Parallel evolutionary pathways to antibiotic resistance selected by biocide exposure by Webber, Mark A, Whitehead, Rebekah N, Mount, Manuella, Loman, Nick J, Pallen, Mark J, Piddock, Laura J V

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Extreme genetic fragility of the HIV-1 capsid by Rihn, Suzannah J, Wilson, Sam J, Loman, Nick J, Alim, Mudathir, Bakker, Saskia E, Bhella, David, Gifford, Robert J, Rixon, Frazer J, Bieniasz, Paul D

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Observations of SARS-CoV-2 variant of concern B.1.1.7 at the UK's largest hospital trust by Garvey, Mark I., McMurray, Claire, Casey, Anna L, Ratcliffe, Liz, Stockton, Joanne, Wilkinson, Martyn A C, Holden, Elisabeth, Osman, Husam, Loman, Nick J

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Details of SARS-CoV-2 reinfections at a major UK tertiary centre by Garvey, Mark I., Casey, Anna L., Wilkinson, Martyn A.C., Ratcliffe, Liz, McMurray, Claire, Stockton, Joanne, Holden, Elisabeth, Osman, Husam, Loman, Nick J

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Genomic detection of a virus lineage replacement event of dengue virus serotype 2 in Brazil, 2019 by de Jesus, Jaqueline Goes, Dutra, Karina Rocha, Sales, Flavia Cristina da Silva, Claro, Ingra Morales, Terzian, Ana Carolina, Candido, Darlan da Silva, Hill, Sarah C, Thézé, Julien, Torres, Celeste, D’Agostini, Tatiana Lang, Felix, Alvina Clara, Reis, Andreia F Negri, Alcantara, Luiz Carlos Junior, de Abreu, André L, Croda, Júlio HR, de Oliveira, Wanderson K, de Filipis, Ana Maria Bispo, Camis, Maria do Carmo Rodrigues dos Santos, Romano, Camila Malta, Loman, Nick J, Pybus, Oliver G, Sabino, Ester Cerdeira, Nogueira, Mauricio L, Faria, Nuno Rodrigues

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Genomic detection of a virus lineage replacement event of dengue virus serotype 2 in Brazil, 2019 by de Jesus, Jaqueline Goes, Dutra, Karina Rocha, Sales, Flavia Cristina da Silva, Claro, Ingra Morales, Terzian, Ana Carolina, Candido, Darlan da Silva, Hill, Sarah C, Thézé, Julien, Torres, Celeste, D'Agostini, Tatiana Lang, Felix, Alvina Clara, Reis, Andreia F Negri, Alcantara, Luiz Carlos Junior, de Abreu, André L, Croda, Júlio Hr, de Oliveira, Wanderson K, de Filipis, Ana Maria Bispo, Camis, Maria do Carmo Rodrigues Dos Santos, Romano, Camila Malta

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Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil by Faria, Nuno R, Mellan, Thomas A, Whittaker, Charles, Claro, Ingra M, Candido, Darlan da S, Mishra, Swapnil, Crispim, Myuki A E, Sales, Flavia C S, Hawryluk, Iwona, McCrone, John T, Hulswit, Ruben J G, Franco, Lucas A M, Ramundo, Mariana S, de Jesus, Jaqueline G, Andrade, Pamela S, Coletti, Thais M, Ferreira, Giulia M, Silva, Camila A M, Manuli, Erika R, Pereira, Rafael H M, Peixoto, Pedro S, Kraemer, Moritz U G, Gaburo, Jr, Nelson, Camilo, Cecilia da C, Hoeltgebaum, Henrique, Souza, William M, Rocha, Esmenia C, de Souza, Leandro M, de Pinho, Mariana C, Araujo, Leonardo J T, Malta, Frederico S V, de Lima, Aline B, Silva, Joice do P, Zauli, Danielle A G, Ferreira, Alessandro C de S, Schnekenberg, Ricardo P, Laydon, Daniel J, Walker, Patrick G T, Schlüter, Hannah M, Dos Santos, Ana L P, Vidal, Maria S, Del Caro, Valentina S, Filho, Rosinaldo M F, Dos Santos, Helem M, Aguiar, Renato S, Proença-Modena, José L, Nelson, Bruce, Hay, James A, Monod, Mélodie, Miscouridou, Xenia, Coupland, Helen, Sonabend, Raphael, Vollmer, Michaela, Gandy, Axel, Prete, Jr, Carlos A, Nascimento, Vitor H, Suchard, Marc A, Bowden, Thomas A, Pond, Sergei L K, Wu, Chieh-Hsi, Ratmann, Oliver, Ferguson, Neil M, Dye, Christopher, Loman, Nick J, Lemey, Philippe, Rambaut, Andrew, Fraiji, Nelson A, Carvalho, Maria do P S S, Pybus, Oliver G, Flaxman, Seth, Bhatt, Samir, Sabino, Ester C

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Evolution and epidemic spread of SARS-CoV-2 in Brazil by Candido, Darlan S, Claro, Ingra M, de Jesus, Jaqueline G, Souza, William M, Moreira, Filipe R R, Dellicour, Simon, Mellan, Thomas A, du Plessis, Louis, Pereira, Rafael H M, Sales, Flavia C S, Manuli, Erika R, Thézé, Julien, Almeida, Luiz, Menezes, Mariane T, Voloch, Carolina M, Fumagalli, Marcilio J, Coletti, Thaís M, da Silva, Camila A M, Ramundo, Mariana S, Amorim, Mariene R, Hoeltgebaum, Henrique H, Mishra, Swapnil, Gill, Mandev S, Carvalho, Luiz M, Buss, Lewis F, Prete, Jr, Carlos A, Ashworth, Jordan, Nakaya, Helder I, Peixoto, Pedro S, Brady, Oliver J, Nicholls, Samuel M, Tanuri, Amilcar, Rossi, Átila D, Braga, Carlos K V, Gerber, Alexandra L, de C Guimarães, Ana Paula, Gaburo, Jr, Nelson, Alencar, Cecila Salete, Ferreira, Alessandro C S, Lima, Cristiano X, Levi, José Eduardo, Granato, Celso, Ferreira, Giulia M, Francisco, Jr, Ronaldo S, Granja, Fabiana, Garcia, Marcia T, Moretti, Maria Luiza, Perroud, Jr, Mauricio W, Castiñeiras, Terezinha M P P, Lazari, Carolina S, Hill, Sarah C, de Souza Santos, Andreza Aruska, Simeoni, Camila L, Forato, Julia, Sposito, Andrei C, Schreiber, Angelica Z, Santos, Magnun N N, de Sá, Camila Zolini, Souza, Renan P, Resende-Moreira, Luciana C, Teixeira, Mauro M, Hubner, Josy, Leme, Patricia A F, Moreira, Rennan G, Nogueira, Maurício L, Ferguson, Neil M, Costa, Silvia F, Proenca-Modena, José Luiz, Vasconcelos, Ana Tereza R, Bhatt, Samir, Lemey, Philippe, Wu, Chieh-Hsi, Rambaut, Andrew, Loman, Nick J, Aguiar, Renato S, Pybus, Oliver G, Sabino, Ester C, Faria, Nuno Rodrigues

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Extreme Genetic Fragility of the HIV-1 Capsid: e1003461 by Rihn, Suzannah J, Wilson, Sam J, Loman, Nick J, Alim, Mudathir, Bakker, Saskia E, Bhella, David, Gifford, Robert J, Rixon, Frazer J, Bieniasz, Paul D

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Identification of Common Deletions in the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2 by Liu, Zhe, Zheng, Huanying, Lin, Huifang, Li, Mingyue, Yuan, Runyu, Peng, Jinju, Xiong, Qianling, Sun, Jiufeng, Li, Baisheng, Wu, Jie, Yi, Lina, Peng, Xiaofang, Zhang, Huan, Zhang, Wei, Hulswit, Ruben J G, Loman, Nick, Rambaut, Andrew, Ke, Changwen, Bowden, Thomas A, Pybus, Oliver G, Lu, Jing

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A cross-sectional survey of bacterial species in plaque from client owned dogs with healthy gingiva, gingivitis or mild periodontitis by Davis, Ian J, Wallis, Corrin, Deusch, Oliver, Colyer, Alison, Milella, Lisa, Loman, Nick, Harris, Stephen

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Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7 by Curran, Martin D., Roy, Sunando, Shaaban, Sharif, de Cesare, Mariateresa, Stark, Richard, Palmer, Steve, Jeffries, Aaron R., da Silva Filipe, Ana, Davis, Thomas, Collins, Jennifer, Williams, Thomas, Haldenby, Sam T., Cook, Kate, Davies, Robert, Kay, Sally, Poplawski, Radoslaw, Reynolds, Nicola, Moll, Robin J., Thornton, Alicia, Gatica-Wilcox, Bree, Louka, Stavroula F., Kraemer, Moritz U.G., Freeman, Timothy M., Abudahab, Khalil, Menegazzo, Mirko, Mason, Jenifer, Holmes, Alison, Curran, Tanya, Mookerjee, Siddharth, Munn, Robert, Davies, Alisha, Smith, Nikki, Cormie, Claire, Lo, Stephanie, Auckland, Cressida, Mollett, Guy, Harper, Katherine L., Bonner, Stephen, Padgett, Debra, Burton-Fanning, Shirelle, Bedford, Luke, Coupland, Lindsay, Wright, Victoria, Ball, Jonathan, Boswell, Tim, Duckworth, Nichola, Williams, Rebecca, Cogger, Benjamin J., Farr, Ben W., Thurston, Scott A.J., Bronner, Iraad F., Aigrain, Louise, Gallagher, Michael D., Miah, Shahjahan, Ramsay, Mary, Schaefer, Ulf, Manesis, Nikos, Allara, Elias, Nichols, Jenna, Vamos, Edith E., Hughes, Margaret, Wilson, Harry D., Wilson, Rebekah E., Thompson, Thomas, O’Brien, Sarah, Rudder, Steven, McCluggage, Kathryn, Bonfield, James, Liddle, Jennifier, Rowe, Will, Bevan, Paul, Clark, Richard, Cutts, Tim, Densem, Aiden, Dodd, David, Griffiths, Coline, Kay, Keely, Lensing, Stefanie, Lewis-Wade, Amanah, Mamun, Irfan, Martin, Matt, McClintock, Jo, Nathwani, Claire, Nicholson, Jon, Patel, Gaurang, Petersen, Arabella, Reynolds, Joe, Rudd, Luke, Sadri, Ramin, Sizer, Dale, Soria, Carmen Diaz, Sousa, Catarina, Squares, Janet, Stickland, Tim, Still, Ian, Symons, Edward, Uphill, James, Van, Philip Jansen, Voak, Paul, Corti, Davide

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Immune gene expression and response to chemotherapy in advanced breast cancer by Foukakis, Theodoros, Lövrot, John, Matikas, Alexios, Zerdes, Ioannis, Lorent, Julie, Tobin, Nick, Suzuki, Chikako, Brage, Suzanne Egyházi, Carlsson, Lena, Einbeigi, Zakaria, Linderholm, Barbro, Loman, Niklas, Malmberg, Martin, Fernö, Mårten, Skoog, Lambert, Bergh, Jonas, Hatschek, Thomas

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Whole-genome comparison of two Acinetobacter baumannii isolates from a single patient, where resistance developed during tigecycline therapy by Hornsey, Michael, Loman, Nick, Wareham, David W., Ellington, Matthew J., Pallen, Mark J., Turton, Jane F., Underwood, Anthony, Gaulton, Tom, Thomas, Claire P., Doumith, Michel, Livermore, David M., Woodford, Neil

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Clinical utilization of genomics data produced by the international Pseudomonas aeruginosa consortium by Freschi, Luca, Jeukens, Julie, Kukavica-Ibrulj, Irena, Boyle, Brian, Dupont, Marie-Josée, Laroche, Jérôme, Larose, Stéphane, Maaroufi, Halim, Fothergill, Joanne L, Moore, Matthew, Winsor, Geoffrey L, Aaron, Shawn D, Barbeau, Jean, Bell, Scott C, Burns, Jane L, Camara, Miguel, Cantin, André, Charette, Steve J, Dewar, Ken, Déziel, Éric, Grimwood, Keith, Hancock, Robert E W, Harrison, Joe J, Heeb, Stephan, Jelsbak, Lars, Jia, Baofeng, Kenna, Dervla T, Kidd, Timothy J, Klockgether, Jens, Lam, Joseph S, Lamont, Iain L, Lewenza, Shawn, Loman, Nick, Malouin, François, Manos, Jim, McArthur, Andrew G, McKeown, Josie, Milot, Julie, Naghra, Hardeep, Nguyen, Dao, Pereira, Sheldon K, Perron, Gabriel G, Pirnay, Jean-Paul, Rainey, Paul B, Rousseau, Simon, Santos, Pedro M, Stephenson, Anne, Taylor, Véronique, Turton, Jane F, Waglechner, Nicholas, Williams, Paul, Thrane, Sandra W, Wright, Gerard D, Brinkman, Fiona S L, Tucker, Nicholas P, Tümmler, Burkhard, Winstanley, Craig, Levesque, Roger C

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Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 - 2018 by Hill, Sarah C, de Souza, Renato, Thézé, Julien, Claro, Ingra, Aguiar, Renato S, Abade, Leandro, Santos, Fabiana C P, Cunha, Mariana S, Nogueira, Juliana S, Salles, Flavia C S, Rocco, Iray M, Maeda, Adriana Y, Vasami, Fernanda G S, du Plessis, Louis, Silveira, Paola P, de Jesus, Jaqueline G, Quick, Joshua, Fernandes, Natália C C A, Guerra, Juliana M, Réssio, Rodrigo A, Giovanetti, Marta, Alcantara, Luiz C J, Cirqueira, Cinthya S, Díaz-Delgado, Josué, Macedo, Fernando L L, Timenetsky, Maria do Carmo S T, de Paula, Regiane, Spinola, Roberta, Telles de Deus, Juliana, Mucci, Luís F, Tubaki, Rosa Maria, de Menezes, Regiane M T, Ramos, Patrícia L, de Abreu, Andre L, Cruz, Laura N, Loman, Nick, Dellicour, Simon, Pybus, Oliver G, Sabino, Ester C, Faria, Nuno R

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A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK by Colquhoun, Rachel, O’Toole, Áine, Hill, Verity, McCrone, J T, Yu, Xiaoyu, Nicholls, Samuel M, Poplawski, Radoslaw, Whalley, Thomas, Groves, Natalie, Ellaby, Nicholas, Loman, Nick, Connor, Tom, Rambaut, Andrew

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Genomics-informed outbreak investigations of SARS-CoV-2 using civet by O'Toole, Áine, Hill, Verity, Jackson, Ben, Dewar, Rebecca, Sahadeo, Nikita, Colquhoun, Rachel, Rooke, Stefan, McCrone, J T, Duggan, Kate, McHugh, Martin P, Nicholls, Samuel M, Poplawski, Radoslaw, Aanensen, David, Holden, Matt, Connor, Tom, Loman, Nick, Goodfellow, Ian, Carrington, Christine V F, Templeton, Kate, Rambaut, Andrew

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Identification and Quantification of Genomic Repeats and Sample Contamination in Assemblies of 454 Pyrosequencing Reads by Nederbragt, Alexander J., Rounge, Trine Ballestad, Kausrud, Kyrre L., Jakobsen, Kjetill S.

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Genomics-informed outbreak investigations of SARS-CoV-2 using civet by Áine O’Toole, Verity Hill, Ben Jackson, Rebecca Dewar, Nikita Sahadeo, Rachel Colquhoun, Stefan Rooke, J. T. McCrone, Kate Duggan, Martin P. McHugh, Samuel M. Nicholls, Radoslaw Poplawski, David Aanensen, Matt Holden, Tom Connor, Nick Loman, Ian Goodfellow, Christine V. F. Carrington, Kate Templeton, Andrew Rambaut

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