Year Item Type Full Text

2022

Risk factors for Crimean-Congo Haemorrhagic Fever (CCHF) virus exposure in farming communities in Uganda. (2022) Atim, Stella A; Ashraf, Shirin; Belij-Rammerstorfer, Sandra; Ademun, Anna R; Vudriko, Patrick; Nakayiki, Teddy; Niebel, Marc; Shepherd, James; Balinandi, Stephen; Nakanjako, Gladys; Abaasa, Andrew; Johnson, Paul CD; Odongo, Steven; Esau, Martin; Bahati, Milton; Kaleebu, Pontiano; Lutwama, Julius J; Masembe, Charles; Lambe, Teresa; Thomson, Emma C; Tweyongyere, Robert

Women in the European Virus Bioinformatics Center. (2022) Hufsky, Franziska; Abecasis, Ana; Agudelo-Romero, Patricia; Bletsa, Magda; Brown, Katherine; Claus, Claudia; Deinhardt-Emmer, Stefanie; Deng, Li; Friedel, Caroline C; Gismondi, María Inés; Kostaki, Evangelia Georgia; Kühnert, Denise; Kulkarni-Kale, Urmila; Metzner, Karin J; Meyer, Irmtraud M; Miozzi, Laura; Nishimura, Luca; Paraskevopoulou, Sofia; Pérez-Cataluña, Alba; Rahlff, Janina; Thomson, Emma; Tumescheit, Charlotte; van der Hoek, Lia; Van Espen, Lore; Vandamme, Anne-Mieke; Zaheri, Maryam; Zuckerman, Neta; Marz, Manja

Persistence of immunogenicity after seven COVID-19 vaccines given as third dose boosters following two doses of ChAdOx1 nCov-19 or BNT162b2 in the UK: Three month analyses of the COV-BOOST trial. (2022) Liu, Xinxue; Munro, Alasdair PS; Feng, Shuo; Janani, Leila; Aley, Parvinder K; Babbage, Gavin; Baxter, David; Bula, Marcin; Cathie, Katrina; Chatterjee, Krishna; Dejnirattisai, Wanwisa; Dodd, Kate; Enever, Yvanne; Qureshi, Ehsaan; Goodman, Anna L; Green, Christopher A; Harndahl, Linda; Haughney, John; Hicks, Alexander; van der Klaauw, Agatha A; Kwok, Jonathan; Libri, Vincenzo; Llewelyn, Martin J; McGregor, Alastair C; Minassian, Angela M; Moore, Patrick; Mughal, Mehmood; Mujadidi, Yama F; Holliday, Kyra; Osanlou, Orod; Osanlou, Rostam; Owens, Daniel R; Pacurar, Mihaela; Palfreeman, Adrian; Pan, Daniel; Rampling, Tommy; Regan, Karen; Saich, Stephen; Serafimova, Teona; Saralaya, Dinesh; Screaton, Gavin R; Sharma, Sunil; Sheridan, Ray; Sturdy, Ann; Supasa, Piyada; Thomson, Emma C; Todd, Shirley; Twelves, Chris; Read, Robert C; Charlton, Sue; Hallis, Bassam; Ramsay, Mary; Andrews, Nick; Lambe, Teresa; Nguyen-Van-Tam, Jonathan S; Cornelius, Victoria; Snape, Matthew D; Faust, Saul N; COV-BOOST study group

SARS-CoV-2 Evolution and Patient Immunological History Shape the Breadth and Potency of Antibody-Mediated Immunity. (2022) Manali, Maria; Bissett, Laura A; Amat, Julien AR; Logan, Nicola; Scott, Sam; Hughes, Ellen C; Harvey, William T; Orton, Richard; Thomson, Emma C; Gunson, Rory N; Viana, Mafalda; Willett, Brian; Murcia, Pablo R

Safety, immunogenicity, and reactogenicity of BNT162b2 and mRNA-1273 COVID-19 vaccines given as fourth-dose boosters following two doses of ChAdOx1 nCoV-19 or BNT162b2 and a third dose of BNT162b2 (COV-BOOST): a multicentre, blinded, phase 2, randomised trial. (2022) Munro, Alasdair PS; Feng, Shuo; Janani, Leila; Cornelius, Victoria; Aley, Parvinder K; Babbage, Gavin; Baxter, David; Bula, Marcin; Cathie, Katrina; Chatterjee, Krishna; Dodd, Kate; Enever, Yvanne; Qureshi, Ehsaan; Goodman, Anna L; Green, Christopher A; Harndahl, Linda; Haughney, John; Hicks, Alexander; van der Klaauw, Agatha A; Kanji, Nasir; Libri, Vincenzo; Llewelyn, Martin J; McGregor, Alastair C; Maallah, Mina; Minassian, Angela M; Moore, Patrick; Mughal, Mehmood; Mujadidi, Yama F; Holliday, Kyra; Osanlou, Orod; Osanlou, Rostam; Owens, Daniel R; Pacurar, Mihaela; Palfreeman, Adrian; Pan, Daniel; Rampling, Tommy; Regan, Karen; Saich, Stephen; Bawa, Tanveer; Saralaya, Dinesh; Sharma, Sunil; Sheridan, Ray; Thomson, Emma C; Todd, Shirley; Twelves, Chris; Read, Robert C; Charlton, Sue; Hallis, Bassam; Ramsay, Mary; Andrews, Nick; Lambe, Teresa; Nguyen-Van-Tam, Jonathan S; Snape, Matthew D; Liu, Xinxue; Faust, Saul N; COV-BOOST study group

Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. (2022) Nickbakhsh, Sema; Hughes, Joseph; Christofidis, Nicolaos; Griffiths, Emily; Shaaban, Sharif; Enright, Jessica; Smollett, Katherine; Nomikou, Kyriaki; Palmalux, Natasha; Tong, Lily; Carmichael, Stephen; Sreenu, Vattipally B; Orton, Richard; Goldstein, Emily J; Tomb, Rachael M; COVID-19 Genomics UK (COG-UK) Consortium; Templeton, Kate; Gunson, Rory N; da Silva Filipe, Ana; Milosevic, Catriona; Thomson, Emma; Robertson, David L; Holden, Matthew TG; Illingworth, Christopher JR; Smith-Palmer, Alison

Characterisation of a Hepatitis C Virus Subtype 2a Cluster in Scottish PWID with a Suboptimal Response to Glecaprevir/Pibrentasvir Treatment. (2022) Shah, Rajiv; Barclay, Stephen T; Peters, Erica S; Fox, Ray; Gunson, Rory; Bradley-Stewart, Amanda; Shepherd, Samantha J; MacLean, Alasdair; Tong, Lily; van Vliet, Vera Jannie Elisabeth; Ngan Chiu Bong, Michael; Filipe, Ana; Thomson, Emma C; Davis, Chris

Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study. (2022) Stirrup, Oliver; Blackstone, James; Mapp, Fiona; MacNeil, Alyson; Panca, Monica; Holmes, Alison; Machin, Nicholas; Shin, Gee Yen; Mahungu, Tabitha; Saeed, Kordo; Saluja, Tranprit; Taha, Yusri; Mahida, Nikunj; Pope, Cassie; Chawla, Anu; Cutino-Moguel, Maria-Teresa; Tamuri, Asif; Williams, Rachel; Darby, Alistair; Robertson, David L; Flaviani, Flavia; Nastouli, Eleni; Robson, Samuel; Smith, Darren; Loose, Matthew; Laing, Kenneth; Monahan, Irene; Kele, Beatrix; Haldenby, Sam; George, Ryan; Bashton, Matthew; Witney, Adam A; Byott, Matthew; Coll, Francesc; Chapman, Michael; Peacock, Sharon J; COG-UK HOCI Investigators; COVID-19 Genomics UK (COG-UK) consortium; Hughes, Joseph; Nebbia, Gaia; Partridge, David G; Parker, Matthew; Price, James Richard; Peters, Christine; Roy, Sunando; Snell, Luke B; de Silva, Thushan I; Thomson, Emma; Flowers, Paul; Copas, Andrew; Breuer, Judith

2021

Real-World Outcomes of Direct-Acting Antiviral Treatment and Retreatment in United Kingdom-Based Patients Infected With Hepatitis C Virus Genotypes/Subtypes Endemic in Africa. (2021) Aranday-Cortes, Elihu; McClure, C Patrick; Davis, Christopher; Irving, William L; Adeboyejo, Kazeem; Tong, Lily; da Silva Filipe, Ana; Sreenu, Vattipally; Agarwal, Kosh; Mutimer, David; Stone, Benjamin; Cramp, Matthew E; Thomson, Emma C; Ball, Jonathan K; McLauchlan, John

Lassa Virus Circulation in Small Mammal Populations in Bo District, Sierra Leone. (2021) Bangura, Umaru; Buanie, Jacob; Lamin, Joyce; Davis, Christopher; Bongo, Gédéon Ngiala; Dawson, Michael; Ansumana, Rashid; Sondufu, Dianah; Thomson, Emma C; Sahr, Foday; Fichet-Calvet, Elisabeth

The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study. (2021) Boshier, Florencia AT; 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; COG-UK HOCI Variant Substudy consortium*, The COVID-19 Genomics

Analysis of an Ebola virus disease survivor whose host and viral markers were predictive of death indicates the effectiveness of medical countermeasures and supportive care. (2021) Bosworth, Andrew; Rickett, Natasha Y; Dong, Xiaofeng; Ng, Lisa FP; García-Dorival, Isabel; Matthews, David A; Fletcher, Tom; Jacobs, Michael; Thomson, Emma C; Carroll, Miles W; Hiscox, Julian A

Age-related immune response heterogeneity to SARS-CoV-2 vaccine BNT162b2. (2021) Collier, Dami A; Ferreira, Isabella ATM; Kotagiri, Prasanti; Datir, Rawlings P; Lim, Eleanor Y; Touizer, Emma; Meng, Bo; Abdullahi, Adam; CITIID-NIHR BioResource COVID-19 Collaboration; Elmer, Anne; Kingston, Nathalie; Graves, Barbara; Le Gresley, Emma; Caputo, Daniela; Bergamaschi, Laura; Smith, Kenneth GC; Bradley, John R; Ceron-Gutierrez, Lourdes; Cortes-Acevedo, Paulina; Barcenas-Morales, Gabriela; Linterman, Michelle A; McCoy, Laura E; Davis, Chris; Thomson, Emma; Lyons, Paul A; McKinney, Eoin; Doffinger, Rainer; Wills, Mark; Gupta, Ravindra K

Reduced neutralisation of the Delta (B.1.617.2) SARS-CoV-2 variant of concern following vaccination. (2021) Davis, Chris; Logan, Nicola; Tyson, Grace; Orton, Richard; Harvey, William T; Perkins, Jonathan S; Mollett, Guy; Blacow, Rachel M; COVID-19 Genomics UK (COG-UK) Consortium; Peacock, Thomas P; Barclay, Wendy S; Cherepanov, Peter; Palmarini, Massimo; Murcia, Pablo R; Patel, Arvind H; Robertson, David L; Haughney, John; Thomson, Emma C; Willett, Brian J; COVID-19 DeplOyed VaccinE (DOVE) Cohort Study investigators

Children develop robust and sustained cross-reactive spike-specific immune responses to SARS-CoV-2 infection. (2021) Dowell, Alexander C; Butler, Megan S; Jinks, Elizabeth; Tut, Gokhan; Lancaster, Tara; Sylla, Panagiota; Begum, Jusnara; Bruton, Rachel; Pearce, Hayden; Verma, Kriti; Logan, Nicola; Tyson, Grace; Spalkova, Eliska; Margielewska-Davies, Sandra; Taylor, Graham S; Syrimi, Eleni; Baawuah, Frances; Beckmann, Joanne; Okike, Ifeanyichukwu O; Ahmad, Shazaad; Garstang, Joanna; Brent, Andrew J; Brent, Bernadette; Ireland, Georgina; Aiano, Felicity; Amin-Chowdhury, Zahin; Jones, Samuel; Borrow, Ray; Linley, Ezra; Wright, John; Azad, Rafaq; Waiblinger, Dagmar; Davis, Chris; Thomson, Emma C; Palmarini, Massimo; Willett, Brian J; Barclay, Wendy S; Poh, John; Amirthalingam, Gayatri; Brown, Kevin E; Ramsay, Mary E; Zuo, Jianmin; Moss, Paul; Ladhani, Shamez

Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 variant of concern 202012/01 (B.1.1.7): an exploratory analysis of a randomised controlled trial. (2021) Emary, Katherine RW; Golubchik, Tanya; Aley, Parvinder K; Ariani, Cristina V; Angus, Brian; Bibi, Sagida; Blane, Beth; Bonsall, David; Cicconi, Paola; Charlton, Sue; Clutterbuck, Elizabeth A; Collins, Andrea M; Cox, Tony; Darton, Thomas C; Dold, Christina; Douglas, Alexander D; Duncan, Christopher JA; Ewer, Katie J; Flaxman, Amy L; Faust, Saul N; Ferreira, Daniela M; Feng, Shuo; Finn, Adam; Folegatti, Pedro M; Fuskova, Michelle; Galiza, Eva; Goodman, Anna L; Green, Catherine M; Green, Christopher A; Greenland, Melanie; Hallis, Bassam; Heath, Paul T; Hay, Jodie; Hill, Helen C; Jenkin, Daniel; Kerridge, Simon; Lazarus, Rajeka; Libri, Vincenzo; Lillie, Patrick J; Ludden, Catherine; Marchevsky, Natalie G; Minassian, Angela M; McGregor, Alastair C; Mujadidi, Yama F; Phillips, Daniel J; Plested, Emma; Pollock, Katrina M; Robinson, Hannah; Smith, Andrew; Song, Rinn; Snape, Matthew D; Sutherland, Rebecca K; Thomson, Emma C; Toshner, Mark; Turner, David PJ; Vekemans, Johan; Villafana, Tonya L; Williams, Christopher J; Hill, Adrian VS; Lambe, Teresa; Gilbert, Sarah C; Voysey, Merryn; Ramasamy, Maheshi N; Pollard, Andrew J; COVID-19 Genomics UK consortium; AMPHEUS Project; Oxford COVID-19 Vaccine Trial Group

Safety and Efficacy of NVX-CoV2373 Covid-19 Vaccine. (2021) Heath, Paul T; Galiza, Eva P; Baxter, David N; Boffito, Marta; Browne, Duncan; Burns, Fiona; Chadwick, David R; Clark, Rebecca; Cosgrove, Catherine; Galloway, James; Goodman, Anna L; Heer, Amardeep; Higham, Andrew; Iyengar, Shalini; Jamal, Arham; Jeanes, Christopher; Kalra, Philip A; Kyriakidou, Christina; McAuley, Daniel F; Meyrick, Agnieszka; Minassian, Angela M; Minton, Jane; Moore, Patrick; Munsoor, Imrozia; Nicholls, Helen; Osanlou, Orod; Packham, Jonathan; Pretswell, Carol H; San Francisco Ramos, Alberto; Saralaya, Dinesh; Sheridan, Ray P; Smith, Richard; Soiza, Roy L; Swift, Pauline A; Thomson, Emma C; Turner, Jeremy; Viljoen, Marianne E; Albert, Gary; Cho, Iksung; Dubovsky, Filip; Glenn, Greg; Rivers, Joy; Robertson, Andreana; Smith, Kathy; Toback, Seth; 2019nCoV-302 Study Group

Harmonizing and publishing heterogeneous premodern manuscript metadata as Linked Open Data. (2021) Koho, Mikko; Burrows, Toby; Hyvönen, Eero; Ikkala, Esko; Page, Kevin; Ransom, Lynn; Tuominen, Jouni; Emery, Doug; Fraas, Mitch; Heller, Benjamin; Lewis, David; Morrison, Andrew; Porte, Guillaume; Thomson, Emma; Velios, Athanasios; Wijsman, Hanno

Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units - A high risk community-hospital interface. (2021) Li, Kathy K; Woo, Y Mun; Stirrup, Oliver; Hughes, Joseph; Ho, Antonia; Filipe, Ana Da Silva; Johnson, Natasha; Smollett, Katherine; Mair, Daniel; Carmichael, Stephen; Tong, Lily; Nichols, Jenna; Aranday-Cortes, Elihu; Brunker, Kirstyn; Parr, Yasmin A; Nomikou, Kyriaki; McDonald, Sarah E; Niebel, Marc; Asamaphan, Patawee; Sreenu, Vattipally B; Robertson, David L; Taggart, Aislynn; Jesudason, Natasha; Shah, Rajiv; Shepherd, James; Singer, Josh; Taylor, Alison HM; Cousland, Zoe; Price, Jonathan; Lees, Jennifer S; Jones, Timothy PW; Lopez, Carlos Varon; MacLean, Alasdair; Starinskij, Igor; Gunson, Rory; Morris, Scott TW; Thomson, Peter C; Geddes, Colin C; Traynor, Jamie P; Breuer, Judith; Thomson, Emma C; Mark, Patrick B; COVID-19 Genomics UK (COG-UK) consortium

SARS-CoV-2 within-host diversity and transmission. (2021) Lythgoe, Katrina A; Hall, Matthew; Ferretti, Luca; de Cesare, Mariateresa; MacIntyre-Cockett, George; Trebes, Amy; Andersson, Monique; Otecko, Newton; Wise, Emma L; Moore, Nathan; Lynch, Jessica; Kidd, Stephen; Cortes, Nicholas; Mori, Matilde; Williams, Rebecca; Vernet, Gabrielle; Justice, Anita; Green, Angie; Nicholls, Samuel M; Ansari, M Azim; Abeler-Dörner, Lucie; Moore, Catrin E; Peto, Timothy EA; Eyre, David W; Shaw, Robert; Simmonds, Peter; Buck, David; Todd, John A; Oxford Virus Sequencing Analysis Group (OVSG); Connor, Thomas R; Ashraf, Shirin; da Silva Filipe, Ana; Shepherd, James; Thomson, Emma C; COVID-19 Genomics UK (COG-UK) Consortium; Bonsall, David; Fraser, Christophe; Golubchik, Tanya

Safety and immunogenicity of seven COVID-19 vaccines as a third dose (booster) following two doses of ChAdOx1 nCov-19 or BNT162b2 in the UK (COV-BOOST): a blinded, multicentre, randomised, controlled, phase 2 trial. (2021) Munro, Alasdair PS; Janani, Leila; Cornelius, Victoria; Aley, Parvinder K; Babbage, Gavin; Baxter, David; Bula, Marcin; Cathie, Katrina; Chatterjee, Krishna; Dodd, Kate; Enever, Yvanne; Gokani, Karishma; Goodman, Anna L; Green, Christopher A; Harndahl, Linda; Haughney, John; Hicks, Alexander; van der Klaauw, Agatha A; Kwok, Jonathan; Lambe, Teresa; Libri, Vincenzo; Llewelyn, Martin J; McGregor, Alastair C; Minassian, Angela M; Moore, Patrick; Mughal, Mehmood; Mujadidi, Yama F; Murira, Jennifer; Osanlou, Orod; Osanlou, Rostam; Owens, Daniel R; Pacurar, Mihaela; Palfreeman, Adrian; Pan, Daniel; Rampling, Tommy; Regan, Karen; Saich, Stephen; Salkeld, Jo; Saralaya, Dinesh; Sharma, Sunil; Sheridan, Ray; Sturdy, Ann; Thomson, Emma C; Todd, Shirley; Twelves, Chris; Read, Robert C; Charlton, Sue; Hallis, Bassam; Ramsay, Mary; Andrews, Nick; Nguyen-Van-Tam, Jonathan S; Snape, Matthew D; Liu, Xinxue; Faust, Saul N; COV-BOOST study group

Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data. (2021) Parker, Matthew D; Lindsey, Benjamin B; Leary, Shay; Gaudieri, Silvana; Chopra, Abha; Wyles, Matthew; Angyal, Adrienn; Green, Luke R; Parsons, Paul; Tucker, Rachel M; Brown, Rebecca; Groves, Danielle; Johnson, Katie; Carrilero, Laura; Heffer, Joe; Partridge, David G; Evans, Cariad; Raza, Mohammad; Keeley, Alexander J; Smith, Nikki; Filipe, Ana Da Silva; Shepherd, James G; Davis, Chris; Bennett, Sahan; Sreenu, Vattipally B; Kohl, Alain; Aranday-Cortes, Elihu; Tong, Lily; Nichols, Jenna; Thomson, Emma C; COVID-19 Genomics UK (COG-UK) Consortium; Wang, Dennis; Mallal, Simon; de Silva, Thushan I

A plasmid DNA-launched SARS-CoV-2 reverse genetics system and coronavirus toolkit for COVID-19 research. (2021) Rihn, Suzannah J; Merits, Andres; Bakshi, Siddharth; Turnbull, Matthew L; Wickenhagen, Arthur; Alexander, Akira JT; Baillie, Carla; Brennan, Benjamin; Brown, Fiona; Brunker, Kirstyn; Bryden, Steven R; Burness, Kerry A; Carmichael, Stephen; Cole, Sarah J; Cowton, Vanessa M; Davies, Paul; Davis, Chris; De Lorenzo, Giuditta; Donald, Claire L; Dorward, Mark; Dunlop, James I; Elliott, Matthew; Fares, Mazigh; da Silva Filipe, Ana; Freitas, Joseph R; Furnon, Wilhelm; Gestuveo, Rommel J; Geyer, Anna; Giesel, Daniel; Goldfarb, Daniel M; Goodman, Nicola; Gunson, Rory; Hastie, C James; Herder, Vanessa; Hughes, Joseph; Johnson, Clare; Johnson, Natasha; Kohl, Alain; Kerr, Karen; Leech, Hannah; Lello, Laura Sandra; Li, Kathy; Lieber, Gauthier; Liu, Xiang; Lingala, Rajendra; Loney, Colin; Mair, Daniel; McElwee, Marion J; McFarlane, Steven; Nichols, Jenna; Nomikou, Kyriaki; Orr, Anne; Orton, Richard J; Palmarini, Massimo; Parr, Yasmin A; Pinto, Rute Maria; Raggett, Samantha; Reid, Elaine; Robertson, David L; Royle, Jamie; Cameron-Ruiz, Natalia; Shepherd, James G; Smollett, Katherine; Stewart, Douglas G; Stewart, Meredith; Sugrue, Elena; Szemiel, Agnieszka M; Taggart, Aislynn; Thomson, Emma C; Tong, Lily; Torrie, Leah S; Toth, Rachel; Varjak, Margus; Wang, Sainan; Wilkinson, Stuart G; Wyatt, Paul G; Zusinaite, Eva; Alessi, Dario R; Patel, Arvind H; Zaid, Ali; Wilson, Sam J; Mahalingam, Suresh

Non-epidemic HCV genotypes in low- and middle-income countries and the risk of resistance to current direct-acting antiviral regimens. (2021) Shah, Rajiv; Ahovegbe, Lucrece; Niebel, Marc; Shepherd, James; Thomson, Emma C

Seoul Virus Associated with Pet Rats, Scotland, UK, 2019. (2021) Shepherd, James G; Blunsum, Andrew E; Carmichael, Stephen; Smollett, Katherine; Maxwell-Scott, Hector; Farmer, Eoghan CW; Osborne, Jane; MacLean, Alasdair; Ashraf, Shirin; Shah, Rajiv; Gunson, Rory; da Silva Filipe, Ana; Aarons, Emma J; Thomson, Emma C

Real world SOF/VEL/VOX retreatment outcomes and viral resistance analysis for HCV patients with prior failure to DAA therapy. (2021) Smith, David A; Bradshaw, Daniel; Mbisa, Jean L; Manso, Carmen F; Bibby, David F; Singer, Joshua B; Thomson, Emma C; da Silva Filipe, Ana; Aranday-Cortes, Elihu; Ansari, M Azim; Brown, Anthony; Hudson, Emma; Benselin, Jennifer; Healy, Brendan; Troke, Phil; McLauchlan, John; Barnes, Eleanor; Irving, William L

SARS-CoV-2 lineage B.1.1.7 is associated with greater disease severity among hospitalised women but not men: multicentre cohort study. (2021) 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; Kele, Beatrix; Monahan, Irene; Mollett, Guy; Parker, Matthew; Pelosi, Emanuela; Randell, Paul; Roy, Sunando; Taylor, Joshua; Weller, Sophie; Wilson-Davies, Eleri; Wade, Phillip; Williams, Rachel; COG-UK-HOCI Variant substudy consortium; COVID-19 Genomics UK (COG-UK) consortium; 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

Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data. (2021) Stirrup, Oliver; Hughes, Joseph; Parker, Matthew; Partridge, David G; Shepherd, James G; Blackstone, James; Coll, Francesc; Keeley, Alexander; Lindsey, Benjamin B; Marek, Aleksandra; Peters, Christine; Singer, Joshua B; COVID-19 Genomics UK (COG-UK) consortium; Tamuri, Asif; de Silva, Thushan I; Thomson, Emma C; Breuer, Judith

In vitro selection of Remdesivir resistance suggests evolutionary predictability of SARS-CoV-2. (2021) Szemiel, Agnieszka M; Merits, Andres; Orton, Richard J; MacLean, Oscar A; Pinto, Rute Maria; Wickenhagen, Arthur; Lieber, Gauthier; Turnbull, Matthew L; Wang, Sainan; Furnon, Wilhelm; Suarez, Nicolas M; Mair, Daniel; da Silva Filipe, Ana; Willett, Brian J; Wilson, Sam J; Patel, Arvind H; Thomson, Emma C; Palmarini, Massimo; Kohl, Alain; Stewart, Meredith E

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. (2021) Thomson, Emma C; Rosen, Laura E; Shepherd, James G; Spreafico, Roberto; da Silva Filipe, Ana; Wojcechowskyj, Jason A; Davis, Chris; Piccoli, Luca; Pascall, David J; Dillen, Josh; Lytras, Spyros; Czudnochowski, Nadine; Shah, Rajiv; Meury, Marcel; Jesudason, Natasha; De Marco, Anna; Li, Kathy; Bassi, Jessica; O'Toole, Aine; Pinto, Dora; Colquhoun, Rachel M; Culap, Katja; Jackson, Ben; Zatta, Fabrizia; Rambaut, Andrew; Jaconi, Stefano; Sreenu, Vattipally B; Nix, Jay; Zhang, Ivy; Jarrett, Ruth F; Glass, William G; Beltramello, Martina; Nomikou, Kyriaki; Pizzuto, Matteo; Tong, Lily; Cameroni, Elisabetta; Croll, Tristan I; Johnson, Natasha; Di Iulio, Julia; Wickenhagen, Arthur; Ceschi, Alessandro; Harbison, Aoife M; Mair, Daniel; Ferrari, Paolo; Smollett, Katherine; Sallusto, Federica; Carmichael, Stephen; Garzoni, Christian; Nichols, Jenna; Galli, Massimo; Hughes, Joseph; Riva, Agostino; Ho, Antonia; Schiuma, Marco; Semple, Malcolm G; Openshaw, Peter JM; Fadda, Elisa; Baillie, J Kenneth; Chodera, John D; ISARIC4C Investigators; COVID-19 Genomics UK (COG-UK) Consortium; Rihn, Suzannah J; Lycett, Samantha J; Virgin, Herbert W; Telenti, Amalio; Corti, Davide; Robertson, David L; Snell, Gyorgy

Single-dose administration and the influence of the timing of the booster dose on immunogenicity and efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine: a pooled analysis of four randomised trials. (2021) Voysey, Merryn; Costa Clemens, Sue Ann; Madhi, Shabir A; Weckx, Lily Y; Folegatti, Pedro M; Aley, Parvinder K; Angus, Brian; Baillie, Vicky L; Barnabas, Shaun L; Bhorat, Qasim E; Bibi, Sagida; Briner, Carmen; Cicconi, Paola; Clutterbuck, Elizabeth A; Collins, Andrea M; Cutland, Clare L; Darton, Thomas C; Dheda, Keertan; Dold, Christina; Duncan, Christopher JA; Emary, Katherine RW; Ewer, Katie J; Flaxman, Amy; Fairlie, Lee; Faust, Saul N; Feng, Shuo; Ferreira, Daniela M; Finn, Adam; Galiza, Eva; Goodman, Anna L; Green, Catherine M; Green, Christopher A; Greenland, Melanie; Hill, Catherine; Hill, Helen C; Hirsch, Ian; Izu, Alane; Jenkin, Daniel; Joe, Carina CD; Kerridge, Simon; Koen, Anthonet; Kwatra, Gaurav; Lazarus, Rajeka; Libri, Vincenzo; Lillie, Patrick J; Marchevsky, Natalie G; Marshall, Richard P; Mendes, Ana VA; Milan, Eveline P; Minassian, Angela M; McGregor, Alastair; Mujadidi, Yama F; Nana, Anusha; Padayachee, Sherman D; Phillips, Daniel J; Pittella, Ana; Plested, Emma; Pollock, Katrina M; Ramasamy, Maheshi N; Ritchie, Adam J; Robinson, Hannah; Schwarzbold, Alexandre V; Smith, Andrew; Song, Rinn; Snape, Matthew D; Sprinz, Eduardo; Sutherland, Rebecca K; Thomson, Emma C; Török, M Estée; Toshner, Mark; Turner, David PJ; Vekemans, Johan; Villafana, Tonya L; White, Thomas; Williams, Christopher J; Douglas, Alexander D; Hill, Adrian VS; Lambe, Teresa; Gilbert, Sarah C; Pollard, Andrew J; Oxford COVID Vaccine Trial Group

Paper microfluidic implementation of loop mediated isothermal amplification for early diagnosis of hepatitis C virus. (2021) Witkowska McConnell, Weronika; Davis, Chris; Sabir, Suleman R; Garrett, Alice; Bradley-Stewart, Amanda; Jajesniak, Pawel; Reboud, Julien; Xu, Gaolian; Yang, Zhugen; Gunson, Rory; Thomson, Emma C; Cooper, Jonathan M

Sharing a household with children and risk of COVID-19: a study of over 300 000 adults living in healthcare worker households in Scotland. (2021) Wood, Rachael; Thomson, Emma; Galbraith, Robert; Gribben, Ciara; Caldwell, David; Bishop, Jennifer; Reid, Martin; Shah, Anoop SV; Templeton, Kate; Goldberg, David; Robertson, Chris; Hutchinson, Sharon J; Colhoun, Helen M; McKeigue, Paul M; McAllister, David A

2020

Remdesivir induced viral RNA and subgenomic RNA suppression, and evolution of viral variants in SARS-CoV-2 infected patients. (2020) Boshier, Florencia AT; Pang, Juanita; Penner, Justin; Hughes, Joseph; Parker, Matthew; Shepherd, James; Alders, Nele; Bamford, Alasdair; Grandjean, Louis; Grunewald, Stephanie; Hatcher, James; Best, Timothy; Dalton, Caroline; Bynoe, Patricia Dyal; Frauenfelder, Claire; Köeglmeier, Jutta; Myerson, Phoebe; Roy, Sunando; Williams, Rachel; Thomson, Emma C; de Silva, Thushan I; Goldstein, Richard A; Breuer, Judith

Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence. (2020) Filipe, Ana da Silva; Shepherd, James; Williams, Thomas; Hughes, Joseph; Aranday-Cortes, Elihu; Asamaphan, Patawee; Balcazar, Carlos; Brunker, Kirstyn; Carmichael, Stephen; Dewar, Rebecca; Gallagher, Michael D; Gunson, Rory; Ho, Antonia; Jesudason, Natasha; Johnson, Natasha; Leitch, E Carol McWilliam; Li, Kathy; MacLean, Alasdair; Mair, Daniel; McDonald, Sarah E; McHugh, Martin; Nichols, Jenna; Niebel, Marc; Nomikou, Kyriaki; Orton, Richard J; O’Toole, Áine; Palmarini, Massimo; Parr, Yasmin A; Rambaut, Andrew; Rooke, Stefan; Shaaban, Sharif; Shah, Rajiv; Singer, Joshua B; Smollett, Katherine; Starinskij, Igor; Tong, Lily; Vattipally, Sreenu; Wastnedge, Elizabeth; Robertson, David L; Holden, Matthew TG; Templeton, Kate; Thomson, Emma C

Distemper, extinction, and vaccination of the Amur tiger. (2020) Gilbert, Martin; Sulikhan, Nadezhda; Uphyrkina, Olga; Goncharuk, Mikhail; Kerley, Linda; Castro, Enrique Hernandez; Reeve, Richard; Seimon, Tracie; McAloose, Denise; Seryodkin, Ivan V; Naidenko, Sergey V; Davis, Christopher A; Wilkie, Gavin S; Vattipally, Sreenu B; Adamson, Walt E; Hinds, Chris; Thomson, Emma C; Willett, Brian J; Hosie, Margaret J; Logan, Nicola; McDonald, Michael; Ossiboff, Robert J; Shevtsova, Elena I; Belyakin, Stepan; Yurlova, Anna A; Osofsky, Steven A; Miquelle, Dale G; Matthews, Louise; Cleaveland, Sarah

Glasgow Early Treatment Arm Favirpiravir (GETAFIX) for adults with early stage COVID-19: A structured summary of a study protocol for a randomised controlled trial. (2020) Hanna, Catherine R; Blyth, Kevin G; Burley, Glenn; Carmichael, Samantha; Evans, Carol; Hinsley, Samantha; Khadra, Ibrahim; Khoo, Saye; Lewsley, Liz-Anne; Jones, Robert R; Sharma, Raman; Taladriz-Sender, Andrea; Thomson, Emma C; Scott, Janet T

Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data. (2020) Stirrup, Oliver T; Hughes, Joseph; Parker, Matthew; Partridge, David G; Shepherd, James G; Blackstone, James; Coll, Francesc; Keeley, Alexander J; Lindsey, Benjamin B; Marek, Aleksandra; Peters, Christine; Singer, Joshua B; Tamuri, Asif; de Silva, Thushan I; Thomson, Emma C; Breuer, Judith

The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity. (2020) Thomson, Emma C; Rosen, Laura E; Shepherd, James G; Spreafico, Roberto; da Silva Filipe, Ana; Wojcechowskyj, Jason A; Davis, Chris; Piccoli, Luca; Pascall, David J; Dillen, Josh; Lytras, Spyros; Czudnochowski, Nadine; Shah, Rajiv; Meury, Marcel; Jesudason, Natasha; De Marco, Anna; Li, Kathy; Bassi, Jessica; O’Toole, Aine; Pinto, Dora; Colquhoun, Rachel M; Culap, Katja; Jackson, Ben; Zatta, Fabrizia; Rambaut, Andrew; Jaconi, Stefano; Sreenu, Vattipally B; Nix, Jay; Jarrett, Ruth F; Beltramello, Martina; Nomikou, Kyriaki; Pizzuto, Matteo; Tong, Lily; Cameroni, Elisabetta; Johnson, Natasha; Wickenhagen, Arthur; Ceschi, Alessandro; Mair, Daniel; Ferrari, Paolo; Smollett, Katherine; Sallusto, Federica; Carmichael, Stephen; Garzoni, Christian; Nichols, Jenna; Galli, Massimo; Hughes, Joseph; Riva, Agostino; Ho, Antonia; Semple, Malcolm G; Openshaw, Peter JM; Baillie, J Kenneth; Rihn, Suzannah J; Lycett, Samantha J; Virgin, Herbert W; Telenti, Amalio; Corti, Davide; Robertson, David L; Snell, Gyorgy

Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity. (2020) Volz, Erik; Hill, Verity; McCrone, John T; Price, Anna; Jorgensen, David; O’Toole, Áine; Southgate, Joel; Johnson, Robert; Jackson, Ben; Nascimento, Fabricia F; Rey, Sara M; Nicholls, Samuel M; Colquhoun, Rachel M; da Silva Filipe, Ana; Shepherd, James; Pascall, David J; Shah, Rajiv; Jesudason, Natasha; Li, Kathy; Jarrett, Ruth; Pacchiarini, Nicole; Bull, Matthew; Geidelberg, Lily; Siveroni, Igor; Goodfellow, Ian; Loman, Nicholas J; Pybus, Oliver G; Robertson, David L; Thomson, Emma C; Rambaut, Andrew; Connor, Thomas R

2019

Suboptimal SVR rates in African patients with atypical genotype 1 subtypes: Implications for global elimination of hepatitis C. (2019) Childs, Kate; Davis, Christopher; Cannon, Mary; Montague, Sarah; Filipe, Ana; Tong, Lily; Simmonds, Peter; Smith, Donald; Thomson, Emma C; Dusheiko, Geoff; Agarwal, Kosh

2018

Highly Diverse Hepatitis C Strains Detected in Sub-Saharan Africa Have Unknown Susceptibility to Direct-Acting Antiviral Treatments. (2018) Davis, Chris; Mgomella, George S; da Silva Filipe, Ana; Frost, Eric H; Giroux, Genevieve; Hughes, Joseph; Hogan, Catherine; Kaleebu, Pontiano; Asiki, Gershim; McLauchlan, John; Niebel, Marc; Ocama, Ponsiano; Pomila, Cristina; Pybus, Oliver G; Pépin, Jacques; Simmonds, Peter; Singer, Joshua B; Sreenu, Vattipally B; Wekesa, Clara; Young, Elizabeth H; Murphy, Donald G; Sandhu, Manj; Thomson, Emma C

2016

Late Ebola virus relapse causing meningoencephalitis: a case report. (2016) Jacobs, Michael; Rodger, Alison; Bell, David J; Bhagani, Sanjay; Cropley, Ian; Filipe, Ana; Gifford, Robert J; Hopkins, Susan; Hughes, Joseph; Jabeen, Farrah; Johannessen, Ingolfur; Karageorgopoulos, Drosos; Lackenby, Angie; Lester, Rebecca; Liu, Rebecca SN; MacConnachie, Alisdair; Mahungu, Tabitha; Martin, Daniel; Marshall, Neal; Mepham, Stephen; Orton, Richard; Palmarini, Massimo; Patel, Monika; Perry, Colin; Peters, S Erica; Porter, Duncan; Ritchie, David; Ritchie, Neil D; Seaton, R Andrew; Sreenu, Vattipally B; Templeton, Kate; Warren, Simon; Wilkie, Gavin S; Zambon, Maria; Gopal, Robin; Thomson, Emma C