Evaluating whole HIV-1 genome sequence for estimation of incidence and migration in a rural South African community [version 1; peer review: 1 approved, 2 approved with reservation... מאת Erik Volz, Anne Derache, Tanya Golubchik, Christophe Fraser, Fabrícia F Nascimento, Siva Danaviah, Manon Ragonnet-Cronin

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Identification of antigens specific to non-tuberculous mycobacteria: the Mce family of proteins as a target of T cell immune responses. מאת Anna M Checkley, David H Wyllie, Thomas J Scriba, Tanya Golubchik, Adrian V S Hill, Willem A Hanekom, Helen McShane

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Recombination and population structure in Salmonella enterica. מאת Xavier Didelot, Rory Bowden, Teresa Street, Tanya Golubchik, Chris Spencer, Gil McVean, Vartul Sangal, Muna F Anjum, Mark Achtman, Daniel Falush, Peter Donnelly

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Asymptomatic Clostridium difficile colonisation and onward transmission. מאת David W Eyre, David Griffiths, Alison Vaughan, Tanya Golubchik, Milind Acharya, Lily O'Connor, Derrick W Crook, A Sarah Walker, Tim E A Peto

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Oxford Screening CSF and Respiratory samples (‘OSCAR’): results of a pilot study to screen clinical samples from a diagnostic microbiology laboratory for viruses using Illumina nex... מאת Colin Sharp, Tanya Golubchik, William F. Gregory, Anna L. McNaughton, Nicholas Gow, Mathyruban Selvaratnam, Alina Mirea, Dona Foster, Monique Andersson, Paul Klenerman, Katie Jeffery, Philippa C. Matthews

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Phylogenetic and Demographic Characterization of Directed HIV-1 Transmission Using Deep Sequences from High-Risk and General Population Cohorts/Groups in Uganda מאת Nicholas Bbosa, Deogratius Ssemwanga, Alfred Ssekagiri, Xiaoyue Xi, Yunia Mayanja, Ubaldo Bahemuka, Janet Seeley, Deenan Pillay, Lucie Abeler-Dörner, Tanya Golubchik, Christophe Fraser, Pontiano Kaleebu, Oliver Ratmann, on behalf of the MRC/UVRI & LSHTM Uganda Research Unit and The PANGEA Consortium

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

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Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial – BCPP/Ya Tsie trial מאת Lerato E Magosi, Yinfeng Zhang, Tanya Golubchik, Victor DeGruttola, Eric Tchetgen Tchetgen, Vladimir Novitsky, Janet Moore, Pam Bachanas, Tebogo Segolodi, Refeletswe Lebelonyane, Molly Pretorius Holme, Sikhulile Moyo, Joseph Makhema, Shahin Lockman, Christophe Fraser, Myron Max Essex, Marc Lipsitch, On behalf of The Botswana Combination Prevention Project and PANGEA consortium

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Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses מאת Sarah Buddle, Leysa Forrest, Naomi Akinsuyi, Luz Marina Martin Bernal, Tony Brooks, Cristina Venturini, Charles Miller, Julianne R. Brown, Nathaniel Storey, Laura Atkinson, Timothy Best, Sunando Roy, Sian Goldsworthy, Sergi Castellano, Peter Simmonds, Heli Harvala, Tanya Golubchik, Rachel Williams, Judith Breuer, Sofia Morfopoulou, Oscar Enrique Torres Montaguth

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A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples. מאת Elizabeth M Batty, T H Nicholas Wong, Amy Trebes, Karène Argoud, Moustafa Attar, David Buck, Camilla L C Ip, Tanya Golubchik, Madeleine Cule, Rory Bowden, Charis Manganis, Paul Klenerman, Eleanor Barnes, A Sarah Walker, David H Wyllie, Daniel J Wilson, Kate E Dingle, Tim E A Peto, Derrick W Crook, Paolo Piazza

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Severe infections emerge from commensal bacteria by adaptive evolution מאת Bernadette C Young, Chieh-Hsi Wu, N Claire Gordon, Kevin Cole, James R Price, Elian Liu, Anna E Sheppard, Sanuki Perera, Jane Charlesworth, Tanya Golubchik, Zamin Iqbal, Rory Bowden, Ruth C Massey, John Paul, Derrick W Crook, Timothy E Peto, A Sarah Walker, Martin J Llewelyn, David H Wyllie, Daniel J Wilson

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Publisher Correction: Distinct patterns of within-host virus populations between two subgroups of human respiratory syncytial virus מאת Gu-Lung Lin, Simon B. Drysdale, Matthew D. Snape, Daniel O’Connor, Anthony Brown, George MacIntyre-Cockett, Esther Mellado-Gomez, Mariateresa de Cesare, David Bonsall, M. Azim Ansari, Deniz Öner, Jeroen Aerssens, Christopher Butler, Louis Bont, Peter Openshaw, Federico Martinón-Torres, Harish Nair, Rory Bowden, RESCEU Investigators, Tanya Golubchik, Andrew J. Pollard

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Distinct patterns of within-host virus populations between two subgroups of human respiratory syncytial virus מאת Gu-Lung Lin, Simon B. Drysdale, Matthew D. Snape, Daniel O’Connor, Anthony Brown, George MacIntyre-Cockett, Esther Mellado-Gomez, Mariateresa de Cesare, David Bonsall, M. Azim Ansari, Deniz Öner, Jeroen Aerssens, Christopher Butler, Louis Bont, Peter Openshaw, Federico Martinón-Torres, Harish Nair, Rory Bowden, RESCEU Investigators, Tanya Golubchik, Andrew J. Pollard

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Within-host evolution of Staphylococcus aureus during asymptomatic carriage. מאת Tanya Golubchik, Elizabeth M Batty, Ruth R Miller, Helen Farr, Bernadette C Young, Hanna Larner-Svensson, Rowena Fung, Heather Godwin, Kyle Knox, Antonina Votintseva, Richard G Everitt, Teresa Street, Madeleine Cule, Camilla L C Ip, Xavier Didelot, Timothy E A Peto, Rosalind M Harding, Daniel J Wilson, Derrick W Crook, Rory Bowden

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Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis מאת Oliver Ratmann, M. Kate Grabowski, Matthew Hall, Tanya Golubchik, Chris Wymant, Lucie Abeler-Dörner, David Bonsall, Anne Hoppe, Andrew Leigh Brown, Tulio de Oliveira, Astrid Gall, Paul Kellam, Deenan Pillay, Joseph Kagaayi, Godfrey Kigozi, Thomas C. Quinn, Maria J. Wawer, Oliver Laeyendecker, David Serwadda, Ronald H. Gray, Christophe Fraser, PANGEA Consortium and Rakai Health Sciences Program

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

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Correction: Corrigendum: Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis מאת Phelim Bradley, N. Claire Gordon, Timothy M. Walker, Laura Dunn, Simon Heys, Bill Huang, Sarah Earle, Louise J. Pankhurst, Luke Anson, Mariateresa de Cesare, Paolo Piazza, Antonina A. Votintseva, Tanya Golubchik, Daniel J. Wilson, David H. Wyllie, Roland Diel, Stefan Niemann, Silke Feuerriegel, Thomas A. Kohl, Nazir Ismail, Shaheed V. Omar, E. Grace Smith, David Buck, Gil McVean, A. Sarah Walker, Tim E. A. Peto, Derrick W. Crook, Zamin Iqbal

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Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil מאת Sue Ann Costa Clemens, Pedro M. Folegatti, Katherine R. W. Emary, Lily Yin Weckx, Jeremy Ratcliff, Sagida Bibi, Ana Verena De Almeida Mendes, Eveline Pipolo Milan, Ana Pittella, Alexandre V. Schwarzbold, Eduardo Sprinz, Parvinder K. Aley, David Bonsall, Christophe Fraser, Michelle Fuskova, Sarah C. Gilbert, Daniel Jenkin, Sarah Kelly, Simon Kerridge, Teresa Lambe, Natalie G. Marchevsky, Yama F. Mujadidi, Emma Plested, Maheshi N. Ramasamy, Peter Simmonds, Tanya Golubchik, Merryn Voysey, Andrew J. Pollard, the AMPHEUS Project, Oxford COVID Vaccine Trial Team

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Correction: Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sa... מאת Helen R Fryer, Tanya Golubchik, Matthew Hall, Christophe Fraser, Robert Hinch, Luca Ferretti, Laura Thomson, Anel Nurtay, Lorenzo Pellis, Thomas House, George MacIntyre-Cockett, Amy Trebes, David Buck, Paolo Piazza, Angie Green, Lorne J Lonie, Darren Smith, Matthew Bashton, Matthew Crown, Andrew Nelson, Clare M McCann, Mohammed Adnan Tariq, Claire J Elstob, Rui Nunes Dos Santos, Zack Richards, Xin Xhang, Joseph Hawley, Mark R Lee, Priscilla Carrillo-Barragan, Isobel Chapman, Sarah Harthern-Flint, COVID-19 Genomics UK (COG-UK) consortium, David Bonsall, Katrina A Lythgoe

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Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias. מאת Helen R Fryer, Tanya Golubchik, Matthew Hall, Christophe Fraser, Robert Hinch, Luca Ferretti, Laura Thomson, Anel Nurtay, Lorenzo Pellis, Thomas House, George MacIntyre-Cockett, Amy Trebes, David Buck, Paolo Piazza, Angie Green, Lorne J Lonie, Darren Smith, Matthew Bashton, Matthew Crown, Andrew Nelson, Clare M McCann, Mohammed Adnan Tariq, Claire J Elstob, Rui Nunes Dos Santos, Zack Richards, Xin Xhang, Joseph Hawley, Mark R Lee, Priscilla Carrillo-Barragan, Isobel Chapman, Sarah Harthern-Flint, COVID-19 Genomics UK (COG-UK) consortium, David Bonsall, Katrina A Lythgoe

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