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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Measurements of Intrahost Viral Diversity Are Extremely Sensitive to Systematic Errors in Variant Calling von McCrone, John T, Lauring, Adam S

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Vaccination has minimal impact on the intrahost diversity of H3N2 influenza viruses von Debbink, Kari, McCrone, John T, Petrie, Joshua G, Truscon, Rachel, Johnson, Emileigh, Mantlo, Emily K, Monto, Arnold S, Lauring, Adam S

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A speed-fidelity trade-off determines the mutation rate and virulence of an RNA virus von Fitzsimmons, William J, Woods, Robert J, McCrone, John T, Woodman, Andrew, Arnold, Jamie J, Yennawar, Madhumita, Evans, Richard, Cameron, Craig E, Lauring, Adam S

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Genetic bottlenecks in intraspecies virus transmission von McCrone, John T, Lauring, Adam S

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The Mutational Robustness of Influenza A Virus von Visher, Elisa, Whitefield, Shawn E, McCrone, John T, Fitzsimmons, William, Lauring, Adam S

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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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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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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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Stochastic processes constrain the within and between host evolution of influenza virus von McCrone, John T, Woods, Robert J, Martin, Emily T, Malosh, Ryan E, Monto, Arnold S, Lauring, Adam S

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Influenza B Viruses Exhibit Lower Within-Host Diversity than Influenza A Viruses in Human Hosts von Valesano, Andrew L, Fitzsimmons, William J, McCrone, John T, Petrie, Joshua G, Monto, Arnold S, Martin, Emily T, Lauring, Adam S

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Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic von Jackson, Ben, Boni, Maciej F., Bull, Matthew J., Colleran, Amy, Colquhoun, Rachel M., Darby, Alistair C., Haldenby, Sam, Hill, Verity, Lucaci, Anita, McCrone, John T., Nicholls, Samuel M., O’Toole, Áine, Pacchiarini, Nicole, Poplawski, Radoslaw, Scher, Emily, Todd, Flora, Webster, Hermione J., Whitehead, Mark, Wierzbicki, Claudia, Loman, Nicholas J., Connor, Thomas R., Robertson, David L., Pybus, Oliver G., Rambaut, Andrew

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Underdetected dispersal and extensive local transmission drove the 2022 mpox epidemic von Paredes, Miguel I., Ahmed, Nashwa, Figgins, Marlin, Colizza, Vittoria, Lemey, Philippe, McCrone, John T., Müller, Nicola, Tran-Kiem, Cécile, Bedford, Trevor

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Computational and Empirical Studies Predict Mycobacterium tuberculosis-Specific T Cells as a Biomarker for Infection Outcome von Marino, Simeone, Gideon, Hannah P, Gong, Chang, Mankad, Shawn, McCrone, John T, Lin, Philana Ling, Linderman, Jennifer J, Flynn, JoAnne L, Kirschner, Denise E

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Context-specific emergence and growth of the SARS-CoV-2 Delta variant von McCrone, John T., Hill, Verity, Bajaj, Sumali, Pena, Rosario Evans, Lambert, Ben C., Inward, Rhys, Bhatt, Samir, Volz, Erik, Ruis, Christopher, Dellicour, Simon, Baele, Guy, Zarebski, Alexander E., Sadilek, Adam, Wu, Neo, Schneider, Aaron, Ji, Xiang, Raghwani, Jayna, Jackson, Ben, Colquhoun, Rachel, O’Toole, Áine, Peacock, Thomas P., Twohig, Kate, Thelwall, Simon, Dabrera, Gavin, Myers, Richard, Faria, Nuno R., Huber, Carmen, Bogoch, Isaac I., Khan, Kamran, du Plessis, Louis, Barrett, Jeffrey C., Aanensen, David M., Barclay, Wendy S., Chand, Meera, Connor, Thomas, Loman, Nicholas J., Suchard, Marc A., Pybus, Oliver G., Rambaut, Andrew, Kraemer, Moritz U. G.

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Friston's theory of everything von McCrone, John

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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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Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1 von Tsui, Joseph L-H, McCrone, John T, Lambert, Ben, Bajaj, Sumali, Inward, Rhys P D, Bosetti, Paolo, Pena, Rosario Evans, Tegally, Houriiyah, Hill, Verity, Zarebski, Alexander E, Peacock, Thomas P, Liu, Luyang, Wu, Neo, Davis, Megan, Bogoch, Isaac I, Khan, Kamran, Kall, Meaghan, Abdul Aziz, Nurin Iwani Binti, Colquhoun, Rachel, O'Toole, Áine, Jackson, Ben, Dasgupta, Abhishek, Wilkinson, Eduan, de Oliveira, Tulio, Connor, Thomas R, Loman, Nicholas J, Colizza, Vittoria, Fraser, Christophe, Volz, Erik, Ji, Xiang, Gutierrez, Bernardo, Chand, Meera, Dellicour, Simon, Cauchemez, Simon, Raghwani, Jayna, Suchard, Marc A, Lemey, Philippe, Rambaut, Andrew, Pybus, Oliver G, Kraemer, Moritz U G

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