ArticleProceedings of the National Academy of Sciences of the United States of America2020
Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.
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In one paragraph
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers, 1 of them a synthesis that pooled it.
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41citing papers in PubMed, 1 pooled it
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Who cites it
41 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Transmissibility and pathogenicity of the severe acute respiratory syndrome coronavirus 2: A systematic review and meta-analysis of secondary attack rate and asymptomatic infection.Journal of infection and public health · 2022Pooled it
- Finding maximum common contractions between phylogenetic networks.Algorithms for molecular biology : AMB · 2025Article
- Comprehensive review on COVID-19: etiology, pathogenicity, and treatment.Frontiers in medicine · 2025Review
- Identifying impacts of contact tracing on HIV epidemiological inference from phylogenetic data.Virus evolution · 2025Article
- Properties and Mechanisms of Deletions, Insertions, and Substitutions in the Evolutionary History of SARS-CoV-2.International journal of molecular sciences · 2024Review
- Application of Phylodynamic Tools to Inform the Public Health Response to COVID-19: Qualitative Analysis of Expert Opinions.JMIR formative research · 2023Article
- A Modified Recombinant DNA-Based SARS-CoV-2 Vaccine Expressing Stabilized Uncleavable Spike Protein Elicits Humoral and Cellular Immunity against Various SARS-CoV-2 Variants of Concern.Transboundary and emerging diseases · 2023Article
- Genomic surveillance of SARS-CoV-2 in Puerto Rico reveals emergence of an autochthonous lineage and early detection of variants.Research square · 2022Article
- Phylodynamics of a regional SARS-CoV-2 rapid spreading event in Colorado in late 2020.PloS one · 2022Article
- Genomic surveillance of SARS-CoV-2 in Puerto Rico enabled early detection and tracking of variants.Communications medicine · 2022Article
- Applicability of several rooted phylogenetic network algorithms for representing the evolutionary history of SARS-CoV-2.BMC ecology and evolution · 2021Article
- The biological and clinical significance of emerging SARS-CoV-2 variants.Nature reviews. Genetics · 2021Review
- Evolutionary analysis and lineage designation of SARS-CoV-2 genomes.Science bulletin · 2021Article
- Mutational spectrum of SARS-CoV-2 during the global pandemic.Experimental & molecular medicine · 2021Article
- An Evolutionary Portrait of the Progenitor SARS-CoV-2 and Its Dominant Offshoots in COVID-19 Pandemic.Molecular biology and evolution · 2021Article
- Ongoing global and regional adaptive evolution of SARS-CoV-2.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Setting the Terms for Zoonotic Diseases: Effective Communication for Research, Conservation, and Public Policy.Viruses · 2021Article
- Integrating Phylogenetic Biomarker Data and Qualitative Approaches: An example of HIV Transmission Clusters as a Sampling Frame for Semistructured Interviews and Implications for the COVID-19 Era.Journal of mixed methods research · 2021Article
- Feline infectious peritonitis (FIP) and coronavirus disease 19 (COVID-19): Are they similar?Transboundary and emerging diseases · 2021Review
- European context of the diversity and phylogenetic position of SARS-CoV-2 sequences from Polish COVID-19 patients.Journal of applied genetics · 2021Article
Corrections and comments
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Authors and funding
36 authors.
Carla MavianEmerging Pathogens Institute, University of Florida, Gainesville, FL 32609; salemi@pathology.ufl.edu cmavian@ufl.edu m.prosperi@ufl.edu.ORCID 0000-0003-3819-5520
Sergei Kosakovsky PondInstitute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122.
Simone MariniEmerging Pathogens Institute, University of Florida, Gainesville, FL 32609.
Brittany Rife MagalisEmerging Pathogens Institute, University of Florida, Gainesville, FL 32609.ORCID 0000-0001-6088-4651
Anne-Mieke VandammeDepartment of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium.
Simon DellicourDepartment of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium.
Samuel V ScarpinoNetwork Science Institute, Northeastern University, Boston, MA 02115.ORCID 0000-0001-5716-2770
Charlotte HouldcroftDepartment of Medicine, University of Cambridge, Cambridge CB2 3QG, United Kingdom.ORCID 0000-0002-1833-5285
Julian Villabona-ArenasCentre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom.
Taylor K PaisieEmerging Pathogens Institute, University of Florida, Gainesville, FL 32609.ORCID 0000-0002-6024-2744
Nídia S TrovãoDivision of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD 20892.ORCID 0000-0002-2106-1166
Christina BoucherDepartment of Computer & Information Science & Engineering, University of Florida, Gainesville, FL 32611.
Yun ZhangDepartment of Informatics, Craig Venter Institute, La Jolla, CA 92037.
Richard H ScheuermannDepartment of Informatics, Craig Venter Institute, La Jolla, CA 92037.
Olivier GascuelUnité Bioinformatique Evolutive, Centre de Bioinformatique, Biostatistique et BiologieIntégrative (C3BI)-USR 3756 CNRS and Institut Pasteur, 75015 Paris, France.
Tommy Tsan-Yuk LamState Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China.
Marc A SuchardDepartment of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095.
Ana AbecasisCenter for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisboa, Portugal.
Eduan WilkinsonKwaZulu-Natal Research Innovation and Sequencing Platform, University of KwaZulu-Natal, Durban 4041, South Africa.
Tulio de OliveiraKwaZulu-Natal Research Innovation and Sequencing Platform, University of KwaZulu-Natal, Durban 4041, South Africa.
Ana I BentoDepartment of Epidemiology and Biostatistics, School of Public Health, Indiana University, Bloomington, IN 47405.ORCID 0000-0001-7728-007X
Heiko A SchmidtMax F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna (CIBIV), Medical University of Vienna, University of Vienna, 1030 Vienna, Austria.ORCID 0000-0002-2311-8592
Darren MartinDepartment of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa.
James HadfieldVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109.
Nuno FariaDepartment of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom.
Nathan D GrubaughDepartment of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510.
Richard A NeherBiozentrum, University of Basel, 4056 Basel, Switzerland.
Guy BaeleDepartment of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium.ORCID 0000-0002-1915-7732
Philippe LemeyDepartment of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium.
Tanja StadlerDepartment of Biosystems Science and Engineering, Swiss Federal Institute of Technology, 4058 Basel, Switzerland.
Jan AlbertDepartment of Microbiology Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden.
Keith A CrandallDepartment of Biostatistics & Bioinformatics, Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC 20052.ORCID 0000-0002-0836-3389
Thomas LeitnerTheoretical Biology & Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545.ORCID 0000-0001-8160-2588
Alexandros StamatakisComputational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany.
Mattia ProsperiEmerging Pathogens Institute, University of Florida, Gainesville, FL 32609; salemi@pathology.ufl.edu cmavian@ufl.edu m.prosperi@ufl.edu.ORCID 0000-0002-9021-5595
Marco SalemiEmerging Pathogens Institute, University of Florida, Gainesville, FL 32609; salemi@pathology.ufl.edu cmavian@ufl.edu m.prosperi@ufl.edu.
Funding
Yale Clinical and Translational Science Award (U Component)UL1TR001863 · NCATS · YALE UNIVERSITY · PI John H. Krystal, LUCILA OHNO-MACHADO · 2016 to 2026
$102.9MReconstructing HIV Epidemics from HIV PhylogeneticsR01AI087520 · NIAID · TRIAD NATIONAL SECURITY, LLC · PI Thomas K. Leitner · 2010 to 2026
$11.2MTurning big data analysis infrastructure for HIV researchR01AI134384 · NIAID · PENNSYLVANIA STATE UNIVERSITY, THE · PI NEKRUTENKO, ANTON, POND, SERGEI L KOSAKOVSKY · 2017 to 2021
$4.2MForecasting trajectories of HIV transmission networks with a novel phylodynamic and deep learning frameworkR01AI145552 · NIAID · UNIVERSITY OF FLORIDA · PI Simone Marini, Mattia Prosperi · 2020 to 2026
$3.6MHIV Dynamic Modelling for Identification of Transmission Epicenters (HIV-DYNAMITE)R21AI138815 · NIAID · UNIVERSITY OF FLORIDA · PI PROSPERI, MATTIA, SALEMI, MARCO · 2018 to 2019
$419kMedical Research Council MR/R015600/1NCATS NIH HHS UL1 TR001863NIAID NIH HHS R01 AI087520NIAID NIH HHS R01 AI134384NIAID NIH HHS R01 AI145552NIAID NIH HHS R21 AI138815Wellcome Trust 204870/Z/16/Z
Abstract
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Indexed as
Coronavirus InfectionsSevere acute respiratory syndrome-related coronavirusBetacoronavirusCOVID-19HumansPandemicsPhylogenyPneumonia, ViralSARS-CoV-2Selection Bias
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