Rates of viral evolution are linked to host geography in bat rabies. by Daniel G Streicker, Philippe Lemey, Andres Velasco-Villa, Charles E Rupprecht

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How fast are viruses spreading in the wild? by Simon Dellicour, Paul Bastide, Pauline Rocu, Denis Fargette, Olivier J Hardy, Marc A Suchard, Stéphane Guindon, Philippe Lemey

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International importance and spread of SARS-CoV-2 variants Alpha, Delta, and Omicron BA.1 into Spain by Pilar Gallego-García, Samuel L. Hong, Nena Bollen, Simon Dellicour, Guy Baele, Marc A. Suchard, Philippe Lemey, David Posada

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Emergence of primary NNRTI resistance mutations without antiretroviral selective pressure in a HAART-treated child. by Elizabeth S Machado, Adriana O Afonso, Dwight V Nissley, Philippe Lemey, Silvia M Cunha, Ricardo H Oliveira, Marcelo A Soares

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Limited evolution of the yellow fever virus 17d in a mouse infection model by Dieudonné Buh Kum, Niraj Mishra, Bram Vrancken, Hendrik Jan Thibaut, Annelies Wilder-Smith, Philippe Lemey, Johan Neyts, Kai Dallmeier

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Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen. by Oscar A MacLean, Spyros Lytras, Steven Weaver, Joshua B Singer, Maciej F Boni, Philippe Lemey, Sergei L Kosakovsky Pond, David L Robertson

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Evaluation of metatranscriptomic sequencing protocols to obtain full-length RNA virus genomes from mammalian tissues by Yiqiao Li, Mariana Polychronopoulou, Ine Boonen, Antonios Fikatas, Sophie Gryseels, Anne Laudisoit, Joelle Gouy de Bellocq, Bram Vrancken, Gkikas Magiorkinis, Philippe Lemey, Magda Bletsa

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Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2. by Philippe Lemey, Andrew Rambaut, Trevor Bedford, Nuno Faria, Filip Bielejec, Guy Baele, Colin A Russell, Derek J Smith, Oliver G Pybus, Dirk Brockmann, Marc A Suchard

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Revealing the Micro-scale Signature of Endemic Zoonotic Disease Transmission in an African Urban Setting. by Hervé Bourhy, Emmanuel Nakouné, Matthew Hall, Pierre Nouvellet, Anthony Lepelletier, Chiraz Talbi, Laurence Watier, Edward C Holmes, Simon Cauchemez, Philippe Lemey, Christl A Donnelly, Andrew Rambaut

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Spatial dynamics of human-origin H1 influenza A virus in North American swine. by Martha I Nelson, Philippe Lemey, Yi Tan, Amy Vincent, Tommy Tsan-Yuk Lam, Susan Detmer, Cécile Viboud, Marc A Suchard, Andrew Rambaut, Edward C Holmes, Marie Gramer

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Genetic variability among complete human respiratory syncytial virus subgroup A genomes: bridging molecular evolutionary dynamics and epidemiology. by Lydia Tan, Philippe Lemey, Lieselot Houspie, Marco C Viveen, Nicolaas J G Jansen, Anton M van Loon, Emmanuel Wiertz, Grada M van Bleek, Darren P Martin, Frank E Coenjaerts

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Phylodynamics and human-mediated dispersal of a zoonotic virus. by Chiraz Talbi, Philippe Lemey, Marc A Suchard, Elbia Abdelatif, Mehdi Elharrak, Jalal Nourlil, Abdellah Faouzi, Juan E Echevarría, Sonia Vazquez Morón, Andrew Rambaut, Nicholas Campiz, Andrew J Tatem, Edward C Holmes, Hervé Bourhy

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An ancient influenza genome from Switzerland allows deeper insights into host adaptation during the 1918 flu pandemic in Europe by Christian Urban, Bram Vrancken, Livia V. Patrono, Ariane Düx, Mathilde Le Vu, Katarina L. Matthes, Nina Maria Burkhard-Koren, Navena Widulin, Thomas Schnalke, Sabina Carraro, Frank Rühli, Philippe Lemey, Kaspar Staub, Sébastien Calvignac-Spencer, Verena J. Schuenemann

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Grains, trade and war in the multimodal transmission of Rice yellow mottle virus: An historical and phylogeographical retrospective. by Innocent Ndikumana, Geoffrey Onaga, Agnès Pinel-Galzi, Pauline Rocu, Judith Hubert, Hassan Karakacha Wéré, Antony Adego, Mariam Nyongesa Wéré, Nils Poulicard, Maxime Hebrard, Simon Dellicour, Philippe Lemey, Erik Gilbert, Marie-José Dugué, François Chevenet, Paul Bastide, Stéphane Guindon, Denis Fargette, Eugénie Hébrard

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Evolutionary genomics of Leishmania braziliensis across the neotropical realm by Senne Heeren, Mandy Sanders, Jeffrey Jon Shaw, Sinval Pinto Brandão-Filho, Mariana Côrtes Boité, Lilian Motta Cantanhêde, Khaled Chourabi, Ilse Maes, Alejandro Llanos-Cuentas, Jorge Arevalo, Jorge D. Marco, Philippe Lemey, James A. Cotton, Jean-Claude Dujardin, Elisa Cupolillo, Frederik Van den Broeck

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Grains, trade and war in the multimodal transmission of Rice yellow mottle virus: An historical and phylogeographical retrospective by Innocent Ndikumana, Geoffrey Onaga, Agnès Pinel-Galzi, Pauline Rocu, Judith Hubert, Hassan Karakacha Wéré, Antony Adego, Mariam Nyongesa Wéré, Nils Poulicard, Maxime Hebrard, Simon Dellicour, Philippe Lemey, Erik Gilbert, Marie-José Dugué, François Chevenet, Paul Bastide, Stéphane Guindon, Denis Fargette, Eugénie Hébrard

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Forecasting framework for dominant SARS-CoV-2 strains before clade replacement using phylogeny-informed genetic distances by Kyuyoung Lee, Atanas V. Demirev, Sangyi Lee, Seunghye Cho, Hyunbeen Kim, Junhyung Cho, Jeong-Sun Yang, Kyung-Chang Kim, Joo-Yeon Lee, Woojin Shin, Soyoung Lee, Sejik Park, Philippe Lemey, Man-Seong Park, Man-Seong Park, Man-Seong Park, Jin Il Kim, Jin Il Kim, Jin Il Kim

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Molecular and genomic investigation of an urban outbreak of dengue virus serotype 2 in Angola, 2017-2019. by Zoraima Neto, Pedro A Martinez, Sarah C Hill, Domingos Jandondo, Julien Thézé, Marinela Mirandela, Renato Santana Aguiar, Joilson Xavier, Cruz Dos Santos Sebastião, Ana Luísa Micolo Cândido, Filipa Vaz, Gisel Reyes Castro, Joana Paula Paixão, Nicholas J Loman, Philippe Lemey, Oliver G Pybus, Jocelyne Vasconcelos, Nuno Rodrigues Faria, Joana de Morais

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Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: an individual-patient- and sequence-level meta-analysis. by Soo-Yon Rhee, Jose Luis Blanco, Michael R Jordan, Jonathan Taylor, Philippe Lemey, Vici Varghese, Raph L Hamers, Silvia Bertagnolio, Tobias F Rinke de Wit, Avelin F Aghokeng, Jan Albert, Radko Avi, Santiago Avila-Rios, Pascal O Bessong, James I Brooks, Charles A B Boucher, Zabrina L Brumme, Michael P Busch, Hermann Bussmann, Marie-Laure Chaix, Bum Sik Chin, Toni T D'Aquin, Cillian F De Gascun, Anne Derache, Diane Descamps, Alaka K Deshpande, Cyrille F Djoko, Susan H Eshleman, Herve Fleury, Pierre Frange, Seiichiro Fujisaki, P Richard Harrigan, Junko Hattori, Africa Holguin, Gillian M Hunt, Hiroshi Ichimura, Pontiano Kaleebu, David Katzenstein, Sasisopin Kiertiburanakul, Jerome H Kim, Sung Soon Kim, Yanpeng Li, Irja Lutsar, Lynn Morris, Nicaise Ndembi, Kee Peng Ng, Ramesh S Paranjape, Martine Peeters, Mario Poljak, Matt A Price, Manon L Ragonnet-Cronin, Gustavo Reyes-Terán, Morgane Rolland, Sunee Sirivichayakul, Davey M Smith, Marcelo A Soares, Vincent V Soriano, Deogratius Ssemwanga, Maja Stanojevic, Mariane A Stefani, Wataru Sugiura, Somnuek Sungkanuparph, Amilcar Tanuri, Kok Keng Tee, Hong-Ha M Truong, David A M C van de Vijver, Nicole Vidal, Chunfu Yang, Rongge Yang, Gonzalo Yebra, John P A Ioannidis, Anne-Mieke Vandamme, Robert W Shafer

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