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

Affiliations

• ¹ Emerging Pathogens Institute, University of Florida, Gainesville, FL 32609; salemi@pathology.ufl.edu cmavian@ufl.edu m.prosperi@ufl.edu.
• ² Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610.
• ³ Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122.
• ⁴ Emerging Pathogens Institute, University of Florida, Gainesville, FL 32609.
• ⁵ Department of Epidemiology, University of Florida, Gainesville, FL 32610.
• ⁶ Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium.
• ⁷ Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisboa, Portugal.
• ⁸ Spatial Epidemiology Laboratory, Université Libre de Bruxelles, 1050 Bruxelles, Belgium.
• ⁹ Network Science Institute, Northeastern University, Boston, MA 02115.
• ¹⁰ Department of Medicine, University of Cambridge, Cambridge CB2 3QG, United Kingdom.
• ¹¹ Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom.
• ¹² Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom.
• ¹³ Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892.
• ¹⁴ Department of Computer & Information Science & Engineering, University of Florida, Gainesville, FL 32611.
• ¹⁵ Department of Informatics, Craig Venter Institute, La Jolla, CA 92037.
• ¹⁶ Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037.
• ¹⁷ Department of Pathology, University of California San Diego, La Jolla, CA 92093.
• ¹⁸ Unité Bioinformatique Evolutive, Centre de Bioinformatique, Biostatistique et BiologieIntégrative (C3BI)-USR 3756 CNRS and Institut Pasteur, 75015 Paris, France.
• ¹⁹ State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China.
• ²⁰ Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095.
• ²¹ Department of Biostatistics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095.
• ²² Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095.
• ²³ KwaZulu-Natal Research Innovation and Sequencing Platform, University of KwaZulu-Natal, Durban 4041, South Africa.
• ²⁴ Department of Epidemiology and Biostatistics, School of Public Health, Indiana University, Bloomington, IN 47405.
• ²⁵ Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna (CIBIV), Medical University of Vienna, University of Vienna, 1030 Vienna, Austria.
• ²⁶ Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa.
• ²⁷ Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109.
• ²⁸ Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom.
• ²⁹ Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510.
• ³⁰ Biozentrum, University of Basel, 4056 Basel, Switzerland.
• ³¹ Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology, 4058 Basel, Switzerland.
• ³² Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden.
• ³³ Department of Biostatistics & Bioinformatics, Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC 20052.
• ³⁴ Theoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545.
• ³⁵ Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany.
• ³⁶ Institute for Theoretical Informatics, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany.