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1. Multiplex MinION sequencing suggests enteric adenovirus F41 genetic diversity comparable to pre-COVID-19 era.

Author

Maes, Mailis, Khokhar, Fahad, Wilkinson, Sam, Smith, Andrew, Kovalenko, Ganna, Dougan, Gordon, Quick, Joshua, Loman, Nicholas, Baker, Stephen, Curran, Martin, Skittrall, Jordan, and Houldcroft, Charlotte

Subjects
DNA virus, adenovirus, genetic epidemiology, genomics, hepatitis, virology, Humans, Child, COVID-19, Pandemics, Sequence Analysis, Adenoviridae, Adenoviridae Infections, Genetic Variation
Abstract

Human adenovirus F41 causes acute gastroenteritis in children, and has recently been associated with an apparent increase in paediatric hepatitis of unknown aetiology in the UK, with further cases reported in multiple countries. Relatively little is known about the genetic diversity of adenovirus F41 in UK children; and it is unclear what, if any, impact the COVID-19 pandemic has had on viral diversity in the UK. Methods that allow F41 to be sequenced from clinical samples without the need for viral culture are required to provide the genomic data to address these questions. Therefore, we evaluated an overlapping-amplicon method of sequencing adenovirus genomes from clinical samples using Oxford Nanopore technology. We applied this method to a small sample of adenovirus-species-F-positive extracts collected as part of standard care in the East of England region in January-May 2022. This method produced genomes with >75 % coverage in 13/22 samples and >50 % coverage in 19/22 samples. We identified two F41 lineages present in paediatric patients in the East of England in 2022. Where F41 genomes from paediatric hepatitis cases were available (n=2), these genomes fell within the diversity of F41 from the UK and continental Europe sequenced before and after the 2020-2021 phase of the COVID-19 pandemic. Our analyses suggest that overlapping amplicon sequencing is an appropriate method for generating F41 genomic data from high-virus-load clinical samples, and currently circulating F41 viral lineages were present in the UK and Europe before the COVID-19 pandemic.

Published
2023

2. Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable

Author

Mavian, Carla, Pond, Sergei Kosakovsky, Marini, Simone, Magalis, Brittany Rife, Vandamme, Anne-Mieke, Dellicour, Simon, Scarpino, Samuel V., Houldcroft, Charlotte, Villabona-Arenas, Julian, Paisie, Taylor K., Trovão, Nídia S., Boucher, Christina, Zhang, Yun, Scheuermann, Richard H., Gascuel, Olivier, Lam, Tommy Tsan-Yuk, Suchard, Marc A., Abecasis, Ana, Wilkinson, Eduan, de Oliveira, Tulio, Bento, Ana I., Schmidt, Heiko A., Martin, Darren, Hadfield, James, Faria, Nuno, Grubaugh, Nathan D., Neher, Richard A., Baele, Guy, Lemey, Philippe, Stadler, Tanja, Albert, Jan, Crandall, Keith A., Leitner, Thomas, Stamatakis, Alexandros, Prosperi, Mattia, and Salemi, Marco

Published
2020

4. Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Author

Koshy, Cherian, Wise, Emma, Cortes, Nick, Lynch, Jessica, Kidd, Stephen, Mori, Matilde, Fairley, Derek J., Curran, Tanya, McKenna, James P., Adams, Helen, Fraser, Christophe, Golubchik, Tanya, Bonsall, David, Moore, Catrin, Caddy, Sarah L., Khokhar, Fahad A., Wantoch, Michelle, Reynolds, Nicola, Warne, Ben, Maksimovic, Joshua, Spellman, Karla, McCluggage, Kathryn, John, Michaela, Beer, Robert, Afifi, Safiah, Morgan, Sian, Marchbank, Angela, Price, Anna, Kitchen, Christine, Gulliver, Huw, Merrick, Ian, Southgate, Joel, Guest, Martyn, Munn, Robert, Workman, Trudy, Connor, Thomas R., Fuller, William, Bresner, Catherine, Snell, Luke B., Charalampous, Themoula, Nebbia, Gaia, Batra, Rahul, Edgeworth, Jonathan, Robson, Samuel C., Beckett, Angela, Loveson, Katie F., Aanensen, David M., Underwood, Anthony P., Yeats, Corin A., Abudahab, Khalil, Taylor, Ben E.W., Menegazzo, Mirko, Clark, Gemma, Smith, Wendy, Khakh, Manjinder, Fleming, Vicki M., Lister, Michelle M., Howson-Wells, Hannah C., Berry, Louise, Boswell, Tim, Joseph, Amelia, Willingham, Iona, Bird, Paul, Helmer, Thomas, Fallon, Karlie, Holmes, Christopher, Tang, Julian, Raviprakash, Veena, Campbell, Sharon, Sheriff, Nicola, Loose, Matthew W., Holmes, Nadine, Moore, Christopher, Carlile, Matthew, Wright, Victoria, Sang, Fei, Debebe, Johnny, Coll, Francesc, Signell, Adrian W., Betancor, Gilberto, Wilson, Harry D., Feltwell, Theresa, Houldcroft, Charlotte J., Eldirdiri, Sahar, Kenyon, Anita, Davis, Thomas, Pybus, Oliver, du Plessis, Louis, Zarebski, Alex, Raghwani, Jayna, Kraemer, Moritz, Francois, Sarah, Attwood, Stephen, Vasylyeva, Tetyana, Torok, M. Estee, Hamilton, William L., Goodfellow, Ian G., Hall, Grant, Jahun, Aminu S., Chaudhry, Yasmin, Hosmillo, Myra, Pinckert, Malte L., Georgana, Iliana, Yakovleva, Anna, Meredith, Luke W., Moses, Samuel, Lowe, Hannah, Ryan, Felicity, Fisher, Chloe L., Awan, Ali R., Boyes, John, Breuer, Judith, Harris, Kathryn Ann, Brown, Julianne Rose, Shah, Divya, Atkinson, Laura, Lee, Jack C.D., Alcolea-Medina, Adela, Moore, Nathan, Cortes, Nicholas, Williams, Rebecca, Chapman, Michael R., Levett, Lisa J., Heaney, Judith, Smith, Darren L., Bashton, Matthew, Young, Gregory R., Allan, John, Loh, Joshua, Randell, Paul A., Cox, Alison, Madona, Pinglawathee, Holmes, Alison, Bolt, Frances, Price, James, Mookerjee, Siddharth, Rowan, Aileen, Taylor, Graham P., Ragonnet-Cronin, Manon, Nascimento, Fabricia F., Jorgensen, David, Siveroni, Igor, Johnson, Rob, Boyd, Olivia, Geidelberg, Lily, Volz, Erik M., Brunker, Kirstyn, Smollett, Katherine L., Loman, Nicholas J., Quick, Joshua, McMurray, Claire, Stockton, Joanne, Nicholls, Sam, Rowe, Will, Poplawski, Radoslaw, Martinez-Nunez, Rocio T., Mason, Jenifer, Robinson, Trevor I., O'Toole, Elaine, Watts, Joanne, Breen, Cassie, Cowell, Angela, Ludden, Catherine, Sluga, Graciela, Machin, Nicholas W., Ahmad, Shazaad S.Y., George, Ryan P., Halstead, Fenella, Sivaprakasam, Venkat, Thomson, Emma C., Shepherd, James G., Asamaphan, Patawee, Niebel, Marc O., Li, Kathy K., Shah, Rajiv N., Jesudason, Natasha G., Parr, Yasmin A., Tong, Lily, Broos, Alice, Mair, Daniel, Nichols, Jenna, Carmichael, Stephen N., Nomikou, Kyriaki, Aranday-Cortes, Elihu, Johnson, Natasha, Starinskij, Igor, da Silva Filipe, Ana, Robertson, David L., Orton, Richard J., Hughes, Joseph, Vattipally, Sreenu, Singer, Joshua B., Hale, Antony D., Macfarlane-Smith, Louissa R., Harper, Katherine L., Taha, Yusri, Payne, Brendan A.I., Burton-Fanning, Shirelle, Waugh, Sheila, Collins, Jennifer, Eltringham, Gary, Templeton, Kate E., McHugh, Martin P., Dewar, Rebecca, Wastenge, Elizabeth, Dervisevic, Samir, Stanley, Rachael, Prakash, Reenesh, Stuart, Claire, Elumogo, Ngozi, Sethi, Dheeraj K., Meader, Emma J., Coupland, Lindsay J., Potter, Will, Graham, Clive, Barton, Edward, Padgett, Debra, Scott, Garren, Swindells, Emma, Greenaway, Jane, Nelson, Andrew, Yew, Wen C., Resende Silva, Paola C., Andersson, Monique, Shaw, Robert, Peto, Timothy, Justice, Anita, Eyre, David, Crooke, Derrick, Hoosdally, Sarah, Sloan, Tim J., Duckworth, Nichola, Walsh, Sarah, Chauhan, Anoop J., Glaysher, Sharon, Bicknell, Kelly, Wyllie, Sarah, Butcher, Ethan, Elliott, Scott, Lloyd, Allyson, Impey, Robert, Levene, Nick, Monaghan, Lynn, Bradley, Declan T., Allara, Elias, Pearson, Clare, Muir, Peter, Vipond, Ian B., Hopes, Richard, Pymont, Hannah M., Hutchings, Stephanie, Curran, Martin D., Parmar, Surendra, Lackenby, Angie, Mbisa, Tamyo, Platt, Steven, Miah, Shahjahan, Bibby, David, Manso, Carmen, Hubb, Jonathan, Chand, Meera, Dabrera, Gavin, Ramsay, Mary, Bradshaw, Daniel, Thornton, Alicia, Myers, Richard, Schaefer, Ulf, Groves, Natalie, Gallagher, Eileen, Lee, David, Williams, David, Ellaby, Nicholas, Harrison, Ian, Hartman, Hassan, Manesis, Nikos, Patel, Vineet, Bishop, Chloe, Chalker, Vicki, Osman, Husam, Bosworth, Andrew, Robinson, Esther, Holden, Matthew T.G., Shaaban, Sharif, Birchley, Alec, Adams, Alexander, Davies, Alisha, Gaskin, Amy, Plimmer, Amy, Gatica-Wilcox, Bree, McKerr, Caoimhe, Moore, Catherine, Williams, Chris, Heyburn, David, De Lacy, Elen, Hilvers, Ember, Downing, Fatima, Shankar, Giri, Jones, Hannah, Asad, Hibo, Coombes, Jason, Watkins, Joanne, Evans, Johnathan M., Fina, Laia, Gifford, Laura, Gilbert, Lauren, Graham, Lee, Perry, Malorie, Morgan, Mari, Bull, Matthew, Cronin, Michelle, Pacchiarini, Nicole, Craine, Noel, Jones, Rachel, Howe, Robin, Corden, Sally, Rey, Sara, Kumziene-Summerhayes, Sara, Taylor, Sarah, Cottrell, Simon, Jones, Sophie, Edwards, Sue, O’Grady, Justin, Page, Andrew J., Wain, John, Webber, Mark A., Mather, Alison E., Baker, David J., Rudder, Steven, Yasir, Muhammad, Thomson, Nicholas M., Aydin, Alp, Tedim, Ana P., Kay, Gemma L., Trotter, Alexander J., Gilroy, Rachel A.J., Alikhan, Nabil-Fareed, de Oliveira Martins, Leonardo, Le-Viet, Thanh, Meadows, Lizzie, Kolyva, Anastasia, Diaz, Maria, Bell, Andrew, Gutierrez, Ana Victoria, Charles, Ian G., Adriaenssens, Evelien M., Kingsley, Robert A., Casey, Anna, Simpson, David A., Molnar, Zoltan, Thompson, Thomas, Acheson, Erwan, Masoli, Jane A.H., Knight, Bridget A., Hattersley, Andrew, Ellard, Sian, Auckland, Cressida, Mahungu, Tabitha W., Irish-Tavares, Dianne, Haque, Tanzina, Bourgeois, Yann, Scarlett, Garry P., Partridge, David G., Raza, Mohammad, Evans, Cariad, Johnson, Kate, Liggett, Steven, Baker, Paul, Essex, Sarah, Lyons, Ronan A., Caller, Laura G., Castellano, Sergi, Williams, Rachel J., Kristiansen, Mark, Roy, Sunando, Williams, Charlotte A., Dyal, Patricia L., Tutill, Helena J., Panchbhaya, Yasmin N., Forrest, Leysa M., Niola, Paola, Findlay, Jacqueline, Brooks, Tony T., Gavriil, Artemis, Mestek-Boukhibar, Lamia, Weeks, Sam, Pandey, Sarojini, Berry, Lisa, Jones, Katie, Richter, Alex, Beggs, Andrew, Smith, Colin P., Bucca, Giselda, Hesketh, Andrew R., Harrison, Ewan M., Peacock, Sharon J., Palmer, Sophie, Churcher, Carol M., Bellis, Katherine L., Girgis, Sophia T., Naydenova, Plamena, Blane, Beth, Sridhar, Sushmita, Ruis, Chris, Forrest, Sally, Cormie, Claire, Gill, Harmeet K., Dias, Joana, Higginson, Ellen E., Maes, Mailis, Young, Jamie, Kermack, Leanne M., Hadjirin, Nazreen F., Aggarwal, Dinesh, Griffith, Luke, Swingler, Tracey, Davidson, Rose K., Rambaut, Andrew, Williams, Thomas, Balcazar, Carlos E., Gallagher, Michael D., O'Toole, Áine, Rooke, Stefan, Jackson, Ben, Colquhoun, Rachel, Ashworth, Jordan, Hill, Verity, McCrone, J.T., Scher, Emily, Yu, Xiaoyu, Williamson, Kathleen A., Stanton, Thomas D., Michell, Stephen L., Bewshea, Claire M., Temperton, Ben, Michelsen, Michelle L., Warwick-Dugdale, Joanna, Manley, Robin, Farbos, Audrey, Harrison, James W., Sambles, Christine M., Studholme, David J., Jeffries, Aaron R., Darby, Alistair C., Hiscox, Julian A., Paterson, Steve, Iturriza-Gomara, Miren, Jackson, Kathryn A., Lucaci, Anita O., Vamos, Edith E., Hughes, Margaret, Rainbow, Lucille, Eccles, Richard, Nelson, Charlotte, Whitehead, Mark, Turtle, Lance, Haldenby, Sam T., Gregory, Richard, Gemmell, Matthew, Kwiatkowski, Dominic, de Silva, Thushan I., Smith, Nikki, Angyal, Adrienn, Lindsey, Benjamin B., Groves, Danielle C., Green, Luke R., Wang, Dennis, Freeman, Timothy M., Parker, Matthew D., Keeley, Alexander J., Parsons, Paul J., Tucker, Rachel M., Brown, Rebecca, Wyles, Matthew, Constantinidou, Chrystala, Unnikrishnan, Meera, Ott, Sascha, Cheng, Jeffrey K.J., Bridgewater, Hannah E., Frost, Lucy R., Taylor-Joyce, Grace, Stark, Richard, Baxter, Laura, Alam, Mohammad T., Brown, Paul E., McClure, Patrick C., Chappell, Joseph G., Tsoleridis, Theocharis, Ball, Jonathan, Grammatopoulos, Dimitris, Buck, David, Todd, John A., Green, Angie, Trebes, Amy, MacIntyre-Cockett, George, de Cesare, Mariateresa, Langford, Cordelia, Alderton, Alex, Amato, Roberto, Goncalves, Sonia, Jackson, David K., Johnston, Ian, Sillitoe, John, Palmer, Steve, Lawniczak, Mara, Berriman, Matt, Danesh, John, Livett, Rich, Shirley, Lesley, Farr, Ben, Quail, Mike, Thurston, Scott, Park, Naomi, Betteridge, Emma, Weldon, Danni, Goodwin, Scott, Nelson, Rachel, Beaver, Charlotte, Letchford, Laura, Jackson, David A., Foulser, Luke, McMinn, Liz, Prestwood, Liam, Kay, Sally, Kane, Leanne, Dorman, Matthew J., Martincorena, Inigo, Puethe, Christoph, Keatley, Jon-Paul, Tonkin-Hill, Gerry, Smith, Christen, Jamrozy, Dorota, Beale, Mathew A., Patel, Minal, Ariani, Cristina, Spencer-Chapman, Michael, Drury, Eleanor, Lo, Stephanie, Rajatileka, Shavanthi, Scott, Carol, James, Keith, Buddenborg, Sarah K., Berger, Duncan J., Patel, Gaurang, Garcia-Casado, Maria V., Dibling, Thomas, McGuigan, Samantha, Rogers, Hazel A., Hunter, Adam D., Souster, Emily, Neaverson, Alexandra S., Volz, Erik, McCrone, John T., O’Toole, Áine, Johnson, Robert, Rey, Sara M., Nicholls, Samuel M., Colquhoun, Rachel M., Shepherd, James, Pascall, David J., Shah, Rajiv, Jesudason, Natasha, Li, Kathy, Jarrett, Ruth, Goodfellow, Ian, and Pybus, Oliver G.

Published
2021
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5. Multispecies Cocirculation of Adenoviruses Identified by Next-Generation Sequencing During an Acute Gastroenteritis Outbreak in Coastal Kenya in 2023.

Author

Lambisia, Arnold W, Mutunga, Martin, Katama, Esther N, Agoti, Charles N, and Houldcroft, Charlotte J

Subjects
HOSPITAL care of children, POLYMERASE chain reaction, NUCLEOTIDE sequencing, BINDING sites, GASTROENTERITIS
Abstract

Background Although 7 human adenovirus (HAdV) species are known to exist, only F (types 40 and 41) and G are identified as diarrheal disease agents. The role of other HAdV species in diarrheal disease remains unclear, and data on their prevalence are limited. We describe HAdV species and types in hospitalized children with diarrhea in coastal Kenya. Methods Three hundred twenty-nine stool samples collected between June 2022 and August 2023 from children aged <13 years were screened for HAdV using quantitative polymerase chain reaction (qPCR). Positive HAdV cases were genotyped by adenovirus primers from the RespiCoV panel by amplification, next-generation sequencing, and phylogenetic analysis. Results Sixty-five samples (20%) tested HadV positive, of which 5 HAdV species were identified. Other than HAdV F, other species included A, B, C, and D; these were detected as either mono-detections or coinfections. Six HAdV F identified by NGS had been missed by our qPCR typing method. This appeared to be as a result of a 133-nucleotide deletion in the long fiber protein, which abrogated a primer and probe binding site. Based on grading of diarrheal disease severity using VESIKARI scores, 93% of the HAdV cases presented with severe disease. One child with an HAdV F infection died. Conclusions Our study shows the enormous diversity and clinical characteristics of HAdV species in children with diarrhea in coastal Kenya. These data offer an opportunity to improve current diagnostic assays and increase knowledge of HAdV in Africa for control of outbreaks in the future. [ABSTRACT FROM AUTHOR]

Published
2024
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6. Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study

Author

Meredith, Luke W, Hamilton, William L, Warne, Ben, Houldcroft, Charlotte J, Hosmillo, Myra, Jahun, Aminu S, Curran, Martin D, Parmar, Surendra, Caller, Laura G, Caddy, Sarah L, Khokhar, Fahad A, Yakovleva, Anna, Hall, Grant, Feltwell, Theresa, Forrest, Sally, Sridhar, Sushmita, Weekes, Michael P, Baker, Stephen, Brown, Nicholas, Moore, Elinor, Popay, Ashley, Roddick, Iain, Reacher, Mark, Gouliouris, Theodore, Peacock, Sharon J, Dougan, Gordon, Török, M Estée, and Goodfellow, Ian

Published
2020
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14. Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

Author

Scheib, Christiana, Houldcroft, Charlotte, Robb, John, Cessford, Craig, Dittmar, Jenna, Inskip, Sarah, Rose, Alice, Hui, Rouyun, Scheib, Christiana [0000-0003-4158-8296], Houldcroft, Charlotte [0000-0002-1833-5285], Cessford, Craig [0000-0001-7291-7828], Apollo - University of Cambridge Repository, Guellil, Meriam [0000-0002-7235-4604], van Dorp, Lucy [0000-0002-6211-2310], Inskip, Sarah A [0000-0001-7424-2094], Dittmar, Jenna M [0000-0003-3514-1869], Saag, Lehti [0000-0002-2274-8138], Tambets, Kristiina [0000-0002-8173-6380], Hui, Ruoyun [0000-0002-5689-7131], Rose, Alice [0000-0003-1755-7174], D'Atanasio, Eugenia [0000-0002-4965-246X], Kriiska, Aivar [0000-0002-0900-7626], Varul, Liivi [0000-0002-8498-3352], Koekkelkoren, A M H C [0000-0003-0721-1727], Goldina, Rimma D [0000-0002-8689-0512], Metspalu, Mait [0000-0003-3099-9161], Krause, Johannes [0000-0001-9144-3920], Herbig, Alexander [0000-0003-1176-1166], Houldcroft, Charlotte J [0000-0002-1833-5285], and Scheib, Christiana L [0000-0003-4158-8296]

Subjects
2 Aetiology, Infectious Diseases, 4301 Archaeology, Sexually Transmitted Infections, 2.2 Factors relating to the physical environment, FOS: Health sciences, Infection, 4303 Historical Studies, 4401 Anthropology, 3105 Genetics, 43 History, Heritage and Archaeology, 31 Biological Sciences, 44 Human Society
Abstract

Funder: Wellcome Trust, Human herpes simplex virus 1 (HSV-1), a lifelong infection spread by oral contact, infects a majority of adults globally. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups has suggested the virus codiverged with human migrations out of Africa, although a much younger origin has also been proposed. We present three full ancient European HSV-1 genomes and one partial genome, dating to the 3rd-17th century CE, sequenced to up to 9.5× with paired human genomes up to 10.16×. Considering a dataset of modern and ancient genomes we apply phylogenetic methods to estimate the age of sampled modern Eurasian HSV-1 diversity to 4.68 (3.87 - 5.65) kya. Extrapolation of estimated rates to a global dataset points to the age of extant sampled HSV-1 as 5.29 (4.60-6.12) kya, suggesting HSV-1 lineage replacement coinciding with the late Neolithic period and following Bronze Age migrations.

Published
2022
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15. Infectious disease in the Pleistocene: Old friends or old foes?

Author

Houldcroft, Charlotte J., Underdown, Simon, Houldcroft, Charlotte J [0000-0002-1833-5285], Apollo - University of Cambridge Repository, and Houldcroft, CJ [0000-0002-1833-5285]

Subjects
metagenomics, human evolution, REVIEW ARTICLES, pandemics, infectious diseases, ancient DNA, REVIEW ARTICLE
Abstract

Funder: Oxford Brookes University; Id: http://dx.doi.org/10.13039/100010053, The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter‐gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.

Published
2023
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17. Using Whole Genome Sequences to Investigate Adenovirus Outbreaks, Including Five Deaths in a Haematopoietic Stem Cell Transplant Unit

Author

Myers, Chloe, Houldcroft, Charlotte, Roy, Sunando, Margetts, Ben, Best, Timothy, Venturini, Cristina, Guerra-Assunção, José, Williams, Charlotte, Williams, Rachel, Dunn, Helen, Hartley, John, Rolfe, Kathryn, Breuer, Judith, Houldcroft, Charlotte [0000-0002-1833-5285], Venturini, Cristina [0000-0002-4769-7912], and Apollo - University of Cambridge Repository

Subjects
Infectious Diseases, Stem Cell Research - Nonembryonic - Human, Clinical Research, FOS: Biological sciences, Human Genome, Genetics, 32 Biomedical and Clinical Sciences, 3 Good Health and Well Being, FOS: Health sciences, Stem Cell Research, Infection, 3202 Clinical Sciences, Biotechnology
Abstract

Background Human mastadenoviruses (HAdV) are associated with significant morbidity and mortality amongst the immunocompromised population. A recent surge in HAdV cases, including five deaths, amongst a haematopoietic stem cell transplant population led us to use whole genome sequencing (WGS) to investigate. Methods To gain a complete transmission picture, we compared outbreak and non-outbreak sequences (54 sequences from 37 patients) with GenBank sequences and our own database of previously sequenced HAdVs (132 sequences from 37 patients). An improved bait set for WGS was used. Maximum likelihood trees and pairwise differences were used to evaluate genotypic relationships paired with epidemiological data from routine Infection, Prevention and Control (IPC) activity. Results Nine monophyletic clusters were identified, seven of which were corroborated by epidemiological evidence and by comparison of single nucleotide polymorphisms. Two incomplete patient clusters were identified by IPC over the same time period. Of the five patients who died, one had a mixed HAdV infection and two were the source of transmission events. Conclusions The clinical consequences of unmitigated HAdV transmission events are high. Focusing on two high risk wards using WGS we identified six transmission events, over prolonged periods, that would have gone unnoticed using traditional polymerase chain reaction and epidemiology. Mixed infection is frequent (10% of patients), providing a sentinel source of recombination and superinfection. Immunosuppressed patients harbouring a high rate of HAdV positivity require comprehensive surveillance. As a consequence of these findings, HAdV WGS is being incorporated routinely into a clinical algorithm to prevent transmission and influence IPC policy in real-time. Summary Whole genome sequencing of adenovirus, direct from clinical samples, can be used to identify cryptic health care associated transmission events, and to resolve transmission suspected by traditional epidemiology. It can also identify mixed genotype infections in immunocompromised patient populations.

Published
2022
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22. Detection of human adenovirus F41 in wastewater and its relationship to clinical cases of acute hepatitis of unknown aetiology

Author

Reyne, Marina I., primary, Allen, Danielle M., additional, Levickas, Ashley, additional, Allingham, Pearce, additional, Lock, Jonathan, additional, Fitzgerald, Arthur, additional, McSparron, Cormac, additional, Nejad, Behnam F., additional, McKinley, Jennifer, additional, Lee, Andrew, additional, Bell, Stephen H., additional, Quick, Joshua, additional, Houldcroft, Charlotte J., additional, Bamford, Connor G.G., additional, Gilpin, Deirdre F., additional, and McGrath, John W., additional

Published
2023
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25. Enteric adenovirus F41 genetic diversity comparable to pre-COVID-19 era: validation of a multiplex amplicon-MinION sequencing method

Author

Maes, Mailis, primary, Khokhar, Fahad, additional, Wilkinson, Sam AJ, additional, Smith, Andrew, additional, Kovalenko, Ganna, additional, Dougan, Gordon, additional, Quick, Joshua, additional, Loman, Nicholas, additional, Baker, Stephen, additional, Curran, Martin D., additional, Skittrall, Jordan, additional, and Houldcroft, Charlotte J., additional

Published
2022
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26. Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia

Author

Guellil, Meriam, primary, van Dorp, Lucy, additional, Inskip, Sarah A., additional, Dittmar, Jenna M., additional, Saag, Lehti, additional, Tambets, Kristiina, additional, Hui, Ruoyun, additional, Rose, Alice, additional, D’Atanasio, Eugenia, additional, Kriiska, Aivar, additional, Varul, Liivi, additional, Koekkelkoren, A. M. H. C., additional, Goldina, Rimma D., additional, Cessford, Craig, additional, Solnik, Anu, additional, Metspalu, Mait, additional, Krause, Johannes, additional, Herbig, Alexander, additional, Robb, John E., additional, Houldcroft, Charlotte J., additional, and Scheib, Christiana L., additional

Published
2022
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27. Patterns of within-host genetic diversity in SARS-CoV-2

Author

Tonkin-Hill, Gerry, Martincorena, Inigo, Amato, Roberto, Lawson, Andrew RJ, Gerstung, Moritz, Johnston, Ian, Jackson, David K, Park, Naomi, Lensing, Stefanie V, Quail, Michael A, Gonçalves, Sónia, Ariani, Cristina, Spencer Chapman, Michael, Hamilton, William L, Meredith, Luke W, Hall, Grant, Jahun, Aminu S, Chaudhry, Yasmin, Hosmillo, Myra, Pinckert, Malte L, Georgana, Iliana, Yakovleva, Anna, Caller, Laura G, Caddy, Sarah L, Feltwell, Theresa, Khokhar, Fahad A, Houldcroft, Charlotte J, Curran, Martin D, Parmar, Surendra, Alderton, Alex, Nelson, Rachel, Harrison, Ewan M, Sillitoe, John, Bentley, Stephen D, Barrett, Jeffrey C, Torok, M Estee, Goodfellow, Ian G, Langford, Cordelia, Kwiatkowski, Dominic, The COVID-19 Genomics UK (COG-UK) Consortium, Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg, McCann, Clare, Tonkin-Hill, Gerry [0000-0003-4397-2224], Gerstung, Moritz [0000-0001-6709-963X], Pinckert, Malte [0000-0002-6072-5949], Caddy, Sarah [0000-0002-9790-7420], Torok, Estee [0000-0001-9098-8590], Apollo - University of Cambridge Repository, Jackson, David K [0000-0002-8090-9462], Spencer Chapman, Michael [0000-0002-5320-8193], Hamilton, William L [0000-0002-3330-353X], Hall, Grant [0000-0003-3928-3979], Jahun, Aminu S [0000-0002-4585-1701], Hosmillo, Myra [0000-0002-3514-7681], Georgana, Iliana [0000-0002-8976-1177], Caddy, Sarah L [0000-0002-9790-7420], Houldcroft, Charlotte J [0000-0002-1833-5285], Torok, M Estee [0000-0001-9098-8590], Goodfellow, Ian G [0000-0002-9483-510X], and Lawson, Andrew Rj [0000-0003-3592-1005]

Subjects
Mutation rate, global health, medicine.disease_cause, Negative selection, 0302 clinical medicine, genetics, Biology (General), Phylogeny, 0303 health sciences, Mutation, Phylogenetic tree, General Neuroscience, C100, transmission, General Medicine, C700, C900, 3. Good health, Host-Pathogen Interactions, Medicine, epidemiology, Research Article, Lineage (genetic), QH301-705.5, Science, mutational spectrum, Genomics, Genome, Viral, Biology, General Biochemistry, Genetics and Molecular Biology, within-host, 03 medical and health sciences, The COVID-19 Genomics UK (COG-UK) Consortium, genomics, medicine, Humans, Pandemics, Allele frequency, 030304 developmental biology, Genetic diversity, Base Sequence, General Immunology and Microbiology, SARS-CoV-2, Wellcome Sanger Institute COVID-19 Surveillance Team, COVID-19, Genetic Variation, Genetics and Genomics, B900, Epidemiology and Global Health, Evolutionary biology, Other, 030217 neurology & neurosurgery
Abstract

Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95.1% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within- and between-host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses., eLife digest The COVID-19 pandemic has had major health impacts across the globe. The scientific community has focused much attention on finding ways to monitor how the virus responsible for the pandemic, SARS-CoV-2, spreads. One option is to perform genetic tests, known as sequencing, on SARS-CoV-2 samples to determine the genetic code of the virus and to find any differences or mutations in the genes between the viral samples. Viruses mutate within their hosts and can develop into variants that are able to more easily transmit between hosts. Genetic sequencing can reveal how genetically similar two SARS-CoV-2 samples are. But tracking how SARS-CoV-2 moves from one person to the next through sequencing can be tricky. Even a sample of SARS-CoV-2 viruses from the same individual can display differences in their genetic material or within-host variants. Could genetic testing of within-host variants shed light on factors driving SARS-CoV-2 to evolve in humans? To get to the bottom of this, Tonkin-Hill, Martincorena et al. probed the genetics of SARS-CoV-2 within-host variants using 1,181 samples. The analyses revealed that 95.1% of samples contained within-host variants. A number of variants occurred frequently in many samples, which were consistent with mutational hotspots in the SARS-CoV-2 genome. In addition, within-host variants displayed mutation patterns that were similar to patterns found between infected individuals. The shared within-host variants between samples can help to reconstruct transmission chains. However, the observed mutational hotspots and the detection of multiple strains within an individual can make this challenging. These findings could be used to help predict how SARS-CoV-2 evolves in response to interventions such as vaccines. They also suggest that caution is needed when using information on within-host variants to determine transmission between individuals.

Published
2021

28. A2B-COVID: A Tool for Rapidly Evaluating Potential SARS-CoV-2 Transmission Events

Author

Illingworth, Christopher J. R., Hamilton, William L., Jackson, Christopher, Warne, Ben, Popay, Ashley, Meredith, Luke, Hosmillo, Myra, Jahun, Aminu, Fieldman, Tom, Routledge, Matthew, Houldcroft, Charlotte J., Caller, Laura, Caddy, Sarah, Yakovleva, Anna, Hall, Grant, Khokhar, Fahad A., Feltwell, Theresa, Pinckert, Malte L., Georgana, Iliana, Chaudhry, Yasmin, Curran, Martin, Parmar, Surendra, Sparkes, Dominic, Rivett, Lucy, Jones, Nick K., Sridhar, Sushmita, Forrest, Sally, Dymond, Tom, Grainger, Kayleigh, Workman, Chris, Gkrania-Klotsas, Effrossyni, Brown, Nicholas M., Weekes, Michael P., Baker, Stephen, Peacock, Sharon J., Gouliouris, Theodore, Goodfellow, Ian, De Angelis, Daniela, Torok, M. Estee, Illingworth, Christopher J. R., Hamilton, William L., Jackson, Christopher, Warne, Ben, Popay, Ashley, Meredith, Luke, Hosmillo, Myra, Jahun, Aminu, Fieldman, Tom, Routledge, Matthew, Houldcroft, Charlotte J., Caller, Laura, Caddy, Sarah, Yakovleva, Anna, Hall, Grant, Khokhar, Fahad A., Feltwell, Theresa, Pinckert, Malte L., Georgana, Iliana, Chaudhry, Yasmin, Curran, Martin, Parmar, Surendra, Sparkes, Dominic, Rivett, Lucy, Jones, Nick K., Sridhar, Sushmita, Forrest, Sally, Dymond, Tom, Grainger, Kayleigh, Workman, Chris, Gkrania-Klotsas, Effrossyni, Brown, Nicholas M., Weekes, Michael P., Baker, Stephen, Peacock, Sharon J., Gouliouris, Theodore, Goodfellow, Ian, De Angelis, Daniela, and Torok, M. Estee

Abstract

Identifying linked cases of infection is a critical component of the public health response to viral infectious diseases. In a clinical context, there is a need to make rapid assessments of whether cases of infection have arrived independently onto a ward, or are potentially linked via direct transmission. Viral genome sequence data are of great value in making these assessments, but are often not the only form of data available. Here, we describe A2B-COVID, a method for the rapid identification of potentially linked cases of COVID-19 infection designed for clinical settings. Our method combines knowledge about infection dynamics, data describing the movements of individuals, and evolutionary analysis of genome sequences to assess whether data collected from cases of infection are consistent or inconsistent with linkage via direct transmission. A retrospective analysis of data from two wards at Cambridge University Hospitals NHS Foundation Trust during the first wave of the pandemic showed qualitatively different patterns of linkage between cases on designated COVID-19 and non-COVID-19 wards. The subsequent real-time application of our method to data from the second epidemic wave highlights its value for monitoring cases of infection in a clinical context.

Published
2022

29. Genomic epidemiology of COVID-19 in care homes in the east of England

Author

Hamilton, William L, Tonkin-Hill, Gerry, Smith, Emily R, Aggarwal, Dinesh, Houldcroft, Charlotte J, Warne, Ben, Meredith, Luke W, Hosmillo, Myra, Jahun, Aminu S, Curran, Martin D, Parmar, Surendra, Caller, Laura G, Caddy, Sarah L, Khokhar, Fahad A, Yakovleva, Anna, Hall, Grant, Feltwell, Theresa, Pinckert, Malte L, Georgana, Iliana, Chaudhry, Yasmin, Brown, Colin S, Gonçalves, Sonia, Amato, Roberto, Harrison, Ewan M, Brown, Nicholas M, Beale, Mathew A, Spencer Chapman, Michael, Jackson, David K, Johnston, Ian, Alderton, Alex, Sillitoe, John, Langford, Cordelia, Dougan, Gordon, Peacock, Sharon J, Kwiatowski, Dominic P, Goodfellow, Ian G, Torok, M Estee, The COVID-19 Genomics Consortium UK, Allan, John, Bashton, Matthew, Loh, Joshua, Nelson, Andrew, Smith, Darren L., Yew, Wen Chyin, Young, Gregory R., Hamilton, William L [0000-0002-3330-353X], Tonkin-Hill, Gerry [0000-0003-4397-2224], Aggarwal, Dinesh [0000-0002-5938-8172], Houldcroft, Charlotte J [0000-0002-1833-5285], Hosmillo, Myra [0000-0002-3514-7681], Jahun, Aminu S [0000-0002-4585-1701], Caddy, Sarah L [0000-0002-9790-7420], Hall, Grant [0000-0003-3928-3979], Georgana, Iliana [0000-0002-8976-1177], Brown, Nicholas M [0000-0002-6657-300X], Beale, Mathew A [0000-0002-4740-3187], Spencer Chapman, Michael [0000-0002-5320-8193], Jackson, David K [0000-0002-8090-9462], Peacock, Sharon J [0000-0002-1718-2782], Goodfellow, Ian G [0000-0002-9483-510X], Torok, M Estee [0000-0001-9098-8590], and Apollo - University of Cambridge Repository

Subjects
Male, 0301 basic medicine, Time Factors, Care homes, Disease Outbreaks, Infectious Disease Transmission, Professional-to-Patient, 0302 clinical medicine, Epidemiology, Global health, Medicine, Infection control, 030212 general & internal medicine, Biology (General), Aged, 80 and over, education.field_of_study, Transmission (medicine), General Neuroscience, General Medicine, 3. Good health, Virus, England, Female, epidemiology, Sequence Analysis, Research Article, medicine.medical_specialty, Infectious Disease Transmission, Patient-to-Professional, Coronavirus disease 2019 (COVID-19), QH301-705.5, Science, Population, Polymorphism, Single Nucleotide, B700, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Environmental health, genomics, Humans, education, General Immunology and Microbiology, business.industry, SARS-CoV-2, Outbreak, COVID-19, Genetics and Genomics, C400, Nursing Homes, 030104 developmental biology, Epidemiology and Global Health, business
Abstract

COVID-19 poses a major challenge to care homes, as SARS-CoV-2 is readily transmitted and causes disproportionately severe disease in older people. Here, 1167 residents from 337 care homes were identified from a dataset of 6600 COVID-19 cases from the East of England. Older age and being a care home resident were associated with increased mortality. SARS-CoV-2 genomes were available for 700 residents from 292 care homes. By integrating genomic and temporal data, 409 viral clusters within the 292 homes were identified, indicating two different patterns – outbreaks among care home residents and independent introductions with limited onward transmission. Approximately 70% of residents in the genomic analysis were admitted to hospital during the study, providing extensive opportunities for transmission between care homes and hospitals. Limiting viral transmission within care homes should be a key target for infection control to reduce COVID-19 mortality in this population.

Published
2021

30. A2B-COVID: A Tool for Rapidly Evaluating Potential SARS-CoV-2 Transmission Events

Author

Illingworth, Christopher J R, primary, Hamilton, William L, additional, Jackson, Christopher, additional, Warne, Ben, additional, Popay, Ashley, additional, Meredith, Luke, additional, Hosmillo, Myra, additional, Jahun, Aminu, additional, Fieldman, Tom, additional, Routledge, Matthew, additional, Houldcroft, Charlotte J, additional, Caller, Laura, additional, Caddy, Sarah, additional, Yakovleva, Anna, additional, Hall, Grant, additional, Khokhar, Fahad A, additional, Feltwell, Theresa, additional, Pinckert, Malte L, additional, Georgana, Iliana, additional, Chaudhry, Yasmin, additional, Curran, Martin, additional, Parmar, Surendra, additional, Sparkes, Dominic, additional, Rivett, Lucy, additional, Jones, Nick K, additional, Sridhar, Sushmita, additional, Forrest, Sally, additional, Dymond, Tom, additional, Grainger, Kayleigh, additional, Workman, Chris, additional, Gkrania-Klotsas, Effrossyni, additional, Brown, Nicholas M, additional, Weekes, Michael P, additional, Baker, Stephen, additional, Peacock, Sharon J, additional, Gouliouris, Theodore, additional, Goodfellow, Ian, additional, Angelis, Daniela De, additional, and Török, M Estée, additional

Published
2022
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31. Contributors

Author

Anderson, Tavis K., Arenas, Miguel, Ayouba, Ahidjo, Barnabé, C., Beshir, Khalid B., Beveridge, Ian, Binyang, Achille, Biron, David G., Brenière, S.F., Cambau, Emmanuelle, Cancino-Muñoz, Irving, Castro-Nallar, Eduardo, Challagundla, Lavanya, Chilton, Neil B., Cochran, G., Cohan, Frederick M., Davidson, Josiah Levi, Delaporte, Eric, Dorn, P.L., Droit, Arnaud, D'arc, Mirela, Dujardin, Jean-Pierre, Etang, Josiane, Etienne, Lucie, García-González, Neris, Gasser, Robin B., Geddes-McAlister, Jennifer, Gibson, Wendy, Gonzalo-Asensio, Jesús, González-Candelas, Fernando, Gostinčar, Cene, Gunde-Cimerman, Nina, Guyeux, Christophe, Hanage, William P., Harpending, H., Holzmuller, Philippe, Houldcroft, Charlotte J., Hu, Ben, Izenour, Katie, Kamel, Mohamed, Kaur, Simerdeep, Kelly, Brenyn, Kopac, Sarah, Kumar, Virendra, La, Kevin, Lewis, Michael D., Liu, Yu-Tsueng, Mbakop, Lili Ranaise, McClure, JoAnn, Medina, Rafael A., Miles, Michael A., Missé, Dorothée, Mokrousov, Igor, Morand, Serge, Munds, Rachel A., Nedelkov, Dobrin, Nelson, Martha I., Nwane, Philippe, Panzera, F., Pardos, Elena Campos, Peeters, Martine, Pita, S., Polley, Spencer D., Pérez-Losada, Marcos, Qiu, Xueting, Refrégier, Guislaine, Robinson, D. Ashley, Roux-Dalvai, Florence, Sahal, Muhammed Rabiu, Sanjuán, Rafael, Senelle, Gaetan, Senghore, Madikay, Seral, Juan Calvet, Shi, Zhengli, Sironi, Manuela, Sola, Christophe, Solano, Philippe, Sánchez-Busó, Leonor, Sutherland, Colin J., Tibayrenc, Michel, van Belkum, Alex, Van Regenmortel, Marc H.V., Verma, Mohit S., Vernet, Guy, Waleckx, E., Wang, Lin-Fa, Wang, Jiangshan, Wille, Michelle, Yeo, Matthew, Zhang, Kunyan, and Zohdy, Sarah

Published
2024
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33. EBV deletions as biomarkers of response to treatment of Chronic Active Epstein Barr Virus

Author

Venturini, Cristina, Houldcroft, Charlotte, Lazareva, Arina, Wegner, Fanny, Morfopoulou, Sofia, Amrolia, Persis, Golwala, Zainab, Rao, Anupama, Marks, Stephen, Simmonds, Jacob, Yoshikawa, Tetsushi, Farrell, Paul, Cohen, Jeffrey, Worth, Austen, Breuer, Judith, Venturini, Cristina [0000-0002-4769-7912], Houldcroft, Charlotte [0000-0002-1833-5285], Wegner, Fanny [0000-0003-4348-5872], Morfopoulou, Sofia [0000-0001-8181-4548], Amrolia, Persis [0000-0003-0480-3911], and Apollo - University of Cambridge Repository

Subjects
Infectious Diseases, Rare Diseases, Lymphoma, Clinical Research, 3207 Medical Microbiology, 32 Biomedical and Clinical Sciences, Hematology, FOS: Health sciences, Infection, Cancer
Abstract

Chronic active Epstein Barr Virus (CAEBV) is a rare condition occurring in previously healthy individuals associated with persistent EBV viraemia, fever, lymphadenopathy and hepatosplenomegaly. Viral deletions have been found in CAEBV and other lymphomas. However, it is unclear how stable these deletions are, whether they are present in different sites and how they evolve overtime. We sequenced fourteen longitudinal blood samples from three European CAEBV patients and compared with CAEBV saliva samples and other sequences from EBV-related conditions. We observed large EBV deletions in blood, but not saliva from CAEBV patients. Deletions were stable over time but were lost following successful treatment. Our results are consistent with the likelihood that certain deletions in the virus from CAEBV patients are associated with the evolution and persistence of haematological clones. We propose that the loss of deletions following successful treatment should be investigated as a potential biomarker to aid CAEBV management.

Published
2020

34. Human Herpesvirus Sequencing in the Genomic Era: The Growing Ranks of the Herpetic Legion

Author

Houldcroft, Charlotte, Houldcroft, Charlotte [0000-0002-1833-5285], and Apollo - University of Cambridge Repository

Subjects
Microbiology (medical), herpesviruses, viruses, lcsh:Medicine, Genomics, clinical sequencing, Review, Disease, Computational biology, Biology, Genome, Virus, Population genomics, 03 medical and health sciences, genomics, Immunology and Allergy, Molecular Biology, 030304 developmental biology, 0303 health sciences, General Immunology and Microbiology, 030306 microbiology, lcsh:R, population genetics, 3. Good health, Transplantation, Infectious Diseases, GenBank, DNA viruses, Human herpesvirus
Abstract

The nine human herpesviruses are some of the most ubiquitous pathogens worldwide, causing life-long latent infection in a variety of different tissues. Human herpesviruses range from mild childhood infections to known tumour viruses and ‘trolls of transplantation’. Epstein-Barr virus was the first human herpesvirus to have its whole genome sequenced; GenBank now includes thousands of herpesvirus genomes. This review will cover some of the recent advances in our understanding of herpesvirus diversity and disease that have come about as a result of new sequencing technologies, such as target enrichment and long-read sequencing. It will also look at the problem of resolving mixed-genotype infections, whether with short or long-read sequencing methods; and conclude with some thoughts on the future of the field as herpesvirus population genomics becomes a reality.

Published
2019

35. Human biology and ancient DNA: exploring disease, domestication and movement

Author

Houldcroft, Charlotte J, Rifkin, Riaan F, Underdown, Simon J, Houldcroft, Charlotte J [0000-0002-1833-5285], Rifkin, Riaan F [0000-0003-1791-3706], Underdown, Simon J [0000-0001-6056-2353], and Apollo - University of Cambridge Repository

Subjects
Domestication, Archaeology, Human Migration, Humans, Genetic Predisposition to Disease, DNA, Ancient, Biological Evolution, History, Ancient
Abstract

The development of ancient DNA (aDNA) analysis has radically transformed how we think about and study the past. The use of aDNA technology has permeated almost every area of anthropology and archaeology and continues to radically alter how we understand the past (Paabo et al. 1989, 2004; Meyer et al. 2016; Slon et al. 2017). Ancient DNA has both vastly enriched and complicated the mosaic picture of the human story from Neanderthals and Homo sapiens interbreeding to the identification of the hitherto unknown Denisovan group (Slon et al. 2017). aDNA has revolutionised the fields of archaeology, population genetics and evolutionary biology, allowing us to directly test hypotheses about past populations which could formerly only be inferred from other lines of evidence. aDNA has also revealed new species, challenged assumptions about admixture and demonstrated that processes such as animal and plant domestication are even more complex than we had assumed. Currently, the oldest aDNA (from a horse) is dated to 700,000 years ago (Orlando et al. 2013) and the oldest human aDNA to 400,000 years ago (Meyer et al. 2016), potentially opening up much of human prehistory to this new field. However, there are also questions which cannot currently be answered by aDNA, whether because of the age or nature of a sample, the preservation conditions or ethical considerations, including engagement with indigenous and marginalised groups. These themes were explored by the participants of the 59th Society for the Study of Human Biology Symposium held in August 2018 at Oxford Brookes University, UK.

Published
2019
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36. Epstein–Barr virus (EBV) deletions as biomarkers of response to treatment of chronic active EBV

Author

Venturini, Cristina, primary, Houldcroft, Charlotte J., additional, Lazareva, Arina, additional, Wegner, Fanny, additional, Morfopoulou, Sofia, additional, Amrolia, Persis J., additional, Golwala, Zainab, additional, Rao, Anupama, additional, Marks, Stephen D., additional, Simmonds, Jacob, additional, Yoshikawa, Tetsushi, additional, Farrell, Paul J., additional, Cohen, Jeffrey I., additional, Worth, Austen J., additional, and Breuer, Judith, additional

Published
2021
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37. Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections

Author

Illingworth, Christopher JR, primary, Hamilton, William L, additional, Warne, Ben, additional, Routledge, Matthew, additional, Popay, Ashley, additional, Jackson, Chris, additional, Fieldman, Tom, additional, Meredith, Luke W, additional, Houldcroft, Charlotte J, additional, Hosmillo, Myra, additional, Jahun, Aminu S, additional, Caller, Laura G, additional, Caddy, Sarah L, additional, Yakovleva, Anna, additional, Hall, Grant, additional, Khokhar, Fahad A, additional, Feltwell, Theresa, additional, Pinckert, Malte L, additional, Georgana, Iliana, additional, Chaudhry, Yasmin, additional, Curran, Martin D, additional, Parmar, Surendra, additional, Sparkes, Dominic, additional, Rivett, Lucy, additional, Jones, Nick K, additional, Sridhar, Sushmita, additional, Forrest, Sally, additional, Dymond, Tom, additional, Grainger, Kayleigh, additional, Workman, Chris, additional, Ferris, Mark, additional, Gkrania-Klotsas, Effrossyni, additional, Brown, Nicholas M, additional, Weekes, Michael P, additional, Baker, Stephen, additional, Peacock, Sharon J, additional, Goodfellow, Ian G, additional, Gouliouris, Theodore, additional, de Angelis, Daniela, additional, and Török, M Estée, additional

Published
2021
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38. Author response: Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections

Author

Illingworth, Christopher JR, primary, Hamilton, William L, additional, Warne, Ben, additional, Routledge, Matthew, additional, Popay, Ashley, additional, Jackson, Chris, additional, Fieldman, Tom, additional, Meredith, Luke W, additional, Houldcroft, Charlotte J, additional, Hosmillo, Myra, additional, Jahun, Aminu S, additional, Caller, Laura G, additional, Caddy, Sarah L, additional, Yakovleva, Anna, additional, Hall, Grant, additional, Khokhar, Fahad A, additional, Feltwell, Theresa, additional, Pinckert, Malte L, additional, Georgana, Iliana, additional, Chaudhry, Yasmin, additional, Curran, Martin D, additional, Parmar, Surendra, additional, Sparkes, Dominic, additional, Rivett, Lucy, additional, Jones, Nick K, additional, Sridhar, Sushmita, additional, Forrest, Sally, additional, Dymond, Tom, additional, Grainger, Kayleigh, additional, Workman, Chris, additional, Ferris, Mark, additional, Gkrania-Klotsas, Effrossyni, additional, Brown, Nicholas M, additional, Weekes, Michael P, additional, Baker, Stephen, additional, Peacock, Sharon J, additional, Goodfellow, Ian G, additional, Gouliouris, Theodore, additional, de Angelis, Daniela, additional, and Török, M Estée, additional

Published
2021
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39. Using Whole Genome Sequences to Investigate Adenovirus Outbreaks in a Hematopoietic Stem Cell Transplant Unit

Author

Myers, Chloe E., primary, Houldcroft, Charlotte J., additional, Roy, Sunando, additional, Margetts, Ben K., additional, Best, Timothy, additional, Venturini, Cristina, additional, Guerra-Assunção, Jose A., additional, Williams, Charlotte A., additional, Williams, Rachel, additional, Dunn, Helen, additional, Hartley, John C., additional, Rao, Kanchan, additional, Rolfe, Kathryn J., additional, and Breuer, Judith, additional

Published
2021
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40. 31,600-year-old human virus genomes support a Pleistocene origin for common childhood infections

Author

Nielsen, Sofie Holtsmark, primary, van Dorp, Lucy, additional, Houldcroft, Charlotte J., additional, Pedersen, Anders G., additional, Allentoft, Morten E., additional, Vinner, Lasse, additional, Margaryan, Ashot, additional, Pavlova, Elena, additional, Chasnyk, Vyacheslav, additional, Nikolskiy, Pavel, additional, Pitulko, Vladimir, additional, Pimenoff, Ville N., additional, Balloux, François, additional, and Sikora, Martin, additional

Published
2021
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41. Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission

Author

Rivett, Lucy, Sridhar, Sushmita, Sparkes, Dominic, Routledge, Matthew, Jones, Nick K, Forrest, Sally, Young, Jamie, Pereira-Dias, Joana, Hamilton, William L, Ferris, Mark, Torok, M Estee, Meredith, Luke, Collaboration, The CITIID-NIHR COVID-19 BioResource, Curran, Martin D, Fuller, Stewart, Chaudhry, Afzal, Shaw, Ashley, Samworth, Richard J, Bradley, John R, Dougan, Gordon, Smith, Kenneth GC, Lehner, Paul J, Matheson, Nicholas J, Wright, Giles, Goodfellow, Ian G, Baker, Stephen, Weekes, Michael P, Gupta, Ravi, Lyons, Paul A, Toshner, Mark, Warne, Ben, Bartholdson Scott, Josefin, Cormie, Claire, Gill, Harmeet, Kean, Iain, Maes, Mailis, Reynolds, Nicola, Wantoch, Michelle, Caddy, Sarah, Caller, Laura, Feltwell, Theresa, Hall, Grant, Hosmillo, Myra, Houldcroft, Charlotte, Jahun, Aminu, Khokhar, Fahad, Yakovleva, Anna, Butcher, Helen, Caputo, Daniela, Clapham-Riley, Debra, Dolling, Helen, Furlong, Anita, Graves, Barbara, Gresley, Emma Le, Kingston, Nathalie, Papadia, Sofia, Stark, Hannah, Stirrups, Kathleen E, Webster, Jennifer, Calder, Joanna, Harris, Julie, Hewitt, Sarah, Kennet, Jane, Meadows, Anne, Rastall, Rebecca, Brien, Criona O, Price, Jo, Publico, Cherry, Rowlands, Jane, Ruffolo, Valentina, Tordesillas, Hugo, Brookes, Karen, Canna, Laura, Cruz, Isabel, Dempsey, Katie, Elmer, Anne, Escoffery, Naidine, Jones, Heather, Ribeiro, Carla, Saunders, Caroline, Wright, Angela, Nyagumbo, Rutendo, Roberts, Anne, Bucke, Ashlea, Hargreaves, Simone, Johnson, Danielle, Narcorda, Aileen, Read, Debbie, Sparke, Christian, Warboys, Lucy, Lagadu, Kirsty, Mactavous, Lenette, Gould, Tim, Raine, Tim, Mather, Claire, Ramenatte, Nicola, Vallier, Anne-Laure, Kasanicki, Mary, Eames, Penelope-Jane, McNicholas, Chris, Thake, Lisa, Bartholomew, Neil, Brown, Nick, Parmar, Surendra, Zhang, Hongyi, Bowring, Ailsa, Martell, Geraldine, Quinnell, Natalie, Wright, Jo, Murphy, Helen, Dunmore, Benjamin J, Legchenko, Ekaterina, Gräf, Stefan, Huang, Christopher, Hodgson, Josh, Hunter, Kelvin, Martin, Jennifer, Mescia, Federica, O'Donnell, Ciara, Pointon, Linda, Shih, Joy, Sutcliffe, Rachel, Tilly, Tobias, Tong, Zhen, Treacy, Carmen, Wood, Jennifer, Bergamaschi, Laura, Betancourt, Ariana, Bowyer, Georgie, De Sa, Aloka, Epping, Maddie, Hinch, Andrew, Huhn, Oisin, Jarvis, Isobel, Lewis, Daniel, Marsden, Joe, McCallum, Simon, Nice, Francescsa, Rivett, Lucy [0000-0002-2781-9345], Lehner, Paul J [0000-0001-9383-1054], Matheson, Nicholas J [0000-0002-3318-1851], Goodfellow, Ian G [0000-0002-9483-510X], Weekes, Michael P [0000-0003-3196-5545], and Apollo - University of Cambridge Repository

Subjects
Epidemiology and Global Health, SARS-CoV-2, infectious disease, education, occupational health, virus diseases, COVID-19, Human Biology and Medicine, Research Article, virology, emerging pathogens, Human, Virus
Abstract

Funder: Addenbrooke's Charitable Trust, Cambridge University Hospitals; FundRef: http://dx.doi.org/10.13039/501100002927, Significant differences exist in the availability of healthcare worker (HCW) SARS-CoV-2 testing between countries, and existing programmes focus on screening symptomatic rather than asymptomatic staff. Over a 3 week period (April 2020), 1032 asymptomatic HCWs were screened for SARS-CoV-2 in a large UK teaching hospital. Symptomatic staff and symptomatic household contacts were additionally tested. Real-time RT-PCR was used to detect viral RNA from a throat+nose self-swab. 3% of HCWs in the asymptomatic screening group tested positive for SARS-CoV-2. 17/30 (57%) were truly asymptomatic/pauci-symptomatic. 12/30 (40%) had experienced symptoms compatible with coronavirus disease 2019 (COVID-19)>7 days prior to testing, most self-isolating, returning well. Clusters of HCW infection were discovered on two independent wards. Viral genome sequencing showed that the majority of HCWs had the dominant lineage B∙1. Our data demonstrates the utility of comprehensive screening of HCWs with minimal or no symptoms. This approach will be critical for protecting patients and hospital staff.

Published
2020
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42. Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections

Author

Illingworth, Christopher J. R., Hamilton, William L., Warne, Ben, Routledge, Matthew, Popay, Ashley, Jackson, Chris, Fieldman, Tom, Meredith, Luke W., Houldcroft, Charlotte J., Hosmillo, Myra, Jahun, Aminu S., Caller, Laura G., Caddy, Sarah L., Yakovleva, Anna, Hall, Grant, Khokhar, Fahad A., Feltwell, Theresa, Pinckert, Malte L., Georgana, Iliana, Chaudhry, Yasmin, Curran, Martin D., Parmar, Surendra, Sparkes, Dominic, Rivett, Lucy, Jones, Nick K., Sridhar, Sushmita, Forrest, Sally, Dymond, Tom, Grainger, Kayleigh, Workman, Chris, Ferris, Mark, Gkrania-Klotsas, Effrossyni, Brown, Nicholas M., Weekes, Michael P., Baker, Stephen, Peacock, Sharon J., Goodfellow, Ian G., Gouliouris, Theodore, de Angelis, Daniela, Torok, M. Estee, Illingworth, Christopher J. R., Hamilton, William L., Warne, Ben, Routledge, Matthew, Popay, Ashley, Jackson, Chris, Fieldman, Tom, Meredith, Luke W., Houldcroft, Charlotte J., Hosmillo, Myra, Jahun, Aminu S., Caller, Laura G., Caddy, Sarah L., Yakovleva, Anna, Hall, Grant, Khokhar, Fahad A., Feltwell, Theresa, Pinckert, Malte L., Georgana, Iliana, Chaudhry, Yasmin, Curran, Martin D., Parmar, Surendra, Sparkes, Dominic, Rivett, Lucy, Jones, Nick K., Sridhar, Sushmita, Forrest, Sally, Dymond, Tom, Grainger, Kayleigh, Workman, Chris, Ferris, Mark, Gkrania-Klotsas, Effrossyni, Brown, Nicholas M., Weekes, Michael P., Baker, Stephen, Peacock, Sharon J., Goodfellow, Ian G., Gouliouris, Theodore, de Angelis, Daniela, and Torok, M. Estee

Abstract

SARS-CoV-2 is notable both for its rapid spread, and for the heterogeneity of its patterns of transmission, with multiple published incidences of superspreading behaviour. Here, we applied a novel network reconstruction algorithm to infer patterns of viral transmission occurring between patients and health care workers (HCWs) in the largest clusters of COVID-19 infection identified during the first wave of the epidemic at Cambridge University Hospitals NHS Foundation Trust, UK. Based upon dates of individuals reporting symptoms, recorded individual locations, and viral genome sequence data, we show an uneven pattern of transmission between individuals, with patients being much more likely to be infected by other patients than by HCWs. Further, the data were consistent with a pattern of superspreading, whereby 21% of individuals caused 80% of transmission events. Our study provides a detailed retrospective analysis of nosocomial SARS-CoV-2 transmission, and sheds light on the need for intensive and pervasive infection control procedures.

Published
2021

44. Latent Cytomegalovirus-Driven Recruitment of Activated CD4+ T Cells Promotes Virus Reactivation

Author

Jackson, Sarah E., primary, Chen, Kevin C., additional, Groves, Ian J., additional, Sedikides, George X., additional, Gandhi, Amar, additional, Houldcroft, Charlotte J., additional, Poole, Emma L., additional, Montanuy, Inmaculada, additional, Mason, Gavin M., additional, Okecha, Georgina, additional, Reeves, Matthew B., additional, Sinclair, John H., additional, and Wills, Mark R., additional

Published
2021
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45. Superspreaders drive the largest outbreaks of hospital onset COVID-19 infection

Author

Illingworth, Chris, primary, Hamilton, William, additional, Warne, Ben, additional, Routledge, Matthew, additional, Popay, Ashley, additional, jackson, christopher, additional, Fieldman, Tom, additional, Meredith, Luke W., additional, Houldcroft, Charlotte J., additional, Hosmillo, Myra, additional, Jahun, Aminu S., additional, Caller, Laura G., additional, Caddy, Sarah L., additional, Yakovleva, Anna, additional, Hall, Grant, additional, Khokhar, Fahad A., additional, Feltwell, Theresa, additional, Pinckert, Malte L., additional, Georgana, Iliana, additional, Chaudhry, Yasmin, additional, Curran, Martin D., additional, Parmar, Surendra, additional, Sparkes, Dominic, additional, Rivett, Lucy, additional, Jones, Nick K., additional, Sridhar, Sushmita, additional, Forrest, Sally, additional, Dymond, Tom, additional, Grainger, Kayleigh, additional, Workman, Chris, additional, Gkrania-Klotsas, Effrossyni, additional, Brown, Nicholas M., additional, Baker, Stephen, additional, Weekes, Michael P., additional, Peacock, Sharon J., additional, Goodfellow, Ian, additional, Gouliouris, Theodore, additional, de Angelis, Daniela, additional, and Török, Estée, additional

Published
2021
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46. Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Author

Volz, Erik, primary, Hill, Verity, additional, McCrone, John T., additional, Price, Anna, additional, Jorgensen, David, additional, O’Toole, Áine, additional, Southgate, Joel, additional, Johnson, Robert, additional, Jackson, Ben, additional, Nascimento, Fabricia F., additional, Rey, Sara M., additional, Nicholls, Samuel M., additional, Colquhoun, Rachel M., additional, da Silva Filipe, Ana, additional, Shepherd, James, additional, Pascall, David J., additional, Shah, Rajiv, additional, Jesudason, Natasha, additional, Li, Kathy, additional, Jarrett, Ruth, additional, Pacchiarini, Nicole, additional, Bull, Matthew, additional, Geidelberg, Lily, additional, Siveroni, Igor, additional, Goodfellow, Ian, additional, Loman, Nicholas J., additional, Pybus, Oliver G., additional, Robertson, David L., additional, Thomson, Emma C., additional, Rambaut, Andrew, additional, Connor, Thomas R., additional, Koshy, Cherian, additional, Wise, Emma, additional, Cortes, Nick, additional, Lynch, Jessica, additional, Kidd, Stephen, additional, Mori, Matilde, additional, Fairley, Derek J., additional, Curran, Tanya, additional, McKenna, James P., additional, Adams, Helen, additional, Fraser, Christophe, additional, Golubchik, Tanya, additional, Bonsall, David, additional, Moore, Catrin, additional, Caddy, Sarah L., additional, Khokhar, Fahad A., additional, Wantoch, Michelle, additional, Reynolds, Nicola, additional, Warne, Ben, additional, Maksimovic, Joshua, additional, Spellman, Karla, additional, McCluggage, Kathryn, additional, John, Michaela, additional, Beer, Robert, additional, Afifi, Safiah, additional, Morgan, Sian, additional, Marchbank, Angela, additional, Kitchen, Christine, additional, Gulliver, Huw, additional, Merrick, Ian, additional, Guest, Martyn, additional, Munn, Robert, additional, Workman, Trudy, additional, Fuller, William, additional, Bresner, Catherine, additional, Snell, Luke B., additional, Charalampous, Themoula, additional, Nebbia, Gaia, additional, Batra, Rahul, additional, Edgeworth, Jonathan, additional, Robson, Samuel C., additional, Beckett, Angela, additional, Loveson, Katie F., additional, Aanensen, David M., additional, Underwood, Anthony P., additional, Yeats, Corin A., additional, Abudahab, Khalil, additional, Taylor, Ben E.W., additional, Menegazzo, Mirko, additional, Clark, Gemma, additional, Smith, Wendy, additional, Khakh, Manjinder, additional, Fleming, Vicki M., additional, Lister, Michelle M., additional, Howson-Wells, Hannah C., additional, Berry, Louise, additional, Boswell, Tim, additional, Joseph, Amelia, additional, Willingham, Iona, additional, Bird, Paul, additional, Helmer, Thomas, additional, Fallon, Karlie, additional, Holmes, Christopher, additional, Tang, Julian, additional, Raviprakash, Veena, additional, Campbell, Sharon, additional, Sheriff, Nicola, additional, Loose, Matthew W., additional, Holmes, Nadine, additional, Moore, Christopher, additional, Carlile, Matthew, additional, Wright, Victoria, additional, Sang, Fei, additional, Debebe, Johnny, additional, Coll, Francesc, additional, Signell, Adrian W., additional, Betancor, Gilberto, additional, Wilson, Harry D., additional, Feltwell, Theresa, additional, Houldcroft, Charlotte J., additional, Eldirdiri, Sahar, additional, Kenyon, Anita, additional, Davis, Thomas, additional, Pybus, Oliver, additional, du Plessis, Louis, additional, Zarebski, Alex, additional, Raghwani, Jayna, additional, Kraemer, Moritz, additional, Francois, Sarah, additional, Attwood, Stephen, additional, Vasylyeva, Tetyana, additional, Torok, M. Estee, additional, Hamilton, William L., additional, Goodfellow, Ian G., additional, Hall, Grant, additional, Jahun, Aminu S., additional, Chaudhry, Yasmin, additional, Hosmillo, Myra, additional, Pinckert, Malte L., additional, Georgana, Iliana, additional, Yakovleva, Anna, additional, Meredith, Luke W., additional, Moses, Samuel, additional, Lowe, Hannah, additional, Ryan, Felicity, additional, Fisher, Chloe L., additional, Awan, Ali R., additional, Boyes, John, additional, Breuer, Judith, additional, Harris, Kathryn Ann, additional, Brown, Julianne Rose, additional, Shah, Divya, additional, Atkinson, Laura, additional, Lee, Jack C.D., additional, Alcolea-Medina, Adela, additional, Moore, Nathan, additional, Cortes, Nicholas, additional, Williams, Rebecca, additional, Chapman, Michael R., additional, Levett, Lisa J., additional, Heaney, Judith, additional, Smith, Darren L., additional, Bashton, Matthew, additional, Young, Gregory R., additional, Allan, John, additional, Loh, Joshua, additional, Randell, Paul A., additional, Cox, Alison, additional, Madona, Pinglawathee, additional, Holmes, Alison, additional, Bolt, Frances, additional, Price, James, additional, Mookerjee, Siddharth, additional, Rowan, Aileen, additional, Taylor, Graham P., additional, Ragonnet-Cronin, Manon, additional, Johnson, Rob, additional, Boyd, Olivia, additional, Volz, Erik M., additional, Brunker, Kirstyn, additional, Smollett, Katherine L., additional, Quick, Joshua, additional, McMurray, Claire, additional, Stockton, Joanne, additional, Nicholls, Sam, additional, Rowe, Will, additional, Poplawski, Radoslaw, additional, Martinez-Nunez, Rocio T., additional, Mason, Jenifer, additional, Robinson, Trevor I., additional, O'Toole, Elaine, additional, Watts, Joanne, additional, Breen, Cassie, additional, Cowell, Angela, additional, Ludden, Catherine, additional, Sluga, Graciela, additional, Machin, Nicholas W., additional, Ahmad, Shazaad S.Y., additional, George, Ryan P., additional, Halstead, Fenella, additional, Sivaprakasam, Venkat, additional, Shepherd, James G., additional, Asamaphan, Patawee, additional, Niebel, Marc O., additional, Li, Kathy K., additional, Shah, Rajiv N., additional, Jesudason, Natasha G., additional, Parr, Yasmin A., additional, Tong, Lily, additional, Broos, Alice, additional, Mair, Daniel, additional, Nichols, Jenna, additional, Carmichael, Stephen N., additional, Nomikou, Kyriaki, additional, Aranday-Cortes, Elihu, additional, Johnson, Natasha, additional, Starinskij, Igor, additional, Orton, Richard J., additional, Hughes, Joseph, additional, Vattipally, Sreenu, additional, Singer, Joshua B., additional, Hale, Antony D., additional, Macfarlane-Smith, Louissa R., additional, Harper, Katherine L., additional, Taha, Yusri, additional, Payne, Brendan A.I., additional, Burton-Fanning, Shirelle, additional, Waugh, Sheila, additional, Collins, Jennifer, additional, Eltringham, Gary, additional, Templeton, Kate E., additional, McHugh, Martin P., additional, Dewar, Rebecca, additional, Wastenge, Elizabeth, additional, Dervisevic, Samir, additional, Stanley, Rachael, additional, Prakash, Reenesh, additional, Stuart, Claire, additional, Elumogo, Ngozi, additional, Sethi, Dheeraj K., additional, Meader, Emma J., additional, Coupland, Lindsay J., additional, Potter, Will, additional, Graham, Clive, additional, Barton, Edward, additional, Padgett, Debra, additional, Scott, Garren, additional, Swindells, Emma, additional, Greenaway, Jane, additional, Nelson, Andrew, additional, Yew, Wen C., additional, Resende Silva, Paola C., additional, Andersson, Monique, additional, Shaw, Robert, additional, Peto, Timothy, additional, Justice, Anita, additional, Eyre, David, additional, Crooke, Derrick, additional, Hoosdally, Sarah, additional, Sloan, Tim J., additional, Duckworth, Nichola, additional, Walsh, Sarah, additional, Chauhan, Anoop J., additional, Glaysher, Sharon, additional, Bicknell, Kelly, additional, Wyllie, Sarah, additional, Butcher, Ethan, additional, Elliott, Scott, additional, Lloyd, Allyson, additional, Impey, Robert, additional, Levene, Nick, additional, Monaghan, Lynn, additional, Bradley, Declan T., additional, Allara, Elias, additional, Pearson, Clare, additional, Muir, Peter, additional, Vipond, Ian B., additional, Hopes, Richard, additional, Pymont, Hannah M., additional, Hutchings, Stephanie, additional, Curran, Martin D., additional, Parmar, Surendra, additional, Lackenby, Angie, additional, Mbisa, Tamyo, additional, Platt, Steven, additional, Miah, Shahjahan, additional, Bibby, David, additional, Manso, Carmen, additional, Hubb, Jonathan, additional, Chand, Meera, additional, Dabrera, Gavin, additional, Ramsay, Mary, additional, Bradshaw, Daniel, additional, Thornton, Alicia, additional, Myers, Richard, additional, Schaefer, Ulf, additional, Groves, Natalie, additional, Gallagher, Eileen, additional, Lee, David, additional, Williams, David, additional, Ellaby, Nicholas, additional, Harrison, Ian, additional, Hartman, Hassan, additional, Manesis, Nikos, additional, Patel, Vineet, additional, Bishop, Chloe, additional, Chalker, Vicki, additional, Osman, Husam, additional, Bosworth, Andrew, additional, Robinson, Esther, additional, Holden, Matthew T.G., additional, Shaaban, Sharif, additional, Birchley, Alec, additional, Adams, Alexander, additional, Davies, Alisha, additional, Gaskin, Amy, additional, Plimmer, Amy, additional, Gatica-Wilcox, Bree, additional, McKerr, Caoimhe, additional, Moore, Catherine, additional, Williams, Chris, additional, Heyburn, David, additional, De Lacy, Elen, additional, Hilvers, Ember, additional, Downing, Fatima, additional, Shankar, Giri, additional, Jones, Hannah, additional, Asad, Hibo, additional, Coombes, Jason, additional, Watkins, Joanne, additional, Evans, Johnathan M., additional, Fina, Laia, additional, Gifford, Laura, additional, Gilbert, Lauren, additional, Graham, Lee, additional, Perry, Malorie, additional, Morgan, Mari, additional, Cronin, Michelle, additional, Craine, Noel, additional, Jones, Rachel, additional, Howe, Robin, additional, Corden, Sally, additional, Rey, Sara, additional, Kumziene-Summerhayes, Sara, additional, Taylor, Sarah, additional, Cottrell, Simon, additional, Jones, Sophie, additional, Edwards, Sue, additional, O’Grady, Justin, additional, Page, Andrew J., additional, Wain, John, additional, Webber, Mark A., additional, Mather, Alison E., additional, Baker, David J., additional, Rudder, Steven, additional, Yasir, Muhammad, additional, Thomson, Nicholas M., additional, Aydin, Alp, additional, Tedim, Ana P., additional, Kay, Gemma L., additional, Trotter, Alexander J., additional, Gilroy, Rachel A.J., additional, Alikhan, Nabil-Fareed, additional, de Oliveira Martins, Leonardo, additional, Le-Viet, Thanh, additional, Meadows, Lizzie, additional, Kolyva, Anastasia, additional, Diaz, Maria, additional, Bell, Andrew, additional, Gutierrez, Ana Victoria, additional, Charles, Ian G., additional, Adriaenssens, Evelien M., additional, Kingsley, Robert A., additional, Casey, Anna, additional, Simpson, David A., additional, Molnar, Zoltan, additional, Thompson, Thomas, additional, Acheson, Erwan, additional, Masoli, Jane A.H., additional, Knight, Bridget A., additional, Hattersley, Andrew, additional, Ellard, Sian, additional, Auckland, Cressida, additional, Mahungu, Tabitha W., additional, Irish-Tavares, Dianne, additional, Haque, Tanzina, additional, Bourgeois, Yann, additional, Scarlett, Garry P., additional, Partridge, David G., additional, Raza, Mohammad, additional, Evans, Cariad, additional, Johnson, Kate, additional, Liggett, Steven, additional, Baker, Paul, additional, Essex, Sarah, additional, Lyons, Ronan A., additional, Caller, Laura G., additional, Castellano, Sergi, additional, Williams, Rachel J., additional, Kristiansen, Mark, additional, Roy, Sunando, additional, Williams, Charlotte A., additional, Dyal, Patricia L., additional, Tutill, Helena J., additional, Panchbhaya, Yasmin N., additional, Forrest, Leysa M., additional, Niola, Paola, additional, Findlay, Jacqueline, additional, Brooks, Tony T., additional, Gavriil, Artemis, additional, Mestek-Boukhibar, Lamia, additional, Weeks, Sam, additional, Pandey, Sarojini, additional, Berry, Lisa, additional, Jones, Katie, additional, Richter, Alex, additional, Beggs, Andrew, additional, Smith, Colin P., additional, Bucca, Giselda, additional, Hesketh, Andrew R., additional, Harrison, Ewan M., additional, Peacock, Sharon J., additional, Palmer, Sophie, additional, Churcher, Carol M., additional, Bellis, Katherine L., additional, Girgis, Sophia T., additional, Naydenova, Plamena, additional, Blane, Beth, additional, Sridhar, Sushmita, additional, Ruis, Chris, additional, Forrest, Sally, additional, Cormie, Claire, additional, Gill, Harmeet K., additional, Dias, Joana, additional, Higginson, Ellen E., additional, Maes, Mailis, additional, Young, Jamie, additional, Kermack, Leanne M., additional, Hadjirin, Nazreen F., additional, Aggarwal, Dinesh, additional, Griffith, Luke, additional, Swingler, Tracey, additional, Davidson, Rose K., additional, Williams, Thomas, additional, Balcazar, Carlos E., additional, Gallagher, Michael D., additional, O'Toole, Áine, additional, Rooke, Stefan, additional, Colquhoun, Rachel, additional, Ashworth, Jordan, additional, McCrone, J.T., additional, Scher, Emily, additional, Yu, Xiaoyu, additional, Williamson, Kathleen A., additional, Stanton, Thomas D., additional, Michell, Stephen L., additional, Bewshea, Claire M., additional, Temperton, Ben, additional, Michelsen, Michelle L., additional, Warwick-Dugdale, Joanna, additional, Manley, Robin, additional, Farbos, Audrey, additional, Harrison, James W., additional, Sambles, Christine M., additional, Studholme, David J., additional, Jeffries, Aaron R., additional, Darby, Alistair C., additional, Hiscox, Julian A., additional, Paterson, Steve, additional, Iturriza-Gomara, Miren, additional, Jackson, Kathryn A., additional, Lucaci, Anita O., additional, Vamos, Edith E., additional, Hughes, Margaret, additional, Rainbow, Lucille, additional, Eccles, Richard, additional, Nelson, Charlotte, additional, Whitehead, Mark, additional, Turtle, Lance, additional, Haldenby, Sam T., additional, Gregory, Richard, additional, Gemmell, Matthew, additional, Kwiatkowski, Dominic, additional, de Silva, Thushan I., additional, Smith, Nikki, additional, Angyal, Adrienn, additional, Lindsey, Benjamin B., additional, Groves, Danielle C., additional, Green, Luke R., additional, Wang, Dennis, additional, Freeman, Timothy M., additional, Parker, Matthew D., additional, Keeley, Alexander J., additional, Parsons, Paul J., additional, Tucker, Rachel M., additional, Brown, Rebecca, additional, Wyles, Matthew, additional, Constantinidou, Chrystala, additional, Unnikrishnan, Meera, additional, Ott, Sascha, additional, Cheng, Jeffrey K.J., additional, Bridgewater, Hannah E., additional, Frost, Lucy R., additional, Taylor-Joyce, Grace, additional, Stark, Richard, additional, Baxter, Laura, additional, Alam, Mohammad T., additional, Brown, Paul E., additional, McClure, Patrick C., additional, Chappell, Joseph G., additional, Tsoleridis, Theocharis, additional, Ball, Jonathan, additional, Grammatopoulos, Dimitris, additional, Buck, David, additional, Todd, John A., additional, Green, Angie, additional, Trebes, Amy, additional, MacIntyre-Cockett, George, additional, de Cesare, Mariateresa, additional, Langford, Cordelia, additional, Alderton, Alex, additional, Amato, Roberto, additional, Goncalves, Sonia, additional, Jackson, David K., additional, Johnston, Ian, additional, Sillitoe, John, additional, Palmer, Steve, additional, Lawniczak, Mara, additional, Berriman, Matt, additional, Danesh, John, additional, Livett, Rich, additional, Shirley, Lesley, additional, Farr, Ben, additional, Quail, Mike, additional, Thurston, Scott, additional, Park, Naomi, additional, Betteridge, Emma, additional, Weldon, Danni, additional, Goodwin, Scott, additional, Nelson, Rachel, additional, Beaver, Charlotte, additional, Letchford, Laura, additional, Jackson, David A., additional, Foulser, Luke, additional, McMinn, Liz, additional, Prestwood, Liam, additional, Kay, Sally, additional, Kane, Leanne, additional, Dorman, Matthew J., additional, Martincorena, Inigo, additional, Puethe, Christoph, additional, Keatley, Jon-Paul, additional, Tonkin-Hill, Gerry, additional, Smith, Christen, additional, Jamrozy, Dorota, additional, Beale, Mathew A., additional, Patel, Minal, additional, Ariani, Cristina, additional, Spencer-Chapman, Michael, additional, Drury, Eleanor, additional, Lo, Stephanie, additional, Rajatileka, Shavanthi, additional, Scott, Carol, additional, James, Keith, additional, Buddenborg, Sarah K., additional, Berger, Duncan J., additional, Patel, Gaurang, additional, Garcia-Casado, Maria V., additional, Dibling, Thomas, additional, McGuigan, Samantha, additional, Rogers, Hazel A., additional, Hunter, Adam D., additional, Souster, Emily, additional, and Neaverson, Alexandra S., additional

Published
2021
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47. EBV deletions as biomarkers of response to treatment of Chronic Active Epstein Barr Virus

Author

Venturini, Cristina, primary, Houldcroft, Charlotte J, additional, Lazareva, Arina, additional, Wegner, Fanny, additional, Morfopoulou, Sofia, additional, Amrolia, Persis J., additional, Golwala, Zainab, additional, Rao, Anupama, additional, Marks, Stephen D., additional, Simmonds, Jacob, additional, Yoshikawa, Tetsushi, additional, Farrell, Paul J., additional, Cohen, Jeffrey I., additional, Worth, Austen J., additional, and Breuer, Judith, additional

Published
2020
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48. Using Whole Genome Sequences to Investigate Adenovirus Outbreaks, Including Five Deaths in a Haematopoietic Stem Cell Transplant Unit

Author

Myers, Chloe E., primary, Houldcroft, Charlotte J., additional, Roy, Sunando, additional, Margetts, Ben K., additional, Best, Timothy, additional, Venturini, Cristina, additional, Guerra-Assunção, José A., additional, Williams, Charlotte A., additional, Williams, Rachel, additional, Dunn, Helen, additional, Hartley, John C., additional, Rolfe, Kathryn J., additional, and Breuer, Judith, additional

Published
2020
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49. A2B-COVID: A method for evaluating potential SARS-CoV-2 transmission events

Author

Illingworth, Christopher J. R., primary, Hamilton, William L., additional, Jackson, Chris, additional, Popay, Ashley, additional, Meredith, Luke, additional, Houldcroft, Charlotte J., additional, Hosmillo, Myra, additional, Jahun, Aminu, additional, Routledge, Matthew, additional, Warne, Ben, additional, Caller, Laura, additional, Caddy, Sarah, additional, Yakovleva, Anna, additional, Hall, Grant, additional, Khokhar, Fahad A., additional, Feltwell, Theresa, additional, Pinckert, Malte L., additional, Georgana, Iliana, additional, Chaudhry, Yasmin, additional, Curran, Martin, additional, Parmar, Surendra, additional, Sparkes, Dominic, additional, Rivett, Lucy, additional, Jones, Nick K., additional, Sridhar, Sushmita, additional, Forrest, Sally, additional, Dymond, Tom, additional, Grainger, Kayleigh, additional, Workman, Chris, additional, Gkrania-Klotsas, Effrossyni, additional, Brown, Nicholas M., additional, Weekes, Michael P., additional, Baker, Stephen, additional, Peacock, Sharon J., additional, Gouliouris, Theodore, additional, Goodfellow, Ian, additional, Angelis, Daniela De, additional, and Török, M. Estée, additional

Published
2020
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50. Assessing Anti-HCMV Cell Mediated Immune Responses in Transplant Recipients and Healthy Controls Using a Novel Functional Assay

Author

Houldcroft, Charlotte J., primary, Jackson, Sarah E., additional, Lim, Eleanor Y., additional, Sedikides, George X., additional, Davies, Emma L., additional, Atkinson, Claire, additional, McIntosh, Megan, additional, Remmerswaal, Ester B. M., additional, Okecha, Georgina, additional, Bemelman, Frederike J., additional, Stanton, Richard J., additional, Reeves, Matthew, additional, and Wills, Mark R., additional

Published
2020
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