The evolutionary dynamics of pathogen emergence and establishment: from Reservoir Detection to Outbreak Control

Publications

Peer reviewed articles (40)

The emergence of SARS-CoV-2 in Europe and North America.

Author(s): Michael Worobey; Jonathan Pekar; Brendan B. Larsen; Martha I. Nelson; Verity Hill; Jeffrey B. Joy; Andrew Rambaut; Marc A. Suchard; Joel O. Wertheim; Philippe Lemey
Published in: Science, 11, 2020, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.abc8169

Large-scale inference of correlation among mixed-type biological traits with phylogenetic multivariate probit models

Author(s): Zhenyu Zhang; Akihiko Nishimura; Paul Bastide; Xiang Ji; Rebecca Payne; Philip J. R. Goulder; Philippe Lemey; Marc A. Suchard
Published in: https://hal.archives-ouvertes.fr/hal-03254483, 18, 2021, ISSN 1932-6157
Publisher: Institute of Mathematical Statistics
DOI: 10.1214/20-aoas1394

Bayesian Phylogeographic Analysis Incorporating Predictors and Individual Travel Histories in BEAST.

Author(s): Samuel L. Hong; Philippe Lemey; Marc A. Suchard; Guy Baele
Published in: Curr Protoc, 7, 2021, ISSN 1934-3396
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/cpz1.98

Symptom evolution following the emergence of maize streak virus

Author(s): Adérito L Monjane, Simon Dellicour, Penelope Hartnady, Kehinde A Oyeniran, Betty E Owor, Marion Bezuidenhout, Daphné Linderme, Rizwan A Syed, Lara Donaldson, Shane Murray, Edward P Rybicki, Anders Kvarnheden, Elham Yazdkhasti, Pierre Lefeuvre, Rémy Froissart, Philippe Roumagnac, Dionne N Shepherd, Gordon W Harkins, Marc A Suchard, Philippe Lemey, Arvind Varsani, Darren P Martin
Published in: eLife, 9, 2020, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.51984

Tracking virus outbreaks in the twenty-first century

Author(s): Nathan D. Grubaugh, Jason T. Ladner, Philippe Lemey, Oliver G. Pybus, Andrew Rambaut, Edward C. Holmes, Kristian G. Andersen
Published in: Nature Microbiology, 4/1, 2019, Page(s) 10-19, ISSN 2058-5276
Publisher: Nature Publishing Group
DOI: 10.1038/s41564-018-0296-2

nosoi: A stochastic agent‐based transmission chain simulation framework in r

Author(s): Sebastian Lequime, Paul Bastide, Simon Dellicour, Philippe Lemey, Guy Baele
Published in: Methods in Ecology and Evolution, 11/8, 2020, Page(s) 1002-1007, ISSN 2041-210X
Publisher: John Wiley and Sons Inc.
DOI: 10.1111/2041-210x.13422

Phylogeographic and phylodynamic approaches to epidemiological hypothesis testing

Author(s): Dellicour, Simon; Lequime, Sebastian; Vrancken, Bram; Gill, Mandev S.; Bastide, Paul; Gangavarapu, Karthik; Matteson, Nate; Tan, Yi; Plessis, Louis du; Fisher, Alexander A.; Nelson, Martha I.; Gilbert, Marius; Suchard, Marc A.; Grubaugh, Nathan D.; Andersen, Kristian G.; Pybus, Oliver G.; Lemey, Philippe
Published in: Nature Communications, 18, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/788059

Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases

Author(s): Kristof Theys; Philippe Lemey; Anne-Mieke Vandamme; Guy Baele
Published in: Frontiers in Public Health, Vol 7 (2019), 17, 2019, ISSN 2296-2565
Publisher: Frontiers Media S.A.
DOI: 10.3389/fpubh.2019.00208

Recent advances in computational phylodynamics

Author(s): Guy Baele, Simon Dellicour, Marc A Suchard, Philippe Lemey, Bram Vrancken
Published in: Current Opinion in Virology, 31, 2018, Page(s) 24-32, ISSN 1879-6257
Publisher: Elsevier BV
DOI: 10.1016/j.coviro.2018.08.009

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

Author(s): Maciej F. Boni, Philippe Lemey, Xiaowei Jiang, Tommy Tsan-Yuk Lam, Blair W. Perry, Todd A. Castoe, Andrew Rambaut, David L. Robertson
Published in: Nature Microbiology, 2020, ISSN 2058-5276
Publisher: Nature Publishing Group
DOI: 10.1038/s41564-020-0771-4

Increasing importance of European lineages in seeding the hepatitis C virus subtype 1a epidemic in Spain

Author(s): Ana Belén Pérez; Bram Vrancken; Natalia Chueca; Antonio Aguilera; Gabriel Reina; Miguel Garcia del Toro; Francisco Vera; Miguel Angel Von Wichman; Juan Arenas; Francisco Téllez; Juan A. Pineda; Mohamed Omar; Enrique Bernal; Antonio Rivero-Juárez; Elisa Fernández-Fuertes; Alberto de la Iglesia; Juan Manuel Pascasio; Philippe Lemey; Federico García; Lize Cuypers
Published in: Eurosurveillance, 2, 2019, ISSN 1560-7917
Publisher: ECDC
DOI: 10.2807/1560-7917.es.2019.24.9.1800227

Temporal signal and the phylodynamic threshold of SARS-CoV-2

Author(s): Sebastián Duchêne; Leo Featherstone; Melina Haritopoulou-Sinanidou; Andrew Rambaut; Philippe Lemey; Guy Baele
Published in: Virus Evolution, 10, 2020, ISSN 2057-1577
Publisher: Oxford University Press
DOI: 10.1093/ve/veaa061

A near full-length HIV-1 genome from 1966 recovered from formalin-fixed paraffin-embedded tissue

Author(s): Sophie Gryseels, Thomas D. Watts, Jean-Marie Kabongo Mpolesha, Brendan B. Larsen, Philippe Lemey, Jean-Jacques Muyembe-Tamfum, Dirk E. Teuwen, Michael Worobey
Published in: Proceedings of the National Academy of Sciences, 117/22, 2020, Page(s) 12222-12229, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1913682117

Earlier initiation of antiretroviral treatment coincides with an initial control of the HIV-1 sub-subtype F1 outbreak among men-having-sex-with-men in Flanders, Belgium

Author(s): Lore Vinken; Katrien Fransen; Lize Cuypers; Ivailo Alexiev; Claudia Balotta; Laurent Debaisieux; Carole Seguin-Devaux; Sergio García Ribas; Perpétua Gomes; Perpétua Gomes; Francesca Incardona; Rolf Kaiser; Jean Ruelle; Murat Sayan; Murat Sayan; Simona Paraschiv; Roger Paredes; Martine Peeters; Anders Sönnerborg; Ellen Vancutsem; Anne-Mieke Vandamme; Anne-Mieke Vandamme; Sigi Van den Wijngaert;
Published in: ISSN: 1664-302X, 10, 2019, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2019.00613

Genomic Epidemiology of 2015–2016 Zika Virus Outbreak in Cape Verde

Author(s): Oumar Faye, Maria de Lourdes Monteiro, Bram Vrancken, Matthieu Prot, Sebastian Lequime, Maryam Diarra, Oumar Ndiaye, Tomas Valdez, Sandra Tavarez, Jessica Ramos, Silvânia da Veiga Leal, Cecilio Pires, Antonio Moreira, Maria Filomena Tavares, Linete Fernandes, Jorge Noel Barreto, Maria do Céu Teixeira, Maria da Luz de Lima Mendonça, Carolina Cardoso da Silva Leite Gomes, Mariano Salazar Castello
Published in: Emerging Infectious Diseases, 26/6, 2020, Page(s) 1084-1090, ISSN 1080-6040
Publisher: US National Center for Infectious Diseases
DOI: 10.3201/eid2606.190928

Genomic and epidemiological monitoring of yellow fever virus transmission potential

Author(s): N. R. Faria, M. U. G. Kraemer, S. C. Hill, J. Goes de Jesus, R. S. Aguiar, F. C. M. Iani, J. Xavier, J. Quick, L. du Plessis, S. Dellicour, J. Thézé, R. D. O. Carvalho, G. Baele, C.-H. Wu, P. P. Silveira, M. B. Arruda, M. A. Pereira, G. C. Pereira, J. Lourenço, U. Obolski, L. Abade, T. I. Vasylyeva, M. Giovanetti, D. Yi, D. J. Weiss, G. R. W. Wint, F. M. Shearer, S. Funk, B. Nikolay, V. Fonseca
Published in: Science, 361/6405, 2018, Page(s) 894-899, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aat7115

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10

Author(s): Marc A Suchard, Philippe Lemey, Guy Baele, Daniel L Ayres, Alexei J Drummond, Andrew Rambaut
Published in: Virus Evolution, 4/1, 2018, ISSN 2057-1577
Publisher: Oxford University Press
DOI: 10.1093/ve/vey016

Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak

Author(s): Simon Dellicour, Guy Baele, Gytis Dudas, Nuno R. Faria, Oliver G. Pybus, Marc A. Suchard, Andrew Rambaut, Philippe Lemey
Published in: Nature Communications, 9/1, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-03763-2

Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak

Author(s): L. E. Kafetzopoulou, S. T. Pullan, P. Lemey, M. A. Suchard, D. U. Ehichioya, M. Pahlmann, A. Thielebein, J. Hinzmann, L. Oestereich, D. M. Wozniak, K. Efthymiadis, D. Schachten, F. Koenig, J. Matjeschk, S. Lorenzen, S. Lumley, Y. Ighodalo, D. I. Adomeh, T. Olokor, E. Omomoh, R. Omiunu, J. Agbukor, B. Ebo, J. Aiyepada, P. Ebhodaghe, B. Osiemi, S. Ehikhametalor, P. Akhilomen, M. Airende, R. Esumeh,
Published in: Science, 363/6422, 2019, Page(s) 74-77, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aau9343

Transmission dynamics of re-emerging rabies in domestic dogs of rural China

Author(s): Huaiyu Tian, Yun Feng, Bram Vrancken, Bernard Cazelles, Hua Tan, Mandev S. Gill, Qiqi Yang, Yidan Li, Weihong Yang, Yuzhen Zhang, Yunzhi Zhang, Philippe Lemey, Oliver G. Pybus, Nils Chr. Stenseth, Hailin Zhang, Simon Dellicour
Published in: PLOS Pathogens, 14/12, 2018, Page(s) e1007392, ISSN 1553-7374
Publisher: PLoS
DOI: 10.1371/journal.ppat.1007392

On the importance of negative controls in viral landscape phylogeography

Author(s): Simon Dellicour, Bram Vrancken, Nídia S Trovão, Denis Fargette, Philippe Lemey
Published in: Virus Evolution, 4/2, 2018, ISSN 2057-1577
Publisher: Oxford University Press
DOI: 10.1093/ve/vey023

Discovery and genome characterization of three new Jeilongviruses, a lineage of paramyxoviruses characterized by their unique membrane proteins

Author(s): Bert Vanmechelen, Magda Bletsa, Lies Laenen, Ana Rita Lopes, Valentijn Vergote, Leen Beller, Ward Deboutte, Miša Korva, Tatjana Avšič Županc, Joëlle Goüy de Bellocq, Sophie Gryseels, Herwig Leirs, Philippe Lemey, Bram Vrancken, Piet Maes
Published in: BMC Genomics, 19/1, 2018, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-018-4995-0

Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling

Author(s): Bram Vrancken, Marc A Suchard, Philippe Lemey
Published in: Virus Evolution, 3/2, 2017, ISSN 2057-1577
Publisher: Oxford University Press
DOI: 10.1093/ve/vex028

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

Author(s): Andrew Rambaut, Alexei J Drummond, Dong Xie, Guy Baele, Marc A Suchard
Published in: Systematic Biology, 67/5, 2018, Page(s) 901-904, ISSN 1063-5157
Publisher: Taylor & Francis
DOI: 10.1093/sysbio/syy032

Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates

Author(s): Jade Vincent Membrebe, Marc A Suchard, Andrew Rambaut, Guy Baele, Philippe Lemey
Published in: Molecular Biology and Evolution, 36/8, 2019, Page(s) 1793-1803, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msz094

BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics

Author(s): Daniel L Ayres, Michael P Cummings, Guy Baele, Aaron E Darling, Paul O Lewis, David L Swofford, John P Huelsenbeck, Philippe Lemey, Andrew Rambaut, Marc A Suchard
Published in: Systematic Biology, 68/6, 2019, Page(s) 1052-1061, ISSN 1063-5157
Publisher: Taylor & Francis
DOI: 10.1093/sysbio/syz020

HIV Rebound Is Predominantly Fueled by Genetically Identical Viral Expansions from Diverse Reservoirs

Author(s): Marie-Angélique De Scheerder, Bram Vrancken, Simon Dellicour, Timothy Schlub, Eunok Lee, Wei Shao, Sofie Rutsaert, Chris Verhofstede, Tessa Kerre, Thomas Malfait, Dimitri Hemelsoet, Marc Coppens, Annemieke Dhondt, Danny De Looze, Frank Vermassen, Philippe Lemey, Sarah Palmer, Linos Vandekerckhove
Published in: Cell Host & Microbe, 26/3, 2019, Page(s) 347-358.e7, ISSN 1931-3128
Publisher: Cell Press
DOI: 10.1016/j.chom.2019.08.003

Divergence dating using mixed effects clock modelling: An application to HIV-1

Author(s): Magda Bletsa, Marc A Suchard, Xiang Ji, Sophie Gryseels, Bram Vrancken, Guy Baele, Michael Worobey, Philippe Lemey
Published in: Virus Evolution, 5/2, 2019, ISSN 2057-1577
Publisher: Oxford University Presss
DOI: 10.1093/ve/vez036

Online Bayesian phylodynamic inference in BEAST with application to epidemic reconstruction

Author(s): Mandev S Gill, Philippe Lemey, Marc A Suchard, Andrew Rambaut, Guy Baele
Published in: Molecular Biology and Evolution, 2020, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msaa047

In Search of Covariates of HIV-1 Subtype B Spread in the United States—A Cautionary Tale of Large-Scale Bayesian Phylogeography

Author(s): Samuel L. Hong, Simon Dellicour, Bram Vrancken, Marc A. Suchard, Michael T. Pyne, David R. Hillyard, Philippe Lemey, Guy Baele
Published in: Viruses, 12/2, 2020, Page(s) 182, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v12020182

Assessing the role of live poultry trade in community-structured transmission of avian influenza in China

Author(s): Qiqi Yang, Xiang Zhao, Philippe Lemey, Marc A. Suchard, Yuhai Bi, Weifeng Shi, Di Liu, Wenbao Qi, Guogang Zhang, Nils Chr. Stenseth, Oliver G. Pybus, Huaiyu Tian
Published in: Proceedings of the National Academy of Sciences, 2020, Page(s) 201906954, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1906954117

Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa

Author(s): Nuno R. Faria, Nicole Vidal, José Lourenco, Jayna Raghwani, Kim C. E. Sigaloff, Andy J. Tatem, David A. M. van de Vijver, Andrea-Clemencia Pineda-Peña, Rebecca Rose, Carole L. Wallis, Steve Ahuka-Mundeke, Jean-Jacques Muyembe-Tamfum, Jérémie Muwonga, Marc A. Suchard, Tobias F. Rinke de Wit, Raph L. Hamers, Nicaise Ndembi, Guy Baele, Martine Peeters, Oliver G. Pybus, Philippe Lemey, Simon Delli
Published in: PLOS Pathogens, 15/12, 2019, Page(s) e1007976, ISSN 1553-7374
Publisher: PLoS
DOI: 10.1371/journal.ppat.1007976

Disentangling the role of Africa in the global spread of H5 highly pathogenic avian influenza

Author(s): Alice Fusaro, Bianca Zecchin, Bram Vrancken, Celia Abolnik, Rose Ademun, Abdou Alassane, Abdelsatar Arafa, Joseph Adongo Awuni, Emmanuel Couacy-Hymann, M.’ Bétiégué Coulibaly, Nicolas Gaidet, Emilie Go-Maro, Tony Joannis, Simon Dickmu Jumbo, Germaine Minoungou, Clement Meseko, Maman Moutari Souley, Deo Birungi Ndumu, Ismaila Shittu, Augustin Twabela, Abel Wade, Lidewij Wiersma, Yao P. Akpeli,
Published in: Nature Communications, 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-13287-y

Phylogeography of Lassa Virus in Nigeria

Author(s): Deborah U. Ehichioya, Simon Dellicour, Meike Pahlmann, Toni Rieger, Lisa Oestereich, Beate Becker-Ziaja, Daniel Cadar, Yemisi Ighodalo, Thomas Olokor, Emmanuel Omomoh, Jennifer Oyakhilome, Racheal Omiunu, Jacqueline Agbukor, Benevolence Ebo, John Aiyepada, Paulson Ebhodaghe, Blessing Osiemi, Solomon Ehikhametalor, Patience Akhilomen, Michael Airende, Rita Esumeh, Ekene Muoebonam, Rosemary Giwa, An
Published in: Journal of Virology, 93/21, 2019, ISSN 0022-538X
Publisher: American Society for Microbiology
DOI: 10.1128/JVI.00929-19

Hamiltonian Monte Carlo sampling to estimate past population dynamics using the skygrid coalescent model in a Bayesian phylogenetics framework.

Author(s): Baele, Guy; Gill, Mandev S.; Lemey, Philippe; Suchard, Marc A.
Published in: Wellcome Open Research, 4, 2020, ISSN 2398-502X
Publisher: F1000 Research
DOI: 10.12688/wellcomeopenres.15770.1

Bayesian Evaluation of Temporal Signal in Measurably Evolving Populations

Author(s): Sebastian Duchene, Philippe Lemey, Tanja Stadler, Simon Y W Ho, David A Duchene, Vijaykrishna Dhanasekaran, Guy Baele
Published in: Molecular Biology and Evolution, 06 July 2020, 2020, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msaa163

Measles virus and rinderpest virus divergence dated to the sixth century BCE

Author(s): Ariane Düx, Sebastian Lequime, Livia Victoria Patrono, Bram Vrancken, Sengül Boral, Jan F. Gogarten, Antonia Hilbig, David Horst, Kevin Merkel, Baptiste Prepoint, Sabine Santibanez, Jasmin Schlotterbeck, Marc A. Suchard, Markus Ulrich, Navena Widulin, Annette Mankertz, Fabian H. Leendertz, Kyle Harper, Thomas Schnalke, Philippe Lemey, Sébastien Calvignac-Spencer
Published in: Science, 368/6497, 2020, Page(s) 1367-1370, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aba9411

Comparing patterns and scales of plant virus phylogeography: Rice yellow mottle virus in Madagascar and in continental Africa

Author(s): Mbolarinosy Rakotomalala, Bram Vrancken, Agnès Pinel-Galzi, Perle Ramavovololona, Eugénie Hébrard, Jean Stéphan Randrianangaly, Simon Dellicour, Philippe Lemey, Denis Fargette
Published in: Virus Evolution, 5/2, 2019, ISSN 2057-1577
Publisher: Oxford Academic
DOI: 10.1093/ve/vez023

Phylogenomic Characterization of Lopma Virus and Praja Virus, Two Novel Rodent-Borne Arteriviruses.

Author(s): Bert Vanmechelen; Zafeiro Zisi; Sophie Gryseels; Joëlle Goüy de Bellocq; Bram Vrancken; Philippe Lemey; Piet Maes; Magda Bletsa
Published in: Volume 13, 1, 2021, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v13091842

Massive Parallelization Boosts Big Bayesian Multidimensional Scaling

Author(s): Andrew J. Holbrook, Philippe Lemey, Guy Baele, Simon Dellicour, Dirk Brockmann, Andrew Rambaut, Marc A. Suchard
Published in: Journal of Computational and Graphical Statistics, 08 Jun 2020, 2020, Page(s) 1-14, ISSN 1061-8600
Publisher: American Statistical Association
DOI: 10.1080/10618600.2020.1754226