Extensive C-U transition biases in the genomes of a wide range of mammalian RNA viruses; potential associations with transcriptional mutations, damage- or host-mediated editing of... von Simmonds, Peter, Ansari, M. Azim

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The impact of pre-existing cross-reactive immunity on SARS-CoV-2 infection and vaccine responses von Murray, Sam M., Ansari, Azim M., Frater, John, Klenerman, Paul, Dunachie, Susanna, Barnes, Eleanor, Ogbe, Ane

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Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree von Ansari, M Azim, Didelot, Xavier

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SARS-CoV-2 within-host diversity and transmission von Lythgoe, Katrina A., Hall, Matthew, Ferretti, Luca, de Cesare, Mariateresa, MacIntyre-Cockett, George, Trebes, Amy, Andersson, Monique, Otecko, Newton, Wise, Emma L., Moore, Nathan, Lynch, Jessica, Kidd, Stephen, Cortes, Nicholas, Mori, Matilde, Williams, Rebecca, Vernet, Gabrielle, Justice, Anita, Green, Angie, Nicholls, Samuel M., Ansari, M. Azim, Abeler-Dorner, Lucie, Moore, Catrin E., Peto, Timothy E. A., Eyre, David W., Shaw, Robert, Simmonds, Peter, Buck, David, Todd, John A., Connor, Thomas R., Ashraf, Shirin, Filipe, Ana da Silva, Shepherd, James, Thomson, Emma C., Bonsall, David, Fraser, Christophe, Golubchik, Tanya

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Testing for dependence on tree structures von Behr, Merle, Ansari, M. Azim, Munk, Axel, Holmes, Chris

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Resistance analysis of genotype 3 hepatitis C virus indicates subtypes inherently resistant to nonstructural protein 5A inhibitors von Smith, David, Magri, Andrea, Bonsall, David, Ip, Camilla L.C., Trebes, Amy, Brown, Anthony, Piazza, Palo, Bowden, Rory, Nguyen, Dung, Ansari, M. Azim, Simmonds, Peter, Barnes, Eleanor

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Inference of the properties of the recombination process from whole bacterial genomes von Ansari, M Azim, Didelot, Xavier

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Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV) von McNaughton, Anna L., Roberts, Hannah E., Bonsall, David, de Cesare, Mariateresa, Mokaya, Jolynne, Lumley, Sheila F., Golubchik, Tanya, Piazza, Paolo, Martin, Jacqueline B., de Lara, Catherine, Brown, Anthony, Ansari, M. Azim, Bowden, Rory, Barnes, Eleanor, Matthews, Philippa C.

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Defining the key intrahepatic gene networks in HCV infection driven by sex von Marchi, Emanuele, Ramamurthy, Narayan, Ansari, M Azim, Harrer, Caroline E, Barnes, Eleanor, Klenerman, Paul

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Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences von McNaughton, Anna L., Revill, Peter A., Littlejohn, Margaret, Matthews, Philippa C., Ansari, M. Azim

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A Comprehensive Genomics Solution for HIV Surveillance and Clinical Monitoring in Low-Income Settings von Bonsall, David, Golubchik, Tanya, de Cesare, Mariateresa, Limbada, Mohammed, Kosloff, Barry, MacIntyre-Cockett, George, Hall, Matthew, Wymant, Chris, Ansari, M. Azim, Abeler-Dorner, Lucie, Schaap, Ab, Brown, Anthony, Barnes, Eleanor, Piwowar-Manning, Estelle, Eshleman, Susan, Wilson, Ethan, Emel, Lynda, Hayes, Richard, Fidler, Sarah, Ayles, Helen, Bowden, Rory, Fraser, Christophe

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Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data von Mayne, Richard, Secret, Shannah, Geoghegan, Cyndi, Trebes, Amy, Kean, Kai, Reid, Kaitlin, Lin, Gu-Lung, Ansari, M Azim, de Cesare, Mariateresa, Bonsall, David, Elliott, Ivo, Piazza, Paolo, Brown, Anthony, Bray, James, Knight, Julian C, Harvala, Heli, Breuer, Judith, Simmonds, Peter, Bowden, Rory J, Golubchik, Tanya

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Impact of Interferon Lambda 4 Genotype on Interferon‐Stimulated Gene Expression During Direct‐Acting Antiviral Therapy for Hepatitis C von Ramamurthy, Narayan, Marchi, Emanuele, Ansari, M. Azim, Pedergnana, Vincent, Mclean, Angela, Hudson, Emma, Bowden, Rory, Spencer, Chris C.A., Barnes, Eleanor, Klenerman, Paul

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Comparison of Next-Generation Sequencing Technologies for Comprehensive Assessment of Full-Length Hepatitis C Viral Genomes von Thomson, Emma, Ip, Camilla L C, Badhan, Anjna, Christiansen, Mette T, Adamson, Walt, Ansari, M Azim, Bibby, David, Breuer, Judith, Brown, Anthony, Bowden, Rory, Bryant, Josie, Bonsall, David, Da Silva Filipe, Ana, Hinds, Chris, Hudson, Emma, Klenerman, Paul, Lythgow, Kieren, Mbisa, Jean L, McLauchlan, John, Myers, Richard, Piazza, Paolo, Roy, Sunando, Trebes, Amy, Sreenu, Vattipally B, Witteveldt, Jeroen, Barnes, Eleanor, Simmonds, Peter

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Global prevalence and phylogeny of hepatitis B virus (HBV) drug and vaccine resistance mutations von Mokaya, Jolynne, Vasylyeva, Tetyana I., Barnes, Eleanor, Ansari, M. Azim, Pybus, Oliver G., Matthews, Philippa C.

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Changes in the prevalence of hepatitis B and C viral infections in Sindh province, Pakistan: Findings from two sero‐surveys in 2007 and 2019 von Alamneh, Tesfa Sewunet, Walker, Josephine G., Lim, Aaron G., Alam, Ejaz, Hamid, Saeed, Foster, Graham R., Choudhry, Naheed, Ansari, M. Azim, Qureshi, Huma, Vickerman, Peter

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Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico von Thézé, Julien, Li, Tony, du Plessis, Louis, Bouquet, Jerome, Kraemer, Moritz U.G., Somasekar, Sneha, Yu, Guixia, de Cesare, Mariateresa, Balmaseda, Angel, Kuan, Guillermina, Harris, Eva, Wu, Chieh-hsi, Ansari, M. Azim, Bowden, Rory, Faria, Nuno R., Yagi, Shigeo, Messenger, Sharon, Brooks, Trevor, Stone, Mars, Bloch, Evan M., Busch, Michael, Muñoz-Medina, José E., González-Bonilla, Cesar R., Wolinsky, Steven, López, Susana, Arias, Carlos F., Bonsall, David, Chiu, Charles Y., Pybus, Oliver G.

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Efficient inference of recombination hot regions in bacterial genomes von Yahara, Koji, Didelot, Xavier, Ansari, M Azim, Sheppard, Samuel K, Falush, Daniel

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Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus von Lin, Gu-Lung, Drysdale, Simon B., Snape, Matthew D., O’Connor, Daniel, Brown, Anthony, MacIntyre-Cockett, George, Mellado-Gomez, Esther, de Cesare, Mariateresa, Ansari, M. Azim, Bonsall, David, Bray, James E., Jolley, Keith A., Bowden, Rory, Aerssens, Jeroen, Bont, Louis, Openshaw, Peter J. M., Martinon-Torres, Federico, Nair, Harish, Golubchik, Tanya, Pollard, Andrew J.

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Real world SOF/VEL/VOX retreatment outcomes and viral resistance analysis for HCV patients with prior failure to DAA therapy von Smith, David A., Bradshaw, Daniel, Mbisa, Jean L, Manso, Carmen F., Bibby, David F, Singer, Joshua B, Thomson, Emma C, da Silva Filipe, Ana, Aranday‐Cortes, Elihu, Ansari, M. Azim, Brown, Anthony, Hudson, Emma, Benselin, Jennifer, Healy, Brendan, Troke, Phil, McLauchlan, John, Barnes, Eleanor, Irving, William L.

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