6 results on '"Poxon C"'
Search Results
2. RT-LAMP has high accuracy for detecting SARS-CoV-2 in saliva and naso/oropharyngeal swabs from asymptomatic and symptomatic individuals
- Author
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Bryony Armson, Andrew D Beggs, Sarah Fouch, Seden Grippon, Nathan Moore, Whalley C, Morant N, Poxon C, Ferguson J, Kidd M, Kerrie Davies, Tom Lewis, Zandra Deans, Ptasinska A, Hannah Love, Bryer C, Walsh C, Zoe Vincent-Mistiaen, Burton J, Emma L. Wise, Alice Goring, Claire Cassar, Rebecca Houghton, Joe Parker, David Cross, Jason Sawyer, Joe James, Samantha Rivers, Amy Sowood, Nicholas Cortes, Howson Ela, Reid Sm, Andreou M, Sue Hill, Stephen P. Kidd, Ian H. Brown, Gemma Snell, Patrick H, Keith M. Godfrey, Veronica L. Fowler, Daniel Burns, Joanne L. Slater-Jefferies, Ashley C. Banyard, Claire Tillyer, Richter Ag, Skinner P, Angela Douglas, Williams A, Andrew Bosworth, Laxman S, Clark D, and Deborah Porter
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medicine.medical_specialty ,2019-20 coronavirus outbreak ,Saliva ,business.industry ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Clinical performance ,Diagnostic Specificity ,Asymptomatic ,Gastroenterology ,stomatognathic system ,Internal medicine ,medicine ,Community setting ,medicine.symptom ,business ,Clinical evaluation - Abstract
Previous studies have described RT-LAMP methodology for the rapid detection of SARS-CoV-2 in nasopharyngeal (NP) and oropharyngeal (OP) swab and saliva samples. This study describes the validation of an improved sample preparation method for extraction free RT-LAMP and defines the clinical performance of four different RT-LAMP assay formats for detection of SARS-CoV-2 within a multisite clinical evaluation. Direct RT-LAMP was performed on 559 swabs and 86,760 saliva samples and RNA RT-LAMP on extracted RNA from 12,619 swabs and 12,521 saliva from asymptomatic and symptomatic individuals across healthcare and community settings. For Direct RT-LAMP, overall diagnostic sensitivity (DSe) of 70.35% (95% CI 63.48-76.60%) on swabs and 84.62% (79.50-88.88%) on saliva was observed, with diagnostic specificity (DSp) of 100% (98.98-100.00%) on swabs and 100% (99.72-100.00%) on saliva when compared to RT-qPCR; analysing samples with RT-qPCR ORF1ab CT values of ≤25 and ≤33, DSe of 100% (96.34-100%) and 77.78% (70.99-83.62%) for swabs were observed, and 99.01% (94.61-99.97%) and 87.61% (82.69-91.54%) for saliva, respectively. For RNA RT-LAMP, overall DSe and DSp were 96.06% (92.88-98.12%) and 99.99% (99.95-100%) for swabs, and 80.65% (73.54-86.54%) and 99.99% (99.95-100%) for saliva, respectively. These findings demonstrate that RT-LAMP is applicable to a variety of use-cases, including frequent, interval-based testing of saliva with Direct RT-LAMP from asymptomatic individuals that may otherwise be missed using symptomatic testing alone.
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- 2021
3. Reverse-Transcription Loop-Mediated Isothermal Amplification Has High Accuracy for Detecting Severe Acute Respiratory Syndrome Coronavirus 2 in Saliva and Nasopharyngeal/Oropharyngeal Swabs from Asymptomatic and Symptomatic Individuals.
- Author
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Kidd SP, Burns D, Armson B, Beggs AD, Howson ELA, Williams A, Snell G, Wise EL, Goring A, Vincent-Mistiaen Z, Grippon S, Sawyer J, Cassar C, Cross D, Lewis T, Reid SM, Rivers S, James J, Skinner P, Banyard A, Davies K, Ptasinska A, Whalley C, Ferguson J, Bryer C, Poxon C, Bosworth A, Kidd M, Richter A, Burton J, Love H, Fouch S, Tillyer C, Sowood A, Patrick H, Moore N, Andreou M, Morant N, Houghton R, Parker J, Slater-Jefferies J, Brown I, Gretton C, Deans Z, Porter D, Cortes NJ, Douglas A, Hill SL, Godfrey KM, and Fowler VL
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- COVID-19 Testing, Humans, Molecular Diagnostic Techniques methods, Nucleic Acid Amplification Techniques methods, RNA, Viral analysis, RNA, Viral genetics, Saliva, Sensitivity and Specificity, COVID-19 diagnosis, SARS-CoV-2 genetics
- Abstract
Previous studies have described reverse-transcription loop-mediated isothermal amplification (RT-LAMP) for the rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in nasopharyngeal/oropharyngeal swab and saliva samples. This multisite clinical evaluation describes the validation of an improved sample preparation method for extraction-free RT-LAMP and reports clinical performance of four RT-LAMP assay formats for SARS-CoV-2 detection. Direct RT-LAMP was performed on 559 swabs and 86,760 saliva samples and RNA RT-LAMP on extracted RNA from 12,619 swabs and 12,521 saliva samples from asymptomatic and symptomatic individuals across health care and community settings. For direct RT-LAMP, overall diagnostic sensitivity (DSe) was 70.35% (95% CI, 63.48%-76.60%) on swabs and 84.62% (95% CI, 79.50%-88.88%) on saliva, with diagnostic specificity of 100% (95% CI, 98.98%-100.00%) on swabs and 100% (95% CI, 99.72%-100.00%) on saliva, compared with quantitative RT-PCR (RT-qPCR); analyzing samples with RT-qPCR ORF1ab C
T values of ≤25 and ≤33, DSe values were 100% (95% CI, 96.34%-100%) and 77.78% (95% CI, 70.99%-83.62%) for swabs, and 99.01% (95% CI, 94.61%-99.97%) and 87.61% (95% CI, 82.69%-91.54%) for saliva, respectively. For RNA RT-LAMP, overall DSe and diagnostic specificity were 96.06% (95% CI, 92.88%-98.12%) and 99.99% (95% CI, 99.95%-100%) for swabs, and 80.65% (95% CI, 73.54%-86.54%) and 99.99% (95% CI, 99.95%-100%) for saliva, respectively. These findings demonstrate that RT-LAMP is applicable to a variety of use cases, including frequent, interval-based direct RT-LAMP of saliva from asymptomatic individuals who may otherwise be missed using symptomatic testing alone., (Copyright © 2022 Association for Molecular Pathology and American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.)- Published
- 2022
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4. Diagnostic accuracy of loop-mediated isothermal amplification coupled to nanopore sequencing (LamPORE) for the detection of SARS-CoV-2 infection at scale in symptomatic and asymptomatic populations.
- Author
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Ptasinska A, Whalley C, Bosworth A, Poxon C, Bryer C, Machin N, Grippon S, Wise EL, Armson B, Howson ELA, Goring A, Snell G, Forster J, Mattocks C, Frampton S, Anderson R, Cleary D, Parker J, Boukas K, Graham N, Cellura D, Garratt E, Skilton R, Sheldon H, Collins A, Ahmad N, Friar S, Burns D, Williams T, Godfrey KM, Deans Z, Douglas A, Hill S, Kidd M, Porter D, Kidd SP, Cortes NJ, Fowler V, Williams T, Richter A, and Beggs AD
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- COVID-19 virology, Cohort Studies, Coronavirus Nucleocapsid Proteins genetics, Humans, Limit of Detection, Nanopore Sequencing, Nasopharynx virology, Polyproteins genetics, Prospective Studies, Reproducibility of Results, Retrospective Studies, SARS-CoV-2 genetics, Saliva virology, Sensitivity and Specificity, Viral Proteins genetics, COVID-19 diagnosis, Molecular Diagnostic Techniques methods, Nucleic Acid Amplification Techniques methods, Pandemics, SARS-CoV-2 isolation & purification
- Abstract
Objectives: Rapid, high throughput diagnostics are a valuable tool, allowing the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in populations so as to identify and isolate people with asymptomatic and symptomatic infections. Reagent shortages and restricted access to high throughput testing solutions have limited the effectiveness of conventional assays such as quantitative RT-PCR (RT-qPCR), particularly throughout the first months of the coronavirus disease 2019 pandemic. We investigated the use of LamPORE, where loop-mediated isothermal amplification (LAMP) is coupled to nanopore sequencing technology, for the detection of SARS-CoV-2 in symptomatic and asymptomatic populations., Methods: In an asymptomatic prospective cohort, for 3 weeks in September 2020, health-care workers across four sites (Birmingham, Southampton, Basingstoke and Manchester) self-swabbed with nasopharyngeal swabs weekly and supplied a saliva specimen daily. These samples were tested for SARS-CoV-2 RNA using the Oxford Nanopore LamPORE system and a reference RT-qPCR assay on extracted sample RNA. A second retrospective cohort of 848 patients with influenza-like illness from March 2020 to June 2020 were similarly tested from nasopharyngeal swabs., Results: In the asymptomatic cohort a total of 1200 participants supplied 23 427 samples (3966 swab, 19 461 saliva) over a 3-week period. The incidence of SARS-CoV-2 detection using LamPORE was 0.95%. Diagnostic sensitivity and specificity of LamPORE was >99.5% (decreasing to approximately 98% when clustered estimation was used) in both swab and saliva asymptomatic samples when compared with the reference RT-qPCR test. In the retrospective symptomatic cohort, the incidence was 13.4% and the sensitivity and specificity were 100%., Conclusions: LamPORE is a highly accurate methodology for the detection of SARS-CoV-2 in both symptomatic and asymptomatic population settings and can be used as an alternative to RT-qPCR., (Copyright © 2021 The Author(s). Published by Elsevier Ltd.. All rights reserved.)
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- 2021
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5. SARS-CoV-2 seroprevalence and asymptomatic viral carriage in healthcare workers: a cross-sectional study.
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Shields A, Faustini SE, Perez-Toledo M, Jossi S, Aldera E, Allen JD, Al-Taei S, Backhouse C, Bosworth A, Dunbar LA, Ebanks D, Emmanuel B, Garvey M, Gray J, Kidd IM, McGinnell G, McLoughlin DE, Morley G, O'Neill J, Papakonstantinou D, Pickles O, Poxon C, Richter M, Walker EM, Wanigasooriya K, Watanabe Y, Whalley C, Zielinska AE, Crispin M, Wraith DC, Beggs AD, Cunningham AF, Drayson MT, and Richter AG
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- Adult, COVID-19 epidemiology, COVID-19 virology, Cross-Sectional Studies, Female, Humans, Male, Middle Aged, RNA, Viral analysis, SARS-CoV-2 genetics, Seroepidemiologic Studies, Antibodies, Viral blood, Asymptomatic Diseases, COVID-19 diagnosis, Health Personnel statistics & numerical data, Pandemics, SARS-CoV-2 immunology
- Abstract
Objective: To determine the rates of asymptomatic viral carriage and seroprevalence of SARS-CoV-2 antibodies in healthcare workers., Design: A cross-sectional study of asymptomatic healthcare workers undertaken on 24/25 April 2020., Setting: University Hospitals Birmingham NHS Foundation Trust (UHBFT), UK., Participants: 545 asymptomatic healthcare workers were recruited while at work. Participants were invited to participate via the UHBFT social media. Exclusion criteria included current symptoms consistent with COVID-19. No potential participants were excluded., Intervention: Participants volunteered a nasopharyngeal swab and a venous blood sample that were tested for SARS-CoV-2 RNA and anti-SARS-CoV-2 spike glycoprotein antibodies, respectively. Results were interpreted in the context of prior illnesses and the hospital departments in which participants worked., Main Outcome Measure: Proportion of participants demonstrating infection and positive SARS-CoV-2 serology., Results: The point prevalence of SARS-CoV-2 viral carriage was 2.4% (n=13/545). The overall seroprevalence of SARS-CoV-2 antibodies was 24.4% (n=126/516). Participants who reported prior symptomatic illness had higher seroprevalence (37.5% vs 17.1%, χ
2 =21.1034, p<0.0001) and quantitatively greater antibody responses than those who had remained asymptomatic. Seroprevalence was greatest among those working in housekeeping (34.5%), acute medicine (33.3%) and general internal medicine (30.3%), with lower rates observed in participants working in intensive care (14.8%). BAME (Black, Asian and minority ethnic) ethnicity was associated with a significantly increased risk of seropositivity (OR: 1.92, 95% CI 1.14 to 3.23, p=0.01). Working on the intensive care unit was associated with a significantly lower risk of seropositivity compared with working in other areas of the hospital (OR: 0.28, 95% CI 0.09 to 0.78, p=0.02)., Conclusions and Relevance: We identify differences in the occupational risk of exposure to SARS-CoV-2 between hospital departments and confirm asymptomatic seroconversion occurs in healthcare workers. Further investigation of these observations is required to inform future infection control and occupational health practices., Competing Interests: Competing interests: MTD reports personal fees from Abingdon Health, outside the submitted work. All other authors declare no competing interests., (© Author(s) (or their employer(s)) 2020. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)- Published
- 2020
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6. Rapid implementation and validation of a cold-chain free SARS-CoV-2 diagnostic testing workflow to support surge capacity.
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Bosworth A, Whalley C, Poxon C, Wanigasooriya K, Pickles O, Aldera EL, Papakonstantinou D, Morley GL, Walker EM, Zielinska AE, McLoughlin D, Webster C, Plant T, Ellis A, Richter A, Kidd IM, and Beggs AD
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- Betacoronavirus genetics, COVID-19, COVID-19 Testing, Coronavirus Infections virology, Humans, Pandemics, Pneumonia, Viral virology, SARS-CoV-2, Saliva virology, Surge Capacity, United Kingdom, Workflow, Betacoronavirus isolation & purification, Clinical Laboratory Techniques methods, Coronavirus Infections diagnosis, Pneumonia, Viral diagnosis, RNA, Viral blood
- Abstract
Background: In January 2020 reports of unidentified severe respiratory illness were described in Wuhan, China. A rapid expansion in cases affecting most countries around the globe led to major changes in the way people live their daily lives. In the United Kingdom, the Department of Health and Social Care directed healthcare providers to establish additional resources to manage the anticipated surge in cases that could overwhelm the health services. A priority area was testing for SARS-CoV-2 RNA and its detection by qualitative RT-PCR., Design: A laboratory workflow twinning research environment with clinical laboratory capabilities was implemented and validated in the University of Birmingham within 4 days of the project initiation. The diagnostic capability was centred on an IVD CE-marked RT-PCR kit and designed to provide surge capacity to the nearby Queen Elizabeth Hospital. The service was initially tasked with testing healthcare workers (HCW) using throat swabs, and subsequently the process investigated the utility of using saliva as an alternative sample type., Results: Between the 8th April 2020 and the 30th April 2020, the laboratory tested a total of 1282 HCW for SARS-CoV-2 RNA in throat swabs. RNA was detected in 54 % of those who reported symptoms compatible with COVID-19, but in only 4% who were asymptomatic., Conclusion: This capability was established rapidly and utilised a cold-chain free methodology, applicable to a wide range of settings, and which can provide surge capacity and support to clinical laboratories facing increasing pressure during periods of national crisis., (Copyright © 2020 The Author(s). Published by Elsevier B.V. All rights reserved.)
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- 2020
- Full Text
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