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Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.
Mavian, Carla; Pond, Sergei Kosakovsky; Marini, Simone; Magalis, Brittany Rife; Vandamme, Anne-Mieke; Dellicour, Simon; Scarpino, Samuel V; Houldcroft, Charlotte; Villabona-Arenas, Julian; Paisie, Taylor K; Trovão, Nídia S; Boucher, Christina; Zhang, Yun; Scheuermann, Richard H; Gascuel, Olivier; Lam, Tommy Tsan-Yuk; Suchard, Marc A; Abecasis, Ana; Wilkinson, Eduan; de Oliveira, Tulio; Bento, Ana I; Schmidt, Heiko A; Martin, Darren; Hadfield, James; Faria, Nuno; Grubaugh, Nathan D; Neher, Richard A; Baele, Guy; Lemey, Philippe; Stadler, Tanja; Albert, Jan; Crandall, Keith A; Leitner, Thomas; Stamatakis, Alexandros; Prosperi, Mattia; Salemi, Marco.
  • Mavian C; Emerging Pathogens Institute, University of Florida, Gainesville, FL 32609; salemi@pathology.ufl.edu cmavian@ufl.edu m.prosperi@ufl.edu.
  • Pond SK; Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610.
  • Marini S; Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122.
  • Magalis BR; Emerging Pathogens Institute, University of Florida, Gainesville, FL 32609.
  • Vandamme AM; Department of Epidemiology, University of Florida, Gainesville, FL 32610.
  • Dellicour S; Emerging Pathogens Institute, University of Florida, Gainesville, FL 32609.
  • Scarpino SV; Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610.
  • Houldcroft C; Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium.
  • Villabona-Arenas J; Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisboa, Portugal.
  • Paisie TK; Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium.
  • Trovão NS; Spatial Epidemiology Laboratory, Université Libre de Bruxelles, 1050 Bruxelles, Belgium.
  • Boucher C; Network Science Institute, Northeastern University, Boston, MA 02115.
  • Zhang Y; Department of Medicine, University of Cambridge, Cambridge CB2 3QG, United Kingdom.
  • Scheuermann RH; Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom.
  • Gascuel O; Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom.
  • Lam TT; Emerging Pathogens Institute, University of Florida, Gainesville, FL 32609.
  • Suchard MA; Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610.
  • Abecasis A; Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892.
  • Wilkinson E; Department of Computer & Information Science & Engineering, University of Florida, Gainesville, FL 32611.
  • de Oliveira T; Department of Informatics, Craig Venter Institute, La Jolla, CA 92037.
  • Bento AI; Department of Informatics, Craig Venter Institute, La Jolla, CA 92037.
  • Schmidt HA; Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037.
  • Martin D; Department of Pathology, University of California San Diego, La Jolla, CA 92093.
  • Hadfield J; Unité Bioinformatique Evolutive, Centre de Bioinformatique, Biostatistique et BiologieIntégrative (C3BI)-USR 3756 CNRS and Institut Pasteur, 75015 Paris, France.
  • Faria N; State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China.
  • Grubaugh ND; Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095.
  • Neher RA; Department of Biostatistics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095.
  • Baele G; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095.
  • Lemey P; Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisboa, Portugal.
  • Stadler T; KwaZulu-Natal Research Innovation and Sequencing Platform, University of KwaZulu-Natal, Durban 4041, South Africa.
  • Albert J; KwaZulu-Natal Research Innovation and Sequencing Platform, University of KwaZulu-Natal, Durban 4041, South Africa.
  • Crandall KA; Department of Epidemiology and Biostatistics, School of Public Health, Indiana University, Bloomington, IN 47405.
  • Leitner T; Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna (CIBIV), Medical University of Vienna, University of Vienna, 1030 Vienna, Austria.
  • Stamatakis A; Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa.
  • Prosperi M; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109.
  • Salemi M; Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom.
Proc Natl Acad Sci U S A ; 117(23): 12522-12523, 2020 06 09.
Article in English | MEDLINE | ID: covidwho-222922
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Coronavirus Infections / Severe acute respiratory syndrome-related coronavirus Type of study: Randomized controlled trials Limits: Humans Language: English Journal: Proc Natl Acad Sci U S A Year: 2020 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Coronavirus Infections / Severe acute respiratory syndrome-related coronavirus Type of study: Randomized controlled trials Limits: Humans Language: English Journal: Proc Natl Acad Sci U S A Year: 2020 Document Type: Article