Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic von Boni, Maciej F., Lemey, Philippe, Jiang, Xiaowei, Lam, Tommy Tsan-Yuk, Perry, Blair W., Castoe, Todd A., Rambaut, Andrew, Robertson, David L.

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The emergence of SARS-CoV-2 in Europe and North America von Worobey, Michael, Pekar, Jonathan, Larsen, Brendan B., Nelson, Martha I., Hill, Verity, Joy, Jeffrey B., Rambaut, Andrew, Suchard, Marc A., Wertheim, Joel O., Lemey, Philippe

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SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes von Bielejec, Filip, Baele, Guy, Vrancken, Bram, Suchard, Marc A, Rambaut, Andrew, Lemey, Philippe

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Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 von Suchard, Marc A, Lemey, Philippe, Baele, Guy, Ayres, Daniel L, Drummond, Alexei J, Rambaut, Andrew

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Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty von Baele, Guy, Lemey, Philippe, Bedford, Trevor, Rambaut, Andrew, Suchard, Marc A, Alekseyenko, Alexander V

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SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics von Bielejec, Filip, Rambaut, Andrew, Suchard, Marc A., Lemey, Philippe

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RDP3: a flexible and fast computer program for analyzing recombination von Martin, Darren P., Lemey, Philippe, Lott, Martin, Moulton, Vincent, Posada, David, Lefeuvre, Pierre

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Integrating influenza antigenic dynamics with molecular evolution von Bedford, Trevor, Suchard, Marc A, Lemey, Philippe, Dudas, Gytis, Gregory, Victoria, Hay, Alan J, McCauley, John W, Russell, Colin A, Smith, Derek J, Rambaut, Andrew

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

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Virome characterization of game animals in China reveals a spectrum of emerging pathogens von He, Wan-Ting, Hou, Xin, Zhao, Jin, Sun, Jiumeng, He, Haijian, Si, Wei, Wang, Jing, Jiang, Zhiwen, Yan, Ziqing, Xing, Gang, Lu, Meng, Suchard, Marc A., Ji, Xiang, Gong, Wenjie, He, Biao, Li, Jun, Lemey, Philippe, Guo, Deyin, Tu, Changchun, Holmes, Edward C., Shi, Mang, Su, Shuo

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The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages von Martin, Darren P., Weaver, Steven, Tegally, Houriiyah, San, James Emmanuel, Shank, Stephen D., Wilkinson, Eduan, Lucaci, Alexander G., Giandhari, Jennifer, Naidoo, Sureshnee, Pillay, Yeshnee, Singh, Lavanya, Lessells, Richard J., Gupta, Ravindra K., Wertheim, Joel O., Nekturenko, Anton, Murrell, Ben, Harkins, Gordon W., Lemey, Philippe, MacLean, Oscar A., Robertson, David L., de Oliveira, Tulio, Kosakovsky Pond, Sergei L.

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Bayesian phylogeography finds its roots von Lemey, Philippe, Rambaut, Andrew, Drummond, Alexei J, Suchard, Marc A

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Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2 von Lemey, Philippe, Hong, Samuel L., Hill, Verity, Baele, Guy, Poletto, Chiara, Colizza, Vittoria, O’Toole, Áine, McCrone, John T., Andersen, Kristian G., Worobey, Michael, Nelson, Martha I., Rambaut, Andrew, Suchard, Marc A.

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Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution von Baele, Guy, Lemey, Philippe, Vansteelandt, Stijn

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The early spread and epidemic ignition of HIV-1 in human populations von Faria, Nuno R., Rambaut, Andrew, Suchard, Marc A., Baele, Guy, Bedford, Trevor, J. Ward, Melissa, Tatem, Andrew J., Sousa, João D., Arinaminpathy, Nimalan, Pépin, Jacques, Posada, David, Peeters, Martine, Pybus, Oliver G., Lemey, Philippe

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SERAPHIM: studying environmental rasters and phylogenetically informed movements von Dellicour, Simon, Rose, Rebecca, Faria, Nuno R, Lemey, Philippe, Pybus, Oliver G

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Genome-wide evolutionary dynamics of influenza B viruses on a global scale von Langat, Pinky, Raghwani, Jayna, Dudas, Gytis, Bowden, Thomas A, Edwards, Stephanie, Gall, Astrid, Bedford, Trevor, Rambaut, Andrew, Daniels, Rodney S, Russell, Colin A, Pybus, Oliver G, McCauley, John, Kellam, Paul, Watson, Simon J

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Resurgence of Ebola virus in 2021 in Guinea suggests a new paradigm for outbreaks von Keita, Alpha Kabinet, Koundouno, Fara R., Faye, Martin, Düx, Ariane, Hinzmann, Julia, Diallo, Haby, Ayouba, Ahidjo, Le Marcis, Frederic, Soropogui, Barré, Ifono, Kékoura, Diagne, Moussa M., Sow, Mamadou S., Bore, Joseph A., Calvignac-Spencer, Sebastien, Vidal, Nicole, Camara, Jacob, Keita, Mamadou B., Renevey, Annick, Diallo, Amadou, Soumah, Abdoul K., Millimono, Saa L., Mari-Saez, Almudena, Diop, Mamadou, Doré, Ahmadou, Soumah, Fodé Y., Kourouma, Kaka, Vielle, Nathalie J., Loucoubar, Cheikh, Camara, Ibrahima, Kourouma, Karifa, Annibaldis, Giuditta, Bah, Assaïtou, Thielebein, Anke, Pahlmann, Meike, Pullan, Steven T., Carroll, Miles W., Quick, Joshua, Formenty, Pierre, Legand, Anais, Pietro, Karla, Wiley, Michael R., Tordo, Noel, Peyrefitte, Christophe, McCrone, John T., Rambaut, Andrew, Sidibé, Youssouf, Barry, Mamadou D., Kourouma, Madeleine, Saouromou, Cé D., Condé, Mamadou, Baldé, Moussa, Povogui, Moriba, Keita, Sakoba, Diakite, Mandiou, Bah, Mamadou S., Sidibe, Amadou, Diakite, Dembo, Sako, Fodé B., Traore, Fodé A., Ki-Zerbo, Georges A., Lemey, Philippe, Günther, Stephan, Kafetzopoulou, Liana E., Sall, Amadou A., Delaporte, Eric, Duraffour, Sophie, Faye, Ousmane, Leendertz, Fabian H., Peeters, Martine, Toure, Abdoulaye, Magassouba, N’. Faly

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

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Mapping the Origins and Expansion of the Indo-European Language Family von Bouckaert, Remco, Lemey, Philippe, Dunn, Michael, Greenhill, Simon J., Alekseyenko, Alexander V., Drummond, Alexei J., Gray, Russell D., Suchard, Marc A., Atkinson, Quentin D.

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