Pre/pro-B cells generate macrophage populations during homeostasis and inflammation by Audzevich, Tatsiana, Bashford-Rogers, Rachael, Mabbott, Neil A., Frampton, Dan, Freeman, Tom C., Potocnik, Alexandre, Kellam, Paul, Gilroy, Derek W.

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Emergence of a novel subclade of influenza A(H3N2) virus in London, December 2016 to January 2017 by Harvala, Heli, Frampton, Dan, Grant, Paul, Raffle, Jade, Ferns, Ruth Bridget, Kozlakidis, Zisis, Kellam, Paul, Pillay, Deenan, Hayward, Andrew, Nastouli, Eleni

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A Rapid Drug Resistance Genotyping Workflow for Mycobacterium tuberculosis, Using Targeted Isothermal Amplification and Nanopore Sequencing by Gliddon, Harriet D, Frampton, Dan, Munsamy, Vanisha, Heaney, Jude, Pataillot-Meakin, Thomas, Nastouli, Eleni, Pym, Alexander S, Steyn, Adrie J C, Pillay, Deenan, McKendry, Rachel A

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A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project by Yebra, Gonzalo, Frampton, Dan, Gallo Cassarino, Tiziano, Raffle, Jade, Hubb, Jonathan, Ferns, R Bridget, Waters, Laura, Tong, C Y William, Kozlakidis, Zisis, Hayward, Andrew, Kellam, Paul, Pillay, Deenan, Clark, Duncan, Nastouli, Eleni, Leigh Brown, Andrew J

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RNA-seq analysis of host and viral gene expression highlights interaction between varicella zoster virus and keratinocyte differentiation by Jones, Meleri, Dry, Inga R, Frampton, Dan, Singh, Manuraj, Kanda, Ravinder K, Yee, Michael B, Kellam, Paul, Hollinshead, Michael, Kinchington, Paul R, O'Toole, Edel A, Breuer, Judith

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Molecular evolution of broadly neutralizing Llama antibodies to the CD4-binding site of HIV-1 by McCoy, Laura E, Rutten, Lucy, Frampton, Dan, Anderson, Ian, Granger, Luke, Bashford-Rogers, Rachael, Dekkers, Gillian, Strokappe, Nika M, Seaman, Michael S, Koh, Willie, Grippo, Vanina, Kliche, Alexander, Verrips, Theo, Kellam, Paul, Fassati, Ariberto, Weiss, Robin A

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Host genetic variants and gene expression patterns associated with Epstein-Barr virus copy number in lymphoblastoid cell lines by Houldcroft, Charlotte J, Petrova, Velislava, Liu, Jimmy Z, Frampton, Dan, Anderson, Carl A, Gall, Astrid, Kellam, Paul

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Genomic characteristics and clinical effect of the emergent SARS-CoV-2 B.1.1.7 lineage in London, UK: a whole-genome sequencing and hospital-based cohort study by Frampton, Dan, Rampling, Tommy, Cross, Aidan, Bailey, Heather, Heaney, Judith, Byott, Matthew, Scott, Rebecca, Sconza, Rebecca, Price, Joseph, Margaritis, Marios, Bergstrom, Malin, Spyer, Moira J, Miralhes, Patricia B, Grant, Paul, Kirk, Stuart, Valerio, Chris, Mangera, Zaheer, Prabhahar, Thaventhran, Moreno-Cuesta, Jeronimo, Arulkumaran, Nish, Singer, Mervyn, Shin, Gee Yen, Sanchez, Emilie, Paraskevopoulou, Stavroula M, Pillay, Deenan, McKendry, Rachel A, Mirfenderesky, Mariyam, Houlihan, Catherine F, Nastouli, Eleni

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Use of Whole-Genome Sequencing in the Investigation of a Nosocomial Influenza Virus Outbreak by Houlihan, Catherine F, Frampton, Dan, Ferns, R Bridget, Raffle, Jade, Grant, Paul, Reidy, Myriam, Hail, Leila, Thomson, Kirsty, Mattes, Frank, Kozlakidis, Zisis, Pillay, Deenan, Hayward, Andrew, Nastouli, Eleni

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Deep sequencing of HIV-1 reveals extensive subtype variation and drug resistance after failure of first-line antiretroviral regimens in Nigeria by El Bouzidi, Kate, Datir, Rawlings P., Kwaghe, Vivian, Roy, Sunando, Frampton, Dan, Breuer, Judith, Ogbanufe, Obinna, Murtala-Ibrahim, Fati, Charurat, Man, Dakum, Patrick, Sabin, Caroline A., Ndembi, Nicaise, Gupta, Ravindra K.

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Limited emergence of resistance to integrase strand transfer inhibitors (INSTIs) in ART-experienced participants failing dolutegravir-based antiretroviral therapy: a cross-sectiona... by Abdullahi, Adam, Kida, Ibrahim Musa, Maina, Umar Abdullahi, Ibrahim, Amina Husaini, Mshelia, James, Wisso, Haruna, Adamu, Abdullahi, Onyemata, James Ezenwa, Edun, Martin, Yusuph, Haruna, Aliyu, Sani H, Charurat, Man, Abimiku, Alash’le, Abeler-Dorner, Lucie, Fraser, Christophe, Bonsall, David, Kemp, Steven A, Gupta, Ravindra K

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Molecular Signatures of Regression of the Canine Transmissible Venereal Tumor by Frampton, Dan, Schwenzer, Hagen, Marino, Gabriele, Butcher, Lee M., Pollara, Gabriele, Kriston-Vizi, Janos, Venturini, Cristina, Austin, Rachel, de Castro, Karina Ferreira, Ketteler, Robin, Chain, Benjamin, Goldstein, Richard A., Weiss, Robin A., Beck, Stephan, Fassati, Ariberto

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High prevalence of integrase mutation L74I in West African HIV-1 subtypes prior to integrase inhibitor treatment by El Bouzidi, Kate, Kemp, Steven A, Datir, Rawlings P, Murtala-Ibrahim, Fati, Aliyu, Ahmad, Kwaghe, Vivian, Frampton, Dan, Roy, Sunando, Breuer, Judith, Sabin, Caroline A, Ogbanufe, Obinna, Charurat, Man E, Bonsall, David, Golubchik, Tanya, Fraser, Christophe, Dakum, Patrick, Ndembi, Nicaise, Gupta, Ravindra K

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Mapping of HIV-1C Transmission Networks Reveals Extensive Spread of Viral Lineages Across Villages in Botswana Treatment-as-Prevention Trial by Novitsky, Vlad, Zahralban-Steele, Melissa, Moyo, Sikhulile, Nkhisang, Tapiwa, Maruapula, Dorcas, McLane, Mary Fran, Leidner, Jean, Bennett, Kara, Wirth, Kathleen E, Gaolathe, Tendani, Kadima, Etienne, Chakalisa, Unoda, Pretorius Holme, Molly, Lockman, Shahin, Mmalane, Mompati, Makhema, Joseph, Gaseitsiwe, Simani, DeGruttola, Victor, Essex, M

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Development of a novel application for visualising infectious diseases in hospital settings by Smith, Catherine M, Kozlakidis, Zisis, Frampton, Dan, Nastouli, Eleni, Coen, Pietro G, Pillay, Deenan, Hayward, Andrew

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The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study by Boshier, Florencia A.T., Venturini, Cristina, Stirrup, Oliver, Guerra-Assunção, José Afonso, Alcolea-Medina, Adela, Becket, Angela H., Byott, Matthew, Charalampous, Themoula, Filipe, Ana da Silva, Frampton, Dan, Glaysher, Sharon, Khan, Tabassum, Kulasegara-Shylini, Raghavendran, Kele, Beatrix, Monahan, Irene M., Mollett, Guy, Parker, Matthew, Pelosi, Emanuela, Randell, Paul, Roy, Sunando, Taylor, Joshua F., Weller, Sophie J., Wilson-Davies, Eleri, Wade, Phillip, Williams, Rachel, Copas, Andrew J., Cutino-Moguel, Teresa, Freemantle, Nick, Hayward, Andrew C., Holmes, Alison, Hughes, Joseph, Mahungu, Tabitha W., Nebbia, Gaia, Nastouli, Eleni, Partridge, David G., Pope, Cassie F., Price, James R., Robson, Samuel C., Saeed, Kordo, Shin, Gee Yen, de Silva, Thushan I., Snell, Luke B., Thomson, Emma C., Witney, Adam A., Breuer, Judith

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Using nearly full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic by Yebra, Gonzalo, Hodcroft, Emma B., Ragonnet-Cronin, Manon L., Pillay, Deenan, Brown, Andrew J. Leigh, Fraser, Christophe, Kellam, Paul, de Oliveira, Tulio, Dennis, Ann, Hoppe, Anne, Kityo, Cissy, Frampton, Dan, Ssemwanga, Deogratius, Tanser, Frank, Keshani, Jagoda, Lingappa, Jairam, Herbeck, Joshua, Wawer, Maria, Essex, Max, Cohen, Myron S., Paton, Nicholas, Ratmann, Oliver, Kaleebu, Pontiano, Hayes, Richard, Fidler, Sarah, Quinn, Thomas, Novitsky, Vladimir, Haywards, Andrew, Nastouli, Eleni, Morris, Steven, Clark, Duncan, Kozlakidis, Zisis

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Immediate T-Helper 17 Polarization Upon Triggering CD11b/c on HIV-Exposed Dendritic Cells by Wilflingseder, Doris, Schroll, Andrea, Hackl, Hubert, Gallasch, Ralf, Frampton, Dan, Lass-Flörl, Cornelia, Pancino, Gianfranco, Saez-Cirion, Asier, Lambotte, Olivier, Weiss, Laurence, Kellam, Paul, Trajanoski, Zlatko, Geijtenbeek, Teunis, Weiss, Günter, Posch, Wilfried

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SARS-CoV-2 lineage B.1.1.7 is associated with greater disease severity among hospitalised women but not men: multicentre cohort study by Stirrup, Oliver, Boshier, Florencia, Venturini, Cristina, Guerra-Assunção, José Afonso, Alcolea-Medina, Adela, Beckett, Angela, Charalampous, Themoula, da Silva Filipe, Ana, Glaysher, Sharon, Khan, Tabassum, Kulasegaran Shylini, Raghavendran, Monahan, Irene, Mollett, Guy, Pelosi, Emanuela, Randell, Paul, Roy, Sunando, Taylor, Joshua, Weller, Sophie, Wade, Phillip, Williams, Rachel, Copas, Andrew, Cutino-Moguel, Maria-Teresa, Freemantle, Nick, Hayward, Andrew C, Holmes, Alison, Hughes, Joseph, Mahungu, Tabitha, Nebbia, Gaia, Partridge, David, Pope, Cassie, Price, James, Robson, Samuel, Saeed, Kordo, de Silva, Thushan, Snell, Luke, Thomson, Emma, Witney, Adam A, Breuer, Judith, Blackstone, James, Hockey, Leanne, Marley, Georgia, Harrington, David, Riddell, Anna, Peters, Christine, Patel, Bindi, Williams, Tom G S, Batra, Rahul, Madona, Pinglawathee, Cox, Alison, Hart, Jennifer, Haque, Tanzina, Irish, Dianne, Pang, Juanita, Williams, Charlotte, Tutill, Helena, Bayzid, Nadua, Cotic, Marius, Green, Luke, Lindsey, Benjamin, State, Amy, Cope, Alison, Johnson, Katie, Angyal, Adrienn, Zhang, Peijun, Whiteley, Max, Ramalho, Marta Gallis, Christou, Stella, Louka, Stavroula, Hornsby, Hailey, Foulkes, Benjamin, Wolverson, Paige, Heffer, Joe, Smith, Nikki, Goudarzi, Salman, Fearn, Chris, Cook, Kate, Loveson, Katie, Elliott, Scott, Samaraweera, Buddhini, Silveira, Siona, Aplin, Stephen, Jeremiah, Sarah, Umpleby, Helen, Wheeler, Helen, Harvey, Matthew, Prieto, Jacqui, Laing, Kenneth, Tan, Ngee Keong, Pereira, Claudia Cardoso, Nastouli, Eleni, Houlihan, Catherine F, Frampton, Dan, Rampling, Tommy, Heaney, Judith, Shin, Gee Yen, Spyer, Moira, Bergstrom, Malin, Sanchez, Emilie, Paraskevopoulou, Stavroula M, Margaritis, Marios

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Nosocomial transmission of influenza: A retrospective cross‐sectional study using next generation sequencing at a hospital in England (2012‐2014) by Blackburn, Ruth M., Frampton, Dan, Smith, Catherine M., Fragaszy, Ellen B., Watson, Simon J., Ferns, R. Bridget, Binter, Špela, Coen, Pietro G., Grant, Paul, Shallcross, Laura J., Kozlakidis, Zisis, Pillay, Deenan, Kellam, Paul, Hué, Stéphane, Nastouli, Eleni, Hayward, Andrew C., Kinghorn, Jane, Wurie, Fatima, Rahman, Saadia, Johnson, Anne, Dunn, David, Leigh‐Brown, Andrew, Morris, Steven, Irving, William, Clark, Duncan, Zambon, Maria

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