Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing by Bram Vrancken, Nídia Sequeira Trovão, Guy Baele, Eric van Wijngaerden, Anne-Mieke Vandamme, Kristel van Laethem, Philippe Lemey

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Phylogenomic Characterization of Lopma Virus and Praja Virus, Two Novel Rodent-Borne Arteriviruses by Bert Vanmechelen, Zafeiro Zisi, Sophie Gryseels, Joëlle Goüy de Bellocq, Bram Vrancken, Philippe Lemey, Piet Maes, Magda Bletsa

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In Search of Covariates of HIV-1 Subtype B Spread in the United States—A Cautionary Tale of Large-Scale Bayesian Phylogeography by Samuel L. Hong, Simon Dellicour, Bram Vrancken, Marc A. Suchard, Michael T. Pyne, David R. Hillyard, Philippe Lemey, Guy Baele

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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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Molecular Epidemiology of HIV-1 Subtype B Infection across Florida Reveals Few Large Superclusters with Metropolitan Origin by Shannan N. Rich, Mattia C. F. Prosperi, Simon Dellicour, Bram Vrancken, Robert L. Cook, Emma C. Spencer, Marco Salemi, Carla Mavian

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Dispersal history and bidirectional human-fish host switching of invasive, hypervirulent Streptococcus agalactiae sequence type 283. by Daniel Schar, Zhenyu Zhang, Joao Pires, Bram Vrancken, Marc A Suchard, Philippe Lemey, Margaret Ip, Marius Gilbert, Thomas Van Boeckel, Simon Dellicour

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Cross-border spread, lineage displacement and evolutionary rate estimation of rabies virus in Yunnan Province, China by Yuzhen Zhang, Bram Vrancken, Yun Feng, Simon Dellicour, Qiqi Yang, Weihong Yang, Yunzhi Zhang, Lu Dong, Oliver G. Pybus, Hailin Zhang, Huaiyu Tian

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<italic toggle="yes">In Vivo</italic> Therapy with M2e-Specific IgG Selects for an Influenza A Virus Mutant with Delayed Matrix Protein 2 Expression by Silvie Van den Hoecke, Marlies Ballegeer, Bram Vrancken, Lei Deng, Emma R. Job, Kenny Roose, Bert Schepens, Lien Van Hoecke, Philippe Lemey, Xavier Saelens

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Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City. by Simon Dellicour, Samuel L Hong, Bram Vrancken, Antoine Chaillon, Mandev S Gill, Matthew T Maurano, Sitharam Ramaswami, Paul Zappile, Christian Marier, Gordon W Harkins, Guy Baele, Ralf Duerr, Adriana Heguy

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New evidence for the east–west spread of the highly pathogenic avian influenza H5N1 virus between Central Asian and east Asian-Australasian flyways in China by Weiyue Meng, Qiqi Yang, Bram Vrancken, Zhuo Chen, Dongping Liu, Lixia Chen, Xiang Zhao, Sarah François, Tian Ma, Ruyi Gao, Wendong Ru, Yunfeng Li, Hongxuan He, Guogang Zhang, Huaiyu Tian, Jun Lu

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

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Evolutionary and genomic insights into the long-term colonization of Shigella flexneri in animals by Junrong Liang, Zhen Zhu, Ruiting Lan, Jing Meng, Bram Vrancken, Shan Lu, Dong Jin, Jing Yang, Jianping Wang, Tian Qin, Ji Pu, Li Zhang, Kui Dong, Mingchao Xu, Huaiyu Tian, Taijiao Jiang, Jianguo Xu

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Accounting for population structure reveals ambiguity in the Zaire Ebolavirus reservoir dynamics. by Bram Vrancken, Tony Wawina-Bokalanga, Bert Vanmechelen, Joan Martí-Carreras, Miles W Carroll, Justus Nsio, Jimmy Kapetshi, Sheila Makiala-Mandanda, Jean-Jacques Muyembe-Tamfum, Guy Baele, Kurt Vermeire, Valentijn Vergote, Steve Ahuka-Mundeke, Piet Maes

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A Comprehensive Molecular Epidemiological Analysis of SARS-CoV-2 Infection in Cyprus from April 2020 to January 2021: Evidence of a Highly Polyphyletic and Evolving Epidemic by Andreas C. Chrysostomou, Bram Vrancken, George Koumbaris, George Themistokleous, Antonia Aristokleous, Christina Masia, Christina Eleftheriou, Costakis Iοannou, Dora C. Stylianou, Marios Ioannides, Panagiotis Petrou, Vasilis Georgiou, Amalia Hatziyianni, Philippe Lemey, Anne-Mieke Vandamme, Philippos P. Patsalis, Leondios G. Kostrikis

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Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework by Simon Dellicour, Sebastian Lequime, Bram Vrancken, Mandev S. Gill, Paul Bastide, Karthik Gangavarapu, Nathaniel L. Matteson, Yi Tan, Louis du Plessis, Alexander A. Fisher, Martha I. Nelson, Marius Gilbert, Marc A. Suchard, Kristian G. Andersen, Nathan D. Grubaugh, Oliver G. Pybus, Philippe Lemey

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Unraveling the Dynamics of Omicron (BA.1, BA.2, and BA.5) Waves and Emergence of the Deltacron Variant: Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus (Oct 2021–Oct 2022... by Andreas C. Chrysostomou, Bram Vrancken, Christos Haralambous, Maria Alexandrou, Ioanna Gregoriou, Marios Ioannides, Costakis Ioannou, Olga Kalakouta, Christos Karagiannis, Markella Marcou, Christina Masia, Michail Mendris, Panagiotis Papastergiou, Philippos C. Patsalis, Despo Pieridou, Christos Shammas, Dora C. Stylianou, Barbara Zinieri, Philippe Lemey, The COMESSAR Network, Leondios G. Kostrikis

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Analyses of Early ZIKV Genomes Are Consistent with Viral Spread from Northeast Brazil to the Americas by Laise de Moraes, Moyra M. Portilho, Bram Vrancken, Frederik Van den Broeck, Luciane Amorim Santos, Marina Cucco, Laura B. Tauro, Mariana Kikuti, Monaise M. O. Silva, Gúbio S. Campos, Mitermayer G. Reis, Aldina Barral, Manoel Barral-Netto, Viviane Sampaio Boaventura, Anne-Mieke Vandamme, Kristof Theys, Philippe Lemey, Guilherme S. Ribeiro, Ricardo Khouri

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A paucigranulocytic asthma host environment promotes the emergence of virulent influenza viral variants by Katina D Hulme, Anjana C Karawita, Cassandra Pegg, Myrna JM Bunte, Helle Bielefeldt-Ohmann, Conor J Bloxham, Silvie Van den Hoecke, Yin Xiang Setoh, Bram Vrancken, Monique Spronken, Lauren E Steele, Nathalie AJ Verzele, Kyle R Upton, Alexander A Khromykh, Keng Yih Chew, Maria Sukkar, Simon Phipps, Kirsty R Short

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Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern by Andreas C. Chrysostomou, Bram Vrancken, Christos Haralambous, Maria Alexandrou, Antonia Aristokleous, Christina Christodoulou, Ioanna Gregoriou, Marios Ioannides, Olga Kalakouta, Christos Karagiannis, George Koumbaris, Charalambos Loizides, Michail Mendris, Panagiotis Papastergiou, Philippos C. Patsalis, Despo Pieridou, Jan Richter, Markus Schmitt, Christos Shammas, Dora C. Stylianou, Giorgos Themistokleous, the COMESSAR Network, Philippe Lemey, Leondios G. Kostrikis

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Phylogenetic relationships of the HA and NA genes between vaccine and seasonal influenza A(H3N2) strains in Korea. by Jin Il Kim, Ilseob Lee, Sehee Park, Joon-Yong Bae, Kirim Yoo, Hee Jin Cheong, Ji Yun Noh, Kyung Wook Hong, Philippe Lemey, Bram Vrancken, Juwon Kim, Misun Nam, Soo-Hyeon Yun, Woo In Cho, Joon Young Song, Woo Joo Kim, Mee Sook Park, Jin-Won Song, Sun-Ho Kee, Ki-Joon Song, Man-Seong Park

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