A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology von Rambaut, Andrew, Holmes, Edward C., O’Toole, Áine, Hill, Verity, McCrone, John T., Ruis, Christopher, du Plessis, Louis, Pybus, Oliver G.

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Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool von O’Toole, Áine, Scher, Emily, Underwood, Anthony, Jackson, Ben, Hill, Verity, McCrone, John T, Colquhoun, Rachel, Ruis, Chris, Abu-Dahab, Khalil, Taylor, Ben, Yeats, Corin, du Plessis, Louis, Maloney, Daniel, Medd, Nathan, Attwood, Stephen W, Aanensen, David M, Holmes, Edward C, Pybus, Oliver G, Rambaut, Andrew

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Constraining the Emission Geometry and Mass of the White Dwarf Pulsar AR Sco Using the Rotating Vector Model von Plessis, Louis du, Wadiasingh, Zorawar, Venter, Christo, Harding, Alice K.

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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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A computationally tractable birth-death model that combines phylogenetic and epidemiological data von Zarebski, Alexander Eugene, du Plessis, Louis, Parag, Kris Varun, Pybus, Oliver George

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Genomic Epidemiology of Early SARS-CoV-2 Transmission Dynamics, Gujarat, India von Raghwani, Jayna, du Plessis, Louis, McCrone, John T, Hill, Sarah C, Parag, Kris V, Thézé, Julien, Kumar, Dinesh, Puvar, Apurva, Pandit, Ramesh, Pybus, Oliver G, Fournié, Guillaume, Joshi, Madhvi, Joshi, Chaitanya

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The effect of human mobility and control measures on the COVID-19 epidemic in China von Kraemer, Moritz U G, Yang, Chia-Hung, Gutierrez, Bernardo, Wu, Chieh-Hsi, Klein, Brennan, Pigott, David M, du Plessis, Louis, Faria, Nuno R, Li, Ruoran, Hanage, William P, Brownstein, John S, Layan, Maylis, Vespignani, Alessandro, Tian, Huaiyu, Dye, Christopher, Pybus, Oliver G, Scarpino, Samuel V

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BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis von Bouckaert, Remco, Vaughan, Timothy G, Barido-Sottani, Joëlle, Duchêne, Sebastián, Fourment, Mathieu, Gavryushkina, Alexandra, Heled, Joseph, Jones, Graham, Kühnert, Denise, De Maio, Nicola, Matschiner, Michael, Mendes, Fábio K, Müller, Nicola F, Ogilvie, Huw A, du Plessis, Louis, Popinga, Alex, Rambaut, Andrew, Rasmussen, David, Siveroni, Igor, Suchard, Marc A, Wu, Chieh-Hsi, Xie, Dong, Zhang, Chi, Stadler, Tanja, Drummond, Alexei J

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Purifying Selection Determines the Short-Term Time Dependency of Evolutionary Rates in SARS-CoV-2 and pH1N1 Influenza von Ghafari, Mahan, du Plessis, Louis, Raghwani, Jayna, Bhatt, Samir, Xu, Bo, Pybus, Oliver G, Katzourakis, Aris

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Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK von du Plessis, Louis, McCrone, John T, Zarebski, Alexander E, Hill, Verity, Ruis, Christopher, Gutierrez, Bernardo, Raghwani, Jayna, Ashworth, Jordan, Colquhoun, Rachel, Connor, Thomas R, Faria, Nuno R, Jackson, Ben, Loman, Nicholas J, O'Toole, Áine, Nicholls, Samuel M, Parag, Kris V, Scher, Emily, Vasylyeva, Tetyana I, Volz, Erik M, Watts, Alexander, Bogoch, Isaac I, Khan, Kamran, Aanensen, David M, Kraemer, Moritz U G, Rambaut, Andrew, Pybus, Oliver G

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Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence von Kraemer, Moritz U G, Hill, Verity, Ruis, Christopher, Dellicour, Simon, Bajaj, Sumali, McCrone, John T, Baele, Guy, Parag, Kris V, Battle, Anya Lindström, Gutierrez, Bernardo, Jackson, Ben, Colquhoun, Rachel, O'Toole, Áine, Klein, Brennan, Vespignani, Alessandro, Volz, Erik, Faria, Nuno R, Aanensen, David M, Loman, Nicholas J, du Plessis, Louis, Cauchemez, Simon, Rambaut, Andrew, Scarpino, Samuel V, Pybus, Oliver G

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Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China von Lu, Jing, du Plessis, Louis, Liu, Zhe, Hill, Verity, Kang, Min, Lin, Huifang, Sun, Jiufeng, François, Sarah, Kraemer, Moritz U.G., Faria, Nuno R., McCrone, John T., Peng, Jinju, Xiong, Qianling, Yuan, Runyu, Zeng, Lilian, Zhou, Pingping, Liang, Chumin, Yi, Lina, Liu, Jun, Xiao, Jianpeng, Hu, Jianxiong, Liu, Tao, Ma, Wenjun, Li, Wei, Su, Juan, Zheng, Huanying, Peng, Bo, Fang, Shisong, Su, Wenzhe, Li, Kuibiao, Sun, Ruilin, Bai, Ru, Tang, Xi, Liang, Minfeng, Quick, Josh, Song, Tie, Rambaut, Andrew, Loman, Nick, Raghwani, Jayna, Pybus, Oliver G., Ke, Changwen

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Clinical, immunological and virological characterization of COVID-19 patients that test re-positive for SARS-CoV-2 by RT-PCR von Lu, Jing, Peng, Jinju, Xiong, Qianling, Liu, Zhe, Lin, Huifang, Tan, Xiaohua, Kang, Min, Yuan, Runyu, Zeng, Lilian, Zhou, Pingping, Liang, Chumin, Yi, Lina, du Plessis, Louis, Song, Tie, Ma, Wenjun, Sun, Jiufeng, Pybus, Oliver G, Ke, Changwen

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Probing the non-thermal emission geometry of AR Sco via optical phase-resolved polarimetry von du Plessis, Louis, Venter, Christo, Wadiasingh, Zorawar, Harding, Alice K, Buckley, David A H, Potter, Stephen B, Meintjes, P J

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

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Gene expression differences underlying genotype-by-genotype specificity in a host–parasite system von Barribeau, Seth M., Sadd, Ben M., du Plessis, Louis, Schmid-Hempel, Paul

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Taming the BEAST—A Community Teaching Material Resource for BEAST 2 von Barido-Sottani, Joëlle, Bošková, Veronika, du Plessis, Louis, Kühnert, Denise, Magnus, Carsten, Mitov, Venelin, Müller, Nicola F., Pečerska, Jūlija, Rasmussen, David A., Zhang, Chi, Drummond, Alexei J., Heath, Tracy A., Pybus, Oliver G., Vaughan, Timothy G., Stadler, Tanja

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COVID-19 pandemic interventions reshaped the global dispersal of seasonal influenza viruses von Chen, Zhiyuan, Tsui, Joseph L-H, Gutierrez, Bernardo, Busch Moreno, Simon, du Plessis, Louis, Deng, Xiaowei, Cai, Jun, Bajaj, Sumali, Suchard, Marc A, Pybus, Oliver G, Lemey, Philippe, Kraemer, Moritz U G, Yu, Hongjie

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A depauperate immune repertoire precedes evolution of sociality in bees von Barribeau, Seth M, Sadd, Ben M, du Plessis, Louis, Brown, Mark J F, Buechel, Severine D, Cappelle, Kaat, Carolan, James C, Christiaens, Olivier, Colgan, Thomas J, Erler, Silvio, Evans, Jay, Helbing, Sophie, Karaus, Elke, Lattorff, H Michael G, Marxer, Monika, Meeus, Ivan, Näpflin, Kathrin, Niu, Jinzhi, Schmid-Hempel, Regula, Smagghe, Guy, Waterhouse, Robert M, Yu, Na, Zdobnov, Evgeny M, Schmid-Hempel, Paul

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The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK von Hill, Verity, Du Plessis, Louis, Peacock, Thomas P, Aggarwal, Dinesh, Colquhoun, Rachel, Carabelli, Alesandro M, Ellaby, Nicholas, Gallagher, Eileen, Groves, Natalie, Jackson, Ben, McCrone, J T, O’Toole, Áine, Price, Anna, Sanderson, Theo, Scher, Emily, Southgate, Joel, Volz, Erik, Barclay, Wendy S, Barrett, Jeffrey C, Chand, Meera, Connor, Thomas, Goodfellow, Ian, Gupta, Ravindra K, Harrison, Ewan M, Loman, Nicholas, Myers, Richard, Robertson, David L, Pybus, Oliver G, Rambaut, Andrew

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