Nuno Faria and {Nathan D.}, Grubaugh, and {Richard A.}, Neherc, and Guy Baele and Lemeye, Philippe and Stadler, Tanja and Jan Albert and {Keith A.}, Crandall, and Thomas Leitner and Stamatakis, Alexandros and Prosperi, Mattia and Marco Salemi",

year = "2020",

month = may,

day = "7",

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, Brittany Rife , M, Vandamme, AM, Simon , D, Samuel V. , S, Charlotte , H, Julian , V-A, Taylor K. , P, Trovão, NS, Christina , B, Yun , Z, Richard H. , S, Olivier , G, Tommy Tsan-Yuk , L, Suchard, MA, Abecasis, AB, Eduan, W, de Oliveira, T, Ana I. , B, Heiko A. , S, Darren , M, James , H, Faria, N, Nathan D. , G, Richard A. , N, Baele, G, Philippe , L, Tanja, S, Albert, J, Keith A. , C, Leitner, T, Alexandros , S, Mattia , P & 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

Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable. / Mavian, Carla; Pond, Sergei Kosakovsky; Marini, Simone; Brittany Rife , Magalis,; Vandamme, AM; Simon , Dellicoure,; Samuel V. , Scarpino,; Charlotte , Houldcroft,; Julian , Villabona-Arenas,; Taylor K. , Paisie,; Trovão, Nídia Sequeira; Christina , Boucher,; Yun , Zhangn,; Richard H. , Scheuermann,; Olivier , Gascuel,; Tommy Tsan-Yuk , Lam,; Suchard, Marc A.; Abecasis, AB; Eduan, Wilkinson,; de Oliveira, Túlio; Ana I. , Bentow,; Heiko A. , Schmidt,; Darren , Martin,; James , Hadfield,; Faria, Nuno; Nathan D. , Grubaugh,; Richard A. , Neherc,; Baele, Guy; Philippe , Lemeye,; Tanja, Stadler, ; Albert, Jan; Keith A. , Crandall,; Leitner, Thomas; Alexandros , Stamatakis,; Mattia , Prosperi,; Salemi, Marco.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 117, No. 23, 07.05.2020, p. 12522-12523.

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

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 - Brittany Rife , Magalis,

AU - Vandamme, AM

AU - Simon , Dellicoure,

AU - Samuel V. , Scarpino,

AU - Charlotte , Houldcroft,

AU - Julian , Villabona-Arenas,

AU - Taylor K. , Paisie,

AU - Trovão, Nídia Sequeira

AU - Christina , Boucher,

AU - Yun , Zhangn,

AU - Richard H. , Scheuermann,

AU - Olivier , Gascuel,

AU - Tommy Tsan-Yuk , Lam,

AU - Suchard, Marc A.

AU - Abecasis, AB

AU - Eduan, Wilkinson,

AU - de Oliveira, Túlio

AU - Ana I. , Bentow,

AU - Heiko A. , Schmidt,

AU - Darren , Martin,

AU - James , Hadfield,

AU - Faria, Nuno

AU - Nathan D. , Grubaugh,

AU - Richard A. , Neherc,

AU - Baele, Guy

AU - Philippe , Lemeye,

AU - Tanja, Stadler,

AU - Albert, Jan

AU - Keith A. , Crandall,

AU - Leitner, Thomas

AU - Alexandros , Stamatakis,

AU - Mattia , Prosperi,

AU - Salemi, Marco

PY - 2020/5/7

Y1 - 2020/5/7

UR - https://www.pnas.org/content/early/2020/05/06/2007295117.long

U2 - 10.1073/pnas.2007295117

DO - 10.1073/pnas.2007295117

M3 - Letter

C2 - 32381734

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

SN - 0027-8424

IS - 23

ER -

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

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