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

Carla Mavian^{1

2}, Sergei Kosakovsky Pond³, Simone Marini^{4

5}, Brittany Rife Magalis^{4

2}, Anne-Mieke Vandamme^{6

7}, Simon Dellicour^{6

8}, Samuel V Scarpino⁹, Charlotte Houldcroft¹⁰, Julian Villabona-Arenas^{11

12}, Taylor K Paisie^{4

2}, Nídia S Trovão¹³, Christina Boucher¹⁴, Yun Zhang¹⁵, Richard H Scheuermann^{15

16

17}, Olivier Gascuel¹⁸, Tommy Tsan-Yuk Lam¹⁹, Marc A Suchard^{20

21

22}, Ana Abecasis⁷, Eduan Wilkinson²³, Tulio de Oliveira²³, Ana I Bento²⁴, Heiko A Schmidt²⁵, Darren Martin²⁶, James Hadfield²⁷, Nuno Faria²⁸, Nathan D Grubaugh²⁹, Richard A Neher³⁰, Guy Baele⁶, Philippe Lemey⁶, Tanja Stadler³¹, Jan Albert³², Keith A Crandall³³, Thomas Leitner³⁴, Alexandros Stamatakis^{35

36}, Mattia Prosperi^{1

5}, Marco Salemi^{1

2}

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.

PMID: 32381734
PMCID: PMC7293693
DOI: 10.1073/pnas.2007295117

Comment

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

Carla Mavian et al. Proc Natl Acad Sci U S A. 2020.

. 2020 Jun 9;117(23):12522-12523.

doi: 10.1073/pnas.2007295117. Epub 2020 May 7.

Authors

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.

PMID: 32381734
PMCID: PMC7293693
DOI: 10.1073/pnas.2007295117

No abstract available

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interest.

Comment on

Phylogenetic network analysis of SARS-CoV-2 genomes.
Forster P, Forster L, Renfrew C, Forster M. Forster P, et al. Proc Natl Acad Sci U S A. 2020 Apr 28;117(17):9241-9243. doi: 10.1073/pnas.2004999117. Epub 2020 Apr 8. Proc Natl Acad Sci U S A. 2020. PMID: 32269081 Free PMC article.

References

1. Forster P., Forster L., Renfrew C., Forster M., Phylogenetic network analysis of SARS-CoV-2 genomes. Proc. Natl. Acad. Sci. U.S.A. 117, 9241–9243 (2020). - PMC - PubMed
1. Salemi M., Vandamme A.-M., Lemey P., The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing (Cambridge University Press, Cambridge, United Kingdom, 2009).
1. Hui D. S., et al. , The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health—The latest 2019 novel coronavirus outbreak in Wuhan, China. Int. J. Infect. Dis. 91, 264–266 (2020). - PMC - PubMed
1. Pybus O. G., Rambaut A., Evolutionary analysis of the dynamics of viral infectious disease. Nat. Rev. Genet. 10, 540–550 (2009). - PMC - PubMed
1. Hadfield J., et al. , Nextstrain: Real-time tracking of pathogen evolution. Bioinformatics 34, 4121–4123 (2018). - PMC - PubMed

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

Affiliations

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

Authors

Affiliations

Conflict of interest statement

Comment on

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Miscellaneous