EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering. by Ciara Judge, Timothy Vaughan, Timothy Russell, Sam Abbott, Louis du Plessis, Tanja Stadler, Oliver Brady, Sarah Hill

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Disruption of seasonal influenza circulation and evolution during the 2009 H1N1 and COVID-19 pandemics in Southeastern Asia by Zhiyuan Chen, Joseph L.-H. Tsui, Jun Cai, Shuo Su, Cécile Viboud, Louis du Plessis, Philippe Lemey, Moritz U. G. Kraemer, Hongjie Yu

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Insights into Treponema pallidum genomics from modern and ancient genomes using a novel mapping strategy by Marta Pla-Díaz, Gülfirde Akgül, Martyna Molak, Louis du Plessis, Hanna Panagiotopoulou, Karolina Doan, Wiesław Bogdanowicz, Paweł Dąbrowski, Maciej Oziembłowski, Barbara Kwiatkowska, Jacek Szczurowski, Joanna Grzelak, Natasha Arora, Kerttu Majander, Fernando González-Candelas, Verena J. Schuenemann

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Inferring enterovirus D68 transmission dynamics from the genomic data of two 2022 North American outbreaks by Martin Grunnill, Alireza Eshaghi, Lambodhar Damodaran, Sandeep Nagra, Ali Gharouni, Thomas Braukmann, Shawn Clark, Adriana Peci, Sandra Isabel, Philip Banh, Louis du Plessis, Carmen Lia Murall, Caroline Colijn, Samira Mubareka, Maan Hasso, Justin Bahl, Heba H. Mostafa, Jonathan B. Gubbay, Samir N. Patel, Jianhong Wu, Venkata R. Duvvuri

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High-resolution epidemiological landscape from  ~290,000 SARS-CoV-2 genomes from Denmark by Mark P. Khurana, Jacob Curran-Sebastian, Neil Scheidwasser, Christian Morgenstern, Morten Rasmussen, Jannik Fonager, Marc Stegger, Man-Hung Eric Tang, Jonas L. Juul, Leandro Andrés Escobar-Herrera, Frederik Trier Møller, The Danish COVID-19 Genome Consortium (DCGC), Mads Albertsen, Moritz U. G. Kraemer, Louis du Plessis, Pikka Jokelainen, Sune Lehmann, Tyra G. Krause, Henrik Ullum, David A. Duchêne, Laust H. Mortensen, Samir Bhatt

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How much should we sequence? An analysis of the Swiss SARS-CoV-2 surveillance effort by Fanny Wegner, Blanca Cabrera-Gil, Araud Tanguy, Christiane Beckmann, Niko Beerenwinkel, Claire Bertelli, Matteo Carrara, Lorenzo Cerutti, Chaoran Chen, Samuel Cordey, Alexis Dumoulin, Louis du Plessis, Marc Friedli, Yannick Gerth, Gilbert Greub, Adrian Härri, Hans Hirsch, Cedric Howald, Michael Huber, Alexander Imhof, Laurent Kaiser, Verena Kufner, Stephen L. Leib, Karoline Leuzinger, Etleva Lleshi, Gladys Martinetti, Mirjam Mäusezahl, Milo Moraz, Richard Neher, Oliver Nolte, Alban Ramette, Maurice Redondo, Lorenz Risch, Lionel Rohner, Tim Roloff, Pascal Schläepfer, Katrin Schneider, Franziska Singer, Valeria Spina, Tanja Stadler, Erik Studer, Ivan Topolsky, Alexandra Trkola, Daniel Walther, Nadia Wohlwend, Cinzia Zehnder, Aitana Neves, Adrian Egli

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