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  1. Article: Antibody Responses to SARS-CoV-2 Infection-Comparative Determination of Seroprevalence in Two High-Throughput Assays versus a Sensitive Spike Protein ELISA.

    Mohanraj, Dinesh / Bicknell, Kelly / Bhole, Malini / Webber, Caroline / Taylor, Lorna / Whitelegg, Alison

    Vaccines

    2021  Volume 9, Issue 11

    Abstract: Robust assay development for SARS-CoV-2 serological testing requires assessment of asymptomatic and non-hospitalised individuals to determine if assays are sensitive to mild antibody responses. Our study evaluated the performance characteristics of two ... ...

    Abstract Robust assay development for SARS-CoV-2 serological testing requires assessment of asymptomatic and non-hospitalised individuals to determine if assays are sensitive to mild antibody responses. Our study evaluated the performance characteristics of two high-throughput SARS-CoV-2 IgG nucleocapsid assays (Abbott Architect and Roche) and The Binding Site (TBS) Anti-Spike IgG/A/M ELISA kit in samples from healthcare workers (HCWs). The 252 samples were collected from multi-site NHS trusts and analysed for SARS-CoV-2 serology. Assay performance was evaluated between these three platforms and ROC curves were used to redefine the Abbott threshold. Concordance between Abbott and TBS was 66%. Any discrepant results were analysed using Roche, which showed 100% concordance with TBS. Analysis conducted in HCWs within 58 days post-PCR result demonstrated 100% sensitivity for both Abbott and Roche. Longitudinal analysis for >100 days post-PCR led to sensitivity of 77.2% and 100% for Abbott and Roche, respectively. A redefined Abbott threshold (0.64) increased sensitivity to 90%, producing results comparable to TBS and Roche. The manufacturer's threshold set by Abbott contributes to lower sensitivity and elevated false-negative occurrences. Abbott performance improved upon re-optimisation of the cut-off threshold. Our findings provided evidence that TBS can be used as bespoke alternative for SARS-CoV-2 serology analysis where high-throughput platforms are not feasible on site.
    Language English
    Publishing date 2021-11-11
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2703319-3
    ISSN 2076-393X
    ISSN 2076-393X
    DOI 10.3390/vaccines9111310
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  2. Article ; Online: Multiple pathways of SARS-CoV-2 nosocomial transmission uncovered by integrated genomic and epidemiological analyses during the second wave of the COVID-19 pandemic in the UK.

    Cook, Kate F / Beckett, Angela H / Glaysher, Sharon / Goudarzi, Salman / Fearn, Christopher / Loveson, Katie F / Elliott, Scott / Wyllie, Sarah / Lloyd, Allyson / Bicknell, Kelly / Lumley, Sally / Chauhan, Anoop J / Robson, Samuel C

    Frontiers in cellular and infection microbiology

    2023  Volume 12, Page(s) 1066390

    Abstract: Introduction: Throughout the global COVID-19 pandemic, nosocomial transmission has represented a major concern for healthcare settings and has accounted for many infections diagnosed within hospitals. As restrictions ease and novel variants continue to ... ...

    Abstract Introduction: Throughout the global COVID-19 pandemic, nosocomial transmission has represented a major concern for healthcare settings and has accounted for many infections diagnosed within hospitals. As restrictions ease and novel variants continue to spread, it is important to uncover the specific pathways by which nosocomial outbreaks occur to understand the most suitable transmission control strategies for the future.
    Methods: In this investigation, SARS-CoV-2 genome sequences obtained from 694 healthcare workers and 1,181 patients were analyzed at a large acute NHS hospital in the UK between September 2020 and May 2021. These viral genomic data were combined with epidemiological data to uncover transmission routes within the hospital. We also investigated the effects of the introduction of the highly transmissible variant of concern (VOC), Alpha, over this period, as well as the effects of the national vaccination program on SARS-CoV-2 infection in the hospital.
    Results: Our results show that infections of all variants within the hospital increased as community prevalence of Alpha increased, resulting in several outbreaks and super-spreader events. Nosocomial infections were enriched amongst older and more vulnerable patients more likely to be in hospital for longer periods but had no impact on disease severity. Infections appeared to be transmitted most regularly from patient to patient and from patients to HCWs. In contrast, infections from HCWs to patients appeared rare, highlighting the benefits of PPE in infection control. The introduction of the vaccine at this time also reduced infections amongst HCWs by over four-times.
    Discussion: These analyses have highlighted the importance of control measures such as regular testing, rapid lateral flow testing alongside polymerase chain reaction (PCR) testing, isolation of positive patients in the emergency department (where possible), and physical distancing of patient beds on hospital wards to minimize nosocomial transmission of infectious diseases such as COVID-19.
    MeSH term(s) Humans ; COVID-19/epidemiology ; SARS-CoV-2/genetics ; Cross Infection/epidemiology ; Pandemics/prevention & control ; Genomics ; United Kingdom/epidemiology
    Language English
    Publishing date 2023-01-20
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2619676-1
    ISSN 2235-2988 ; 2235-2988
    ISSN (online) 2235-2988
    ISSN 2235-2988
    DOI 10.3389/fcimb.2022.1066390
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  3. Article ; Online: Comparative assessment of SARS-CoV-2 serology in healthcare workers with Abbott Architect, Roche Elecsys and The Binding site ELISA immunoassays.

    Mohanraj, Dinesh / Whitelegg, Alison / Bicknell, Kelly / Bhole, Malini / Webber, Caroline / Taylor, Lorna

    medRxiv

    Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serology testing is key for assessing seroprevalence and antibody response post-vaccination in immunocompromised patients. Here we performed a comparison between two high-throughput ... ...

    Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serology testing is key for assessing seroprevalence and antibody response post-vaccination in immunocompromised patients. Here we performed a comparison between two high-throughput nucleocapsid assays (Abbott SARS-CoV-2 IgG and Roche Elecsys Anti-SARS-CoV-2) and The Binding Site (TBS) anti-Spike IgG/A/M- SARS-CoV-2 ELISA kit. 236 samples were collected across 2 sites, Portsmouth Hospital University NHS Trust (PHU) and The Dudley Group NHS Trust. We derived concordance, agreement and assay performance as well as using receiver operating characteristic (ROC) curves to redefine the assay threshold of the Abbott assay. Result concordance between the Abbott and TBS was 66%. Discrepant samples were analysed using the Roche assay which showed 100% agreement with the TBS assay. In samples analysed >58 days post-PCR, the sensitivity of Abbott and Roche was 100%. In samples analysed >100 days post-PCR the sensitivity of the Abbott assay dropped to 77.2% but remained at 100% for the Roche assay. A redefined Abbott threshold of 0.64 increased the sensitivity to 90% giving results similar to the Roche and TBS assays. In conclusion, this study demonstrated Abbott assay had a lower sensitivity in comparison to TBS and Roche. This study established TBS can be implemented as a viable alternative for SARS-CoV-2 serology testing where high-throughput assays are not available on site. Furthermore, anti-spike assays, such as TBS, could be used to monitor vaccination responses to deduce SARS-CoV-2 population-immunity. Further optimization studies are required to evaluate the performance characteristics of these assays which could facilitate widescale sero-epidemiological surveillance.
    Keywords covid19
    Language English
    Publishing date 2021-03-24
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2021.03.19.21253518
    Database COVID19

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  4. Article: Evaluation of a primary to secondary care referral pathway and novel nurse-led one-stop clinic for patients with suspected non-alcoholic fatty liver disease.

    Fowell, Andrew J / Fancey, Kirsty / Gamble, Karen / Bicknell, Kelly / Dowman, Joanna K / Howden, Paul / Aspinall, Richard J

    Frontline gastroenterology

    2020  Volume 12, Issue 2, Page(s) 102–107

    Abstract: Objective: Non-alcoholic fatty liver disease (NAFLD) affects approximately one in four adults of the general population, with an important minority of cases at high risk of developing cirrhosis. We evaluated the utility of a primary care NAFLD pathway ... ...

    Abstract Objective: Non-alcoholic fatty liver disease (NAFLD) affects approximately one in four adults of the general population, with an important minority of cases at high risk of developing cirrhosis. We evaluated the utility of a primary care NAFLD pathway incorporating a specialist nurse-led NAFLD clinic and a two-step testing approach for advanced liver fibrosis.
    Design/method: We performed a retrospective evaluation of prospectively collected demographic and clinical data on all patients diagnosed with NAFLD and intermediate NAFLD fibrosis score seen in our nurse-led NAFLD clinic between 1 May 2014 and 30 April 2017. Patients were assessed using a specific clerking pro forma and transient elastography (TE). Discharge to primary care with lifestyle advice was considered where TE<7.9 kPa.
    Results: 904 patients were identified, 114 (12.6%) of whom did not meet NAFLD criteria. Among the NAFLD population (n=790 (87.4%)), TE<7.9 kPa was present in 558 patients (70.6%), 519 of whom were discharged to primary care. Selected patients were followed up in secondary care despite TE<7.9 kPa or discharged with TE≥7.9 kPa. TE was unreliable in 22 patients (2.7%). Overall, 559 (70.8%) of patients with confirmed NAFLD were discharged from the nurse-led clinic. Introduction of the new pathway was associated with increased screening for hepatitis B and C viruses in primary care, and 17 new cases of alpha-1-antitrypsin deficiency were identified.
    Conclusion: An integrated primary/secondary care NAFLD pathway, including a specialist nurse-led clinic may be a useful way of managing increasing demand on secondary care hepatology services.
    Language English
    Publishing date 2020-04-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 2521857-8
    ISSN 2041-4137
    ISSN 2041-4137
    DOI 10.1136/flgastro-2019-101304
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  5. Article ; Online: Combining viral genomics and clinical data to assess risk factors for severe COVID-19 (mortality, ICU admission, or intubation) amongst hospital patients in a large acute UK NHS hospital Trust.

    Foxley-Marrable, Max / D'Cruz, Leon / Meredith, Paul / Glaysher, Sharon / Beckett, Angela H / Goudarzi, Salman / Fearn, Christopher / Cook, Kate F / Loveson, Katie F / Dent, Hannah / Paul, Hannah / Elliott, Scott / Wyllie, Sarah / Lloyd, Allyson / Bicknell, Kelly / Lumley, Sally / McNicholas, James / Prytherch, David / Lundgren, Andrew /
    Graur, Or / Chauhan, Anoop J / Robson, Samuel C

    PloS one

    2023  Volume 18, Issue 3, Page(s) e0283447

    Abstract: Throughout the COVID-19 pandemic, valuable datasets have been collected on the effects of the virus SARS-CoV-2. In this study, we combined whole genome sequencing data with clinical data (including clinical outcomes, demographics, comorbidity, treatment ... ...

    Abstract Throughout the COVID-19 pandemic, valuable datasets have been collected on the effects of the virus SARS-CoV-2. In this study, we combined whole genome sequencing data with clinical data (including clinical outcomes, demographics, comorbidity, treatment information) for 929 patient cases seen at a large UK hospital Trust between March 2020 and May 2021. We identified associations between acute physiological status and three measures of disease severity; admission to the intensive care unit (ICU), requirement for intubation, and mortality. Whilst the maximum National Early Warning Score (NEWS2) was moderately associated with severe COVID-19 (A = 0.48), the admission NEWS2 was only weakly associated (A = 0.17), suggesting it is ineffective as an early predictor of severity. Patient outcome was weakly associated with myriad factors linked to acute physiological status and human genetics, including age, sex and pre-existing conditions. Overall, we found no significant links between viral genomics and severe outcomes, but saw evidence that variant subtype may impact relative risk for certain sub-populations. Specific mutations of SARS-CoV-2 appear to have little impact on overall severity risk in these data, suggesting that emerging SARS-CoV-2 variants do not result in more severe patient outcomes. However, our results show that determining a causal relationship between mutations and severe COVID-19 in the viral genome is challenging. Whilst improved understanding of the evolution of SARS-CoV-2 has been achieved through genomics, few studies on how these evolutionary changes impact on clinical outcomes have been seen due to complexities associated with data linkage. By combining viral genomics with patient records in a large acute UK hospital, this study represents a significant resource for understanding risk factors associated with COVID-19 severity. However, further understanding will likely arise from studies of the role of host genetics on disease progression.
    MeSH term(s) Humans ; COVID-19/epidemiology ; SARS-CoV-2/genetics ; Pandemics ; State Medicine ; Trust ; Intensive Care Units ; Risk Factors ; Hospitals ; Intubation, Intratracheal ; United Kingdom/epidemiology
    Language English
    Publishing date 2023-03-23
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0283447
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  6. Article ; Online: Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

    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, Dave / Thomson, Emma C. / Rambaut, Andrew / Connor, Thomas R. / 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 / Beér, Robert / Afifi, Safiah / Morgan, Siân / Marchbank, Angela / Kitchen, C. / Gulliver, Huw / Merrick, Ian / Guest, Martyn / Munn, Robert / Workman, Trudy / 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, L. / Zarebski, Alex / Raghwani, Jayna / Kraemer, Moritz / Francois, Sarah / Attwood, Stephen / Vasylyeva, Tetyana / Török, Estée / 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, S. / 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, Ali / Madona, Pinglawathee / Holmes, Alison / Bolt, Frances / Price, James / Mookerjee, Siddharth / Rowan, Aileen / Taylor, Graham P. / Ragonnet-Cronin, Manon / Johnson, Rob / Boyd, Olivia / Volz, Erik M. / Brunker, Kirstyn / Smollett, Katherine L. / Quick, Joshua / McMurray, Claire / Stockton, Joanne / Nicholls, Sam / Rowe, William / 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 / 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 / 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, Shâhjahân / 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 / Cronin, Michelle / 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 / Yāsir, Muḥammad / 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, D. A. / Molnár, Zoltán / 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, K. E. / Richter, Alex / Beggs, Andrew / Smith, Colin P. / Bucca, Giselda / Hesketh, Andrew R. / Harrison, Ewan M. / Peacock, Sharon J. / Eser, 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. / Williams, Thomas / Balcazar, Carlos E. / Gallagher, Michael D. / O'Toole, Áine / Rooke, Stefan / Colquhoun, Rachel / Ashworth, Jordan / 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 / Gramatopoulos, 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.

    Cell. 2021 Jan. 07, v. 184, no. 1 p.64-75.e11

    2021  

    Abstract: Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the ... ...

    Institution COG-UK Consortium
    Abstract Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant.
    Keywords COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; data collection ; founder effect ; genetic analysis ; genome ; mortality ; mutation ; pathogenicity ; phylogeny ; viral load ; United Kingdom ; COVID-19 ; SARS-CoV-2 ; evolution ; epidemiology ; spike
    Language English
    Dates of publication 2021-0107
    Size p. 64-75.e11.
    Publishing place Elsevier Inc.
    Document type Article ; Online
    Note NAL-AP-2-clean
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2020.11.020
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

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  7. Article ; Online: Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

    E., Alm / E. K., Broberg / T., Connor / E. B., Hodcroft / A. B., Komissarov / S., Maurer-Stroh / A., Melidou / R. A., Neher / A., O'Toole / Niko Beerenwinkel, Pereyaslov D. / Posada-Céspedes, Susana / Philipp Jablonski, Kim / Falé Ferreira, Pedro / Topolsky, Ivan / Avšič-Županc, Tatjana / Korva, Miša / Poljak, Mario / Zakotnik, Samo / Mark Zorec, Tomaž /
    Bragstad, Karoline / Hungnes, Olav / Stene-Johansen, Kathrine / Reusken, Chantal / Meijer, Adam / Vennema, Harry / Ruiz-Roldán, Lidia / Alma Bracho, María / García-González, Neris / Chiner-Oms, Álvaro / Cancino-Muñoz, Irving / Comas, Iñaki / A Goig, Galo / Torres-Puente, Manuela / G López, Mariana / Martínez-Priego, Llúcia / D'Auria, Giuseppe / Ferrús-Abad, Loreto / de Marco, Griselda / Galan-Vendrell, Inmaculada / Carbó-Ramirez, Sandra / Ruíz-Hueso, Paula / Coscollá, Mireia / Polackova, Katerina / Kramna, Lenka / Cinek, Ondrej / Richter, Jan / Krashias, George / Tryfonos, Christina / Bashiardes, Stavros / Koptides, Dana / Christodoulou, Christina / Bartolini, Barbara / Em Gruber, Cesare / Di Caro, Antonino / Castilletti, Concetta / Stefani, Fabrizio / Giordana Rimoldi, Sara / Romeri, Francesca / Salerno, Franco / Polesello, Stefano / Nagy, Alexander / Jirincova, Helena / Vecerova, Jaromira / Novakova, Ludmila / Cordey, Samuel / Murtskhvaladze, Marine / Kotaria, Nato / Schär, Tobias / Beisel, Christian / Vugrek, Oliver / Rokić, Filip / Trgovec-Greif, Lovro / Jurak, Igor / Rukavina, Tomislav / Sučić, Neven / Schønning, Kristian / M Karst, Søren / H Kirkegaard, Rasmus / Y Michaelsen, Thomas / Aa Sørensen, Emil / Knutson, Simon / Brandt, Jakob / Le-Quy, Vang / Sørensen, Trine / Petersen, Celine / Schou Pedersen, Martin / Løkkegaard Larsen, Sanne / Nielsine Skov, Marianne / Rasmussen, Morten / Fonager, Jannik / Fomsgaard, Anders / Amirovich Maksyutov, Rinat / Vasil'Evna Gavrilova, Elena / Victorovich Pyankov, Oleg / Alexandrovich Bodnev, Sergey / Vladimirovna Tregubchak, Tatyana / Nikolayevich Shvalov, Alexander / Victorovich Antonets, Denis / Cristina Resende, Paola / Goya, Stephanie / Perrin, Amandine / Tc Lee, Raphael / Yadahalli, Shilpa / X Han, Alvin / A Russell, Colin / Schmutz, Stefan / Zaheri, Maryam / Kufner, Verena / Huber, Michael / Trkola, Alexandra / Antwerpen, Markus / C Walter, Mathias / van der Werf, Sylvie / Gambaro, Fabiana / Behillil, Sylvie / Enouf, Vincent / Donati, Flora / Ustinova, Monta / Rovite, Vita / Klovins, Janis / Savicka, Oksana / K Wienecke-Baldacchino, Anke / Ragimbeau, Catherine / Fournier, Guillaume / Mossong, Joël / W Aberle, Stephan / Haukland, Mattias / Enkirch, Theresa / Advani, Abdolreza / Lind Karlberg, Maria / Karlsson Lindsjö, Oskar / Broddesson, Sandra / Sláviková, Monika / Ličková, Martina / Klempa, Boris / Staroňová, Edita / Tichá, Elena / Szemes, Tomáš / Rusňáková, Diana / Stadler, Tanja / Quer, Josep / Anton, Andres / Andres, Cristina / Piñana, Maria / Garcia-Cehic, Damir / Pumarola, Tomas / Izopet, Jacques / Gioula, Georgia / Exindari, Maria / Papa, Anna / Chatzidimitriou, Dimitrios / Metallidis, Symeon / Pappa, Stella / Macek Jr, Milan / Geryk, Jan / Brož, Petr / Briksí, Aleš / Hubáček, Petr / Dřevínek, Pavel / Zajac, Miroslav / Kvapil, Petr / Holub, Michal / Kvapilová, Kateřina / Novotný, Adam / Kašný, Martin / Klempt, Petr / Vapalahti, Olli / Smura, Teemu / Sironen, Tarja / Selhorst, Philippe / Anthony, Colin / Ariën, Kevin / Simon-Loriere, Etienne / Rabalski, Lukasz / Bienkowska-Szewczyk, Krystyna / Borges, Vítor / Isidro, Joana / Paulo Gomes, João / Guiomar, Raquel / Pechirra, Pedro / Costa, Inês / Duarte, Sílvia / Vieira, Luís / Pyrc, Krzysztof / S Zuckerman, Neta / Turdikulova, Shahlo / Abdullaev, Alisher / Dalimova, Dilbar / Abdurakhimov, Abror / Tagliabracci, Adriano / Alessandrini, Federica / Melchionda, Filomena / Onofri, Valerio / Turchi, Chiara / Bagnarelli, Patrizia / Menzo, Stefano / Caucci, Sara / Di Sante, Laura / Popa, Alexandra / Genger, Jakob-Wendelin / Agerer, Benedikt / Lercher, Alexander / Endler, Lukas / Smyth, Mark / Penz, Thomas / Schuster, Michael / Senekowitsch, Martin / Laine, Jan / Bock, Christoph / Bergthaler, Andreas / Shevtsov, Alexandr / Kalendar, Ruslan / Ramanculov, Yerlan / Graf, Alexander / Muenchhoff, Maximilian / T Keppler, Oliver / Krebs, Stefan / Blum, Helmut / Marcello, Alessandro / Licastro, Danilo / D'Agaro, Pierlanfranco / Laubscher, Florian / Vidanovic, Dejan / Tesovic, Bojana / Volkening, Jeremy / Clementi, Nicola / Mancini, Nicasio / Rupnik, Maja / Mahnic, Aleksander / Walker, Andreas / Houwaart, Torsten / Wienemann, Tobias / Kohns Vasconcelos, Malte / Strelow, Daniel / Ole Jensen, Björn-Erik / Senff, Tina / Hülse, Lisanna / Adams, Ortwin / Andree, Marcel / Hauka, Sandra / Feldt, Torsten / Keitel, Verena / Kindgen-Milles, Detlef / Timm, Jörg / Pfeffer, Klaus / T Dilthey, Alexander / Moore, Catherine / Ozdarendeli, Aykut / Terkis Islam Pavel, Shaikh / Yetiskin, Hazel / Aydin, Gunsu / Holyavkin, Can / Ali Uygut, Muhammet / Cevik, Ceren / Shchetinin, Alexey / Gushchin, Vladimir / Dinler-Doganay, Gizem / Doganay, Levent / Kizilboga-Akgun, Tugba / Karacan, Ilker / Pancer, Katarzyna / Maes, Piet / Martí-Carreras, Joan / Wawina-Bokalanga, Tony / Vanmechelen, Bert / Thürmer, Andrea / Wedde, Marianne / Dürrwald, Ralf / Von Kleist, Max / Drechsel, Oliver / Wolff, Thorsten / Fuchs, Stephan / Kmiecinski, Rene / Michel, Janine / Nitsche, Andreas / Casas, Inmaculada / Iglesias Caballero, María / Zaballos, Ángel / Jiménez, Pilar / Jiménez, Mercedes / Monzón Fernández, Sara / Varona Fernández, Sarai / Cuesta De La Plaza, Isabel / Fadeev, Artem / Ivanova, Anna / Sergeeva, Mariia / Stefanelli, Paola / Estee Torok, M / Hall, Grant / da Silva Filipe, Ana / Turtle, Lance / Afifi, Safiah / Mccluggage, Kathryn / Beer, Robert / Ledesma, Juan / Maksimovic, Joshua / Spellman, Karla / L Hamilton, William / Marchbank, Angela / Alexander Southgate, Joel / Underwood, Anthony / Taylor, Ben / Yeats, Corin / Abudahab, Khalil / R Gemmell, Matthew / Eccles, Richard / Lucaci, Anita / Abigail Nelson, Charlotte / Rainbow, Lucille / Whitehead, Mark / Gregory, Richard / Haldenby, Sam / Paterson, Steve / A Hughes, Margaret / D Curran, Martin / Baker, David / Tucker, Rachel / R Green, Luke / Feltwell, Theresa / D Halstead, Fenella / Wyles, Matthew / S Jahun, Aminu / Y Ahmad, Shazaad S / Georgana, Iliana / Goodfellow, Ian / Yakovleva, Anna / W Meredith, Luke / Gavriil, Artemis / Raza Awan, Ali / Fisher, Chloe / Edgeworth, Jonathan / Lynch, Jessica / Moore, Nathan / Williams, Rebecca / P Kidd, Stephen / Cortes, Nicholas / Brunker, Kirstyn / T Mccrone, John / Quick, Joshua / Duckworth, Nichola / Walsh, Sarah / Sloan, Tim / Ludden, Catherine / P George, Ryan / Eltringham, Gary / R Brown, Julianne / Aranday-Cortes, Elihu / G Shepherd, James / Hughes, Joseph / K Li, Kathy / C Williams, Thomas / Johnson, Natasha / Jesudason, Natasha / Mair, Daniel / Thomson, Emma / Shah, Rajiv / A Parr, Yasmin / Carmichael, Stephen / L Robertson, David / Nomikou, Kyriaki / Broos, Alice / Niebel, Marc / Smollett, Katherine / Tong, Lily / Miah, Shahjahan / Wittner, Anita / Phillips, Nicole / Payne, Brendan / Dewar, Rebecca / Holmes, Alison / Bolt, Frances / R Price, James / Mookerjee, Siddharth / K Sethi, Dheeraj / Potter, Will / Stanley, Rachael / Prakash, Reenesh / Dervisevic, Samir / Clive Graham, Jonathan / Nelson, Andrew / Smith, Darren / R Young, Gregory / Chyin Yew, Wen / A Todd, John / Trebes, Amy / Andersson, Monique / Bull, Matthew / Watkins, Joanne / Birchley, Alec / Gatica-Wilcox, Bree / Gilbert, Lauren / Kumžiene-Summerhayes, Sara / Rey, Sara / Chauhan, Anoop / Butcher, Ethan / Bicknell, Kelly / Elliott, Scott / Glaysher, Sharon / Lackenby, Angie / Bibby, David / Platt, Steven / Mohamed, Hodan / William Machin, Nicholas / Lutamyo Mbisa, Jean / Evans, Jonathan / Perry, Malorie / Pacchiarini, Nicole / Corden, Sally / Geraint Adams, Alexander / Gaskin, Amy / Coombs, Jason / John Graham, Lee / Cottrell, Simon / Morgan, Mari / Gifford, Laura / Kolyva, Anastasia / John Rudder, Steven / J Trotter, Alexander / E Mather, Alison / Aydin, Alp / J Page, Andrew / L Kay, Gemma / de Oliveira Martins, Leonardo / Yasir, Muhammad / Alikhan, Nabil-Fareed / M Thomson, Nicholas / Gilroy, Rachel / A Kingsley, Robert / O'Grady, Justin / Victoria Gutierrez, Ana / Diaz, Maria / Le Viet, Thanh / P Tedim, Ana / M Adriaenssens, Evelien / Patrick Mcclure, C / Moore, Christopher / Sang, Fei / Clark, Gemma / C Howson-Wells, Hannah / Debebe, Johnny / Ball, Jonathan / Chappell, Joseph / Khakh, Manjinder / Carlile, Matthew / Loose, Matthew / M Lister, Michelle / Holmes, Nadine / Tsoleridis, Theocharis / M Fleming, Vicki / Wright, Victoria / Smith, Wendy / D Gallagher, Michael / Parker, Matthew / G Partridge, David / Evans, Cariad / Baker, Paul / Essex, Sarah / Liggett, Steven / J Keeley, Alexander / Bashton, Matthew / Rooke, Stefan / Jane Meader, Emma / Enrique Balcazar Lopez, Carlos / Angyal, Adrienn / Kristiansen, Mark / J Tutill, Helena / Findlay, Jacqueline / Mestek-Boukhibar, Lamia / Forrest, Leysa / Dyal, Patricia / J Williams, Rachel / Panchbhaya, Yasmin / A Williams, Charlotte / Roy, Sunando / Pandey, Sarojini / Stockton, Jo / J Loman, Nicholas / Poplawski, Radoslaw / Nicholls, Samuel / M Rowe, W P / Khokhar, Fahad / Lars Pinckert, Malte / Hosmillo, Myra / Chaudhry, Yasmin / G Caller, Laura / K Davidson, Rose / Griffith, Luke / Rambaut, Andrew / Jackson, Ben / Colquhoun, Rachel / Hill, Verity / Nichols, Jenna / Asamaphan, Patawee / Darby, Alistair / A Jackson, Kathryn / Iturriza-Gomara, Miren / Edith Vamos, Ecaterina / Green, Angie / Aanensen, David / Bonsall, David / Buck, David / Macintyre-Cockett, George / de Cesare, Mariateresa / Pybus, Oliver / Golubchik, Tanya / Scarlett, Garry / F Loveson, Katie / C Robson, Samuel / Beckett, Angela / Lindsey, Benjamin / C Groves, Danielle / J Parsons, Paul / P Mchugh, Martin / Daniel Barnes, James / F Manso, Carmen / Grammatopoulos, Dimitris / Elisabeth Menger, Katja / Harrison, Ewan / Gunson, Rory / J Peacock, Sharon / Gonzalez, Gabriel / Carr, Michael / Mihaela, Lazar / Popovici, Odette / Brytting, Mia / Bresner, Catherine / Fuller, William / Workman, Trudy / F Mentis, Andreas / Kossyvakis, Athanasios / Karamitros, Timokratis / Pogka, Vasiliki / Kalliaropoulos, Antonios / Horefti, Elina / Kontou, Aspasia / Martinez-Gonzalez, Beatriz / Labropoulou, Voula / Voulgari-Kokota, Androniki / Evangelidou, Maria / Bizta, Panagiota / Belimezi, Maria / Lambrechts, Laurens / Z Doymaz, Mehmet / Kalkan Yazici, Merve / S Cetin, Nesibe / Karaaslan, Elif / Kallio-Kokko, Hannimari / Virtanen, Jenni / Suvanto, Maija / Truong Nguyen, Phuoc / Ellonen, Pekka / Hannula, Sari / Kangas, Harri / B Sreenu, Vattipally / Burián, Katalin / Terhes, Gabriella / Gombos, Katalin / Gyenesei, Attila / Urbán, Péter / Herczeg, Róbert / Jakab, Ferenc / Kemenesi, Gábor / Endre Tóth, Gábor / Somogyi, Balázs / Zana, Brigitta / Zeghbib, Safia / Kuczmog, Anett / Földes, Fanni / Lanszki, Zsófia / Madai, Mónika / Papp, Henrietta / Nagy, Ágnes / István Pereszlényi, Csaba / Csaba Babinszky, Gergely / Dudás, Gábor / Csoma, Eszter / N Abou Tayoun, Ahmad / A Alsheikh-Ali, Alawi / Loney, Tom / Nowotny, Norbert / Abdul-Wahab, Osama / Gonzalez-Candelas, Fernando / H Andersen, Martin / Sarah Taylor, And

    2020  

    Abstract: We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence ... ...

    Abstract We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.
    Keywords COVID-19 ; Europe ; NGS ; nomenclature ; SARS-CoV-2 ; sequencing ; WGS ; Base Sequence ; Betacoronavirus ; Coronavirus ; Coronavirus Infections ; Genome ; Viral ; Humans ; Phylogeography ; Pneumonia ; RNA Replicase ; RNA ; Severe Acute Respiratory Syndrome ; Spatio-Temporal Analysis ; World Health Organization ; Pandemics ; covid19
    Language English
    Publishing country it
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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