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

Publications

SPREAD 4: online visualisation of pathogen phylogeographic reconstructions

Author(s): Kanika D Nahata, Filip Bielejec, Juan Monetta, Simon Dellicour, Andrew Rambaut, Marc A Suchard, Guy Baele, Philippe Lemey
Published in: Virus Evolution, 2022, ISSN 2057-1577
Publisher: Oxford Academic
DOI: 10.1093/ve/veac088

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, Issue 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, Issue 18, 2021, ISSN 1932-6157
Publisher: Institute of Mathematical Statistics
DOI: 10.1214/20-aoas1394

Global spatial dynamics and vaccine-induced fitness changes of Bordetella pertussis.

Author(s): Noémie Lefrancq; Valérie Bouchez; Nadia Fernandes; Alex-Mikael Barkoff; Thijs Bosch; Tine Dalby; Thomas Åkerlund; Jessica Darenberg; Katerina Fabianova; Didrik F. Vestrheim; Norman K. Fry; Juan José González-López; Karolina Gullsby; Adele Habington; Qiushui He; David Litt; Helena Martini; Denis Piérard; Paola Stefanelli; Marc Stegger; Jana Zavadilova; Nathalie Armatys; Annie Landier; Sophie
Published in: Science Translational Medicine, Issue 14, 2022, ISSN 1946-6234
Publisher: American Association for the Advancement of Science
DOI: 10.17863/cam.82478

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, Issue 7, 2021, ISSN 1934-3396
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/cpz1.98

Predicting the evolution of Lassa Virus endemic area and population at risk over the next decades

Author(s): Raphaëlle Klitting; Liana E. Kafetzopoulou; Liana E. Kafetzopoulou; W. Thiery; G. Dudas; Sophie Gryseels; A. Kotamarthi; Bram Vrancken; Karthik Gangavarapu; Mambu Momoh; J. Demby Sandy; Augustine Goba; F. Alhasan; Don Grant; Robert F. Garry; Allison R. Smither; Mark Zeller; Matthias Pauthner; Michelle McGraw; Laura D. Hughes; Sophie Duraffour; Stephan Günther; Marc A. Suchard; Marc A. Suchard; P
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/2021.09.22.461380

Untangling introductions and persistence in COVID-19 resurgence in Europe

Author(s): Philippe Lemey, Nick Ruktanonchai, Samuel L. Hong, Vittoria Colizza, Chiara Poletto, Frederik Van den Broeck, Mandev S. Gill, Xiang Ji, Anthony Levasseur, Bas B. Oude Munnink, Marion Koopmans, Adam Sadilek, Shengjie Lai, Andrew J. Tatem, Guy Baele, Marc A. Suchard, Simon Dellicour
Published in: Nature, Issue 595, 2021, Page(s) 713–717, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-021-03754-2

Scalable Bayesian Divergence Time Estimation With Ratio Transformations

Author(s): X., Fisher A.A., Su S., Thorne J.L., Potter B., Lemey P., Baele G., Suchard M.A
Published in: Systematic Biology, 2023, ISSN 1063-5157
Publisher: Taylor & Francis
DOI: 10.1093/sysbio/syad039

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, Issue 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, Issue 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, Issue 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, Issue 18, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/788059

SANTA-SIM: simulating viral sequence evolution dynamics under selection and recombination.

Author(s): Abbas Jariani; Christopher Warth; Koen Deforche; Pieter Libin; Pieter Libin; Alexei J. Drummond; Alexei J. Drummond; Andrew Rambaut; Frederick A. Matsen; Kristof Theys
Published in: Virus Evolution, Issue 19, 2019, ISSN 2057-1577
Publisher: Oxford Academic
DOI: 10.1093/ve/vez003

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), Issue 17, 2019, ISSN 2296-2565
Publisher: Frontiers Media S.A.
DOI: 10.3389/fpubh.2019.00208

Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1

Author(s): Tsui, Joseph L-H; McCrone, John T; Lambert, Ben; Bajaj, Sumali; Inward, Rhys PD; Bosetti, Paolo; Pena, Rosario Evans; Tegally, Houriiyah; Hill, Verity; Zarebski, Alexander E; Peacock, Thomas P; Liu, Luyang; Wu, Neo; Davis, Megan; Bogoch, Isaac I; Khan, Kamran; Kall, Meaghan; Aziz, Nurin Iwani Binti Abdul; Colquhoun, Rachel; O'Toole, Aine; Jackson, Ben; Dasgupta, Abhishek; Wilkinson, Eduan; de Oliv
Published in: Science, 2023, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.adg660

Efficient Bayesian inference of general Gaussian models on large phylogenetic trees

Author(s): Paul Bastide; Lam Si Tung Ho; Guy Baele; Philippe Lemey; Marc A. Suchard
Published in: Annals of Applied Statistics, Issue 15(2), 2021, ISSN 1932-6157
Publisher: Institute of Mathematical Statistics
DOI: 10.1214/20-aoas1419

Recent advances in computational phylodynamics

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

Reconstruction of SARS-CoV-2 outbreaks in a primary school using epidemiological and genomic data.

Author(s): Kremer C., Torneri A., Libin P.J.K., Meex C., Hayette M.P., Bontems S., Durkin K., Artesi M., Bours V., Lemey P., Darcis G., Hens N., Meuris C
Published in: Epidemics, 2023, ISSN 1755-4365
Publisher: Elsevier BV
DOI: 10.1016/j.epidem.2023.100701

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, Issue 2, 2019, ISSN 1560-7917
Publisher: ECDC
DOI: 10.2807/1560-7917.es.2019.24.9.1800227

Data Integration in Bayesian Phylogenetics

Author(s): Hassler, G.W., Magee, A.F., Zhang, Z., Baele, G., Lemey P., Ji, X., Fourment, M. and Suchard, M.A.
Published in: Annual Review of Statistics and Its Application, Issue 10(1), 2023, Page(s) 353-377, ISSN 2326-8298
Publisher: Annual Reviews
DOI: 10.1146/annurev-statistics-033021-112532

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, Issue 10, 2020, ISSN 2057-1577
Publisher: Oxford University Press
DOI: 10.1093/ve/veaa061

Inferring Phenotypic Trait Evolution on Large Trees With Many Incomplete Measurements

Author(s): Gabriel W. Hassler; Max R. Tolkoff; William L. Allen; Lam Si Tung Ho; Philippe Lemey; Marc A. Suchard
Published in: Journal of the American Statistical Association, Issue vol 117, iss 538, 2022, ISSN 0162-1459
Publisher: American Statistical Association
DOI: 10.1080/01621459.2020.1799812

The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape.

Author(s): Darren P, Martin; Steven, Weaver; Houryiah, Tegally; Emmanuel James, San; Stephen D, Shank; Eduan, Wilkinson; Alexander G, Lucaci; Jennifer, Giandhari; Sureshnee, Naidoo; Yeshnee, Pillay; Lavanya, Singh; Richard J, Lessells; Ravindra K, Gupta; Joel O, Wertheim; Anton, Nekturenko; Ben, Murrell; Gordon W, Harkins; Philippe, Lemey; Oscar A, MacLean; David L, Robertson; Tulio, de Oliveira; Sergei L, K
Published in: Cell, Issue Volume 184, Issue 20, 2021, Page(s) 5189-5200.e7, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1101/2021.02.23.21252268

Accelerating Bayesian inference of dependency between complex biological traits

Author(s): Zhang, Zhenyu; Nishimura, Akihiko; Trovão, Nídia S.; Cherry, Joshua L.; Holbrook, Andrew J.; Ji, Xiang; Lemey, Philippe; Suchard, Marc A.
Published in: Plos Computational Biology, Issue 3, 2023, ISSN 1553-734X
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1011419

Molecular detection and genomic characterization of diverse hepaciviruses in African rodents

Author(s): Magda Bletsa, Bram Vrancken, Sophie Gryseels, Ine Boonen, Antonios Fikatas, Yiqiao Li, Anne Laudisoit, Sebastian Lequime, Josef Bryja, Rhodes Makundi, Yonas Meheretu, Benjamin Dudu Akaibe, Sylvestre Gambalemoke Mbalitini, Frederik Van de Perre, Natalie Van Houtte, Jana Těšíková, Elke Wollants, Marc Van Ranst, Oliver G Pybus, Jan Felix Drexler, Erik Verheyen, H
Published in: Virus Evolution, Issue Volume 7, Issue 1, 2021, Page(s) veab036, ISSN 2057-1577
Publisher: Oxford Academic
DOI: 10.1093/ve/veab036

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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-13287-y

Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen.

Author(s): Oscar A. MacLean; Spyros Lytras; Steven Weaver; Joshua B Singer; Maciej F. Boni; Philippe Lemey; Sergei L Kosakovsky Pond; David Robertson
Published in: PLoS Biology, Issue Vol 19, Iss 3, 2021, Page(s) e3001115, ISSN 1544-9173
Publisher: Public Library of Science
DOI: 10.1371/journal.pbio.3001115

Principled, practical, flexible, fast: A new approach to phylogenetic factor analysis

Author(s): Gabriel W. Hassler; Brigida Gallone; Leandro Aristide; William L. Allen; Max R. Tolkoff; Andrew J. Holbrook; Guy Baele; Philippe Lemey; Marc A. Suchard
Published in: Methods in ecology and evolution, Issue 13, 2023, ISSN 2041-210X
Publisher: John Wiley and Sons Inc.
DOI: 10.1111/2041-210x.13920

Gradients do grow on trees: a linear-time ${\cal O}\hspace{-0.2em}\left( N \right)$-dimensional gradient for statistical phylogenetics

Author(s): Ji, Xiang; Zhang, Zhenyu; Holbrook, Andrew; Nishimura, Akihiko; Baele, Guy; Rambaut, Andrew; Lemey, Philippe; Suchard, Marc A.
Published in: Molecular Biology and Evolution, 2020, ISSN 1537-1719
Publisher: Oxford University Press
DOI: 10.1093/molbev/msaa130

Uncovering the endemic circulation of rabies in Cambodia

Author(s): Layan M., Dacheux L, Lemey P., Brunker K., Ma L., Troupin C., Dussart P., Chevalier V., Wood J.L.N., Ly S., Duong V., Bourhy H., Dellicour S
Published in: Molecular Ecology, 2022, ISSN 1365-294X
Publisher: John Wiley & Sons Ltd
DOI: 10.1111/mec.17087

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, Issue 93/21, 2019, ISSN 0022-538X
Publisher: American Society for Microbiology
DOI: 10.1128/JVI.00929-19

Analyses of Early ZIKV Genomes Are Consistent with Viral Spread from Northeast Brazil to the Americas

Author(s): de Moraes L., Portilho M.M., Vrancken B., Van den Broeck F., Santos L.A., Cucco M., Tauro L.B., Kikuti M., Silva M.M.O., Campos G.S., Reis M.G., Barral A., Barral-Netto M., Boaventura V.S., Vandamme A.M., Theys K., Lemey P., Ribeiro G.S. and Khouri R
Published in: Viruses, 2023, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v15061236

Scalable Bayesian phylogenetics

Author(s): Alexander A. Fisher; Gabriel W. Hassler; Xiang Ji; Guy Baele; Marc A. Suchard; Philippe Lemey
Published in: PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B, Issue Volume 377Issue 1861, 2022, ISSN 0962-8436
Publisher: Royal Society of London
DOI: 10.1098/rstb.2021.0242

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, Issue 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, Issue 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, Issue 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, Issue 5/2, 2019, ISSN 2057-1577
Publisher: Oxford Academic
DOI: 10.1093/ve/vez023

Relaxed random walks at scale

Author(s): Fisher, Alexander A.; Ji, Xiang; Lemey, Philippe; Suchard, Marc A.
Published in: Systematic Biology, 2021, ISSN 1063-5157
Publisher: Taylor & Francis
DOI: 10.1093/sysbio/syaa056

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, Issue 1, 2021, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v13091842

In Vivo Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression.

Author(s): Silvie Van den Hoecke; Marlies Ballegeer; Bram Vrancken; Lei Deng; Emma R. Job; Kenny Roose; Bert Schepens; Lien Van Hoecke; Philippe Lemey; Xavier Saelens
Published in: MBIO, Issue 15, 2021, ISSN 2150-7511
Publisher: American Society for Microbiology
DOI: 10.1128/mbio.00745-21

Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study

Author(s): George M Nduva; Frederick Otieno; Joshua Kimani; Elizabeth Wahome; Lyle R McKinnon; Francois Cholette; Maxwell Majiwa; Moses Masika; Gaudensia Mutua; Omu Anzala; Susan M Graham; Larry Gelmon; Matt A Price; Adrian D Smith; Robert C Bailey; Guy Baele; Philippe Lemey; Amin S Hassan; Eduard J Sanders; Joakim Esbjörnsson
Published in: Virus Evolution, Issue Volume 8, Issue 1, 2022, Page(s) veac016, ISSN 2057-1577
Publisher: Oxford University Press
DOI: 10.1093/ve/veac016

Detection of Marburg Virus Disease in Guinea

Author(s): Fara R. Koundouno; Liana E. Kafetzopoulou; Martin Faye; Annick Renevey; Barrè Soropogui; Kékoura Ifono; Emily V. Nelson; Aly A. Kamano; Charles Tolno; Giuditta Annibaldis; Saa L. Millimono; Jacob Camara; Karifa Kourouma; Ahmadou Doré; Tamba E. Millimouno; Fernand M.B. Tolno; Julia Hinzmann; Hugo Soubrier; Mette Hinrichs; Anke Thielebein; Glaucia Herzer; Meike Pahlmann; Georges A. Ki-Zerbo; Pier
Published in: The New England Journal of Medicine, 2022, ISSN 0028-4793
Publisher: Massachusetts Medical Society
DOI: 10.1056/nejmc2120183

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, Issue 08 Jun 2020, 2020, Page(s) 1-14, ISSN 1061-8600
Publisher: American Statistical Association
DOI: 10.1080/10618600.2020.1754226

Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2

Author(s): Philippe Lemey, Samuel L. Hong, Verity Hill, Guy Baele, Chiara Poletto, Vittoria Colizza, Áine O’Toole, John T. McCrone, Kristian G. Andersen, Michael Worobey, Martha I. Nelson, Andrew Rambaut & Marc A. Suchard
Published in: Nature Communications, Issue 11, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-18877-9

The evolutionary history of hepaciviruses

Author(s): YQ Li, M Ghafari, AJ Holbrook, I Boonen, N Amor, S Catalano, JP Webster, YY Li, HT Li, V Vergote, P Maes, YL Chong, A Laudisoit, P Baelo, S Ngoy, SG Mbalitini, GC Gembu, P Musaba Akawa, J Goüy de Bellocq, H Leirs, E Verheyen, OG Pybus, A Katzourakis, AN Alagaili, S Gryseels, YC Li, MA Suchard, M Bletsa, P Lemey
Published in: bioRxiv, 2023
Publisher: Cold Spring Harbour Laboratory
DOI: 10.1101/2023.06.30.547218

The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2

Author(s): Lytras, Spyros ; Ghafari, Mahan ; Magee, Andrew F ; Parker, Edyth ; Havens, Jennifer L ; Katzourakis, Aris ; Vasylyeva, Tetyana I ; Suchard, Marc A ; Hughes, Alice C ; Hughes, Joseph ; Robertson, David L ; Dellicour, Simon ; Worobey, Michael ; Wertheim, Joel O ; Lemey, Philippe
Published in: bioArxiv, 2023
Publisher: Cold Spring Harbour Laboratory
DOI: 10.1101/2023.07.12.548617

The International Virus Bioinformatics Meeting 2022

Author(s): Franziska Hufsky; Denis Beslic; Dimitri Boeckaerts; Sebastian Duchene; Enrique González-Tortuero; Andreas J. Gruber; Jiarong Guo; Daan Jansen; John Juma; Kunaphas Kongkitimanon; Antoni Luque; Muriel Ritsch; Gabriel Lencioni Lovate; Luca Nishimura; Célia Pas; Esteban Domingo; Emma Hodcroft; Philippe Lemey; Matthew B. Sullivan; Friedemann Weber; Fernando González-Candelas; Sarah Krautwurst; Alba
Published in: VIRUSES, Issue 14(5), 2022, ISSN 1999-4915
Publisher: MDPI
DOI: 10.48350/170316

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