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Start Over Author "State, Amy" Topic sars-cov-2
5 results on '"State, Amy"'

1. Characterising within-hospitalSARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves.

Author

Lindsey BB, Villabona-Arenas CJ, Campbell F, Keeley AJ, Parker MD, Shah DR, Parsons H, Zhang P, Kakkar N, Gallis M, Foulkes BH, Wolverson P, Louka SF, Christou S, State A, Johnson K, Raza M, Hsu S, Jombart T, Cori A, Evans CM, Partridge DG, Atkins KE, Hué S, and de Silva TI

Subjects
Bayes Theorem, Cohort Studies, Cross Infection epidemiology, Cross Infection transmission, Disease Outbreaks, Genomics, Health Personnel, Hospitals, Humans, United Kingdom epidemiology, COVID-19 epidemiology, COVID-19 transmission, Genome, Viral, Molecular Epidemiology, Pandemics, SARS-CoV-2 genetics
Abstract

Hospital outbreaks of COVID19 result in considerable mortality and disruption to healthcare services and yet little is known about transmission within this setting. We characterise within hospital transmission by combining viral genomic and epidemiological data using Bayesian modelling amongst 2181 patients and healthcare workers from a large UK NHS Trust. Transmission events were compared between Wave 1 (1st March to 25th J'uly 2020) and Wave 2 (30th November 2020 to 24th January 2021). We show that staff-to-staff transmissions reduced from 31.6% to 12.9% of all infections. Patient-to-patient transmissions increased from 27.1% to 52.1%. 40%-50% of hospital-onset patient cases resulted in onward transmission compared to 4% of community-acquired cases. Control measures introduced during the pandemic likely reduced transmissions between healthcare workers but were insufficient to prevent increasing numbers of patient-to-patient transmissions. As hospital-acquired cases drive most onward transmission, earlier identification of nosocomial cases will be required to break hospital transmission chains., (© 2022. The Author(s).)

Published
2022
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2. Improved sensitivity using a dual target, E and RdRp assay for the diagnosis of SARS-CoV-2 infection: Experience at a large NHS Foundation Trust in the UK.

Author

Colton H, Ankcorn M, Yavuz M, Tovey L, Cope A, Raza M, Keeley AJ, State A, Poller B, Parker M, de Silva TI, and Evans C

Subjects
Humans, RNA-Dependent RNA Polymerase, Reverse Transcriptase Polymerase Chain Reaction, Sensitivity and Specificity, State Medicine, United Kingdom, COVID-19, SARS-CoV-2
Published
2021
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3. Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7/Alpha variant infections

Author

Parker, Matthew D, Shaw, Hazel, Shehata, Ola M, Lindsey, Benjamin B, Shah, Dhruv R, Hsu, Sharon, Keeley, Alexander J, Partridge, David G, Leary, Shay, Cope, Alison, State, Amy, Johnson, Katie, Ali, Nasar, Raghei, Rasha, Heffer, Joe, Smith, Nikki, Zhang, Peijun, Gallis, Marta, Louka, Stavroula F, Hornsby, Hailey R, Alamri, Hatoon, Whiteley, Max, Foulkes, Benjamin H, Christou, Stella, Wolverson, Paige, Pohare, Manoj, Hansford, Samantha E, Green, Luke R, Evans, Cariad, Raza, Mohammad, Wang, Dennis, Firth, Andrew, Edgar, James, Gaudieri, Silvana, Mallal, Simon, COVID-19 Genomics UK (COG-UK) Consortium, Collins, Mark O, Peden, Andrew A, De Silva, Thushan I, Parker, Matthew D [0000-0003-2999-3870], Shaw, Hazel [0000-0003-1438-1089], Lindsey, Benjamin B [0000-0003-4227-2592], Shah, Dhruv R [0000-0002-6198-8273], Keeley, Alexander J [0000-0001-9386-1157], Partridge, David G [0000-0002-0417-2016], Heffer, Joe [0000-0001-8733-1117], Louka, Stavroula F [0000-0003-3000-3504], Hornsby, Hailey R [0000-0002-6657-9743], Christou, Stella [0000-0002-8287-788X], Wolverson, Paige [0000-0003-2709-0686], Pohare, Manoj [0000-0003-2272-9946], Hansford, Samantha E [0000-0003-3042-8748], Green, Luke R [0000-0002-2836-2041], Wang, Dennis [0000-0003-0068-1005], Firth, Andrew [0000-0002-7986-9520], Edgar, James [0000-0001-7903-8199], Collins, Mark O [0000-0002-7656-4975], Peden, Andrew A [0000-0003-0144-7712], de Silva, Thushan I [0000-0002-6498-9212], Apollo - University of Cambridge Repository, Stewart, Hazel [0000-0003-1438-1089], and Edgar, James R [0000-0001-7903-8199]

Subjects
SARS-CoV-2, article, COVID-19, Humans, RNA, 45/23, 631/114, 631/326/596/4130, 45/90
Abstract

B.1.1.7 lineage SARS-CoV-2 is more transmissible, leads to greater clinical severity, and results in modest reductions in antibody neutralization. Subgenomic RNA (sgRNA) is produced by discontinuous transcription of the SARS-CoV-2 genome. Applying our tool (periscope) to ARTIC Network Oxford Nanopore Technologies genomic sequencing data from 4400 SARS-CoV-2 positive clinical samples, we show that normalised sgRNA is significantly increased in B.1.1.7 (alpha) infections (n = 879). This increase is seen over the previous dominant lineage in the UK, B.1.177 (n = 943), which is independent of genomic reads, E cycle threshold and days since symptom onset at sampling. A noncanonical sgRNA which could represent ORF9b is found in 98.4% of B.1.1.7 SARS-CoV-2 infections compared with only 13.8% of other lineages, with a 16-fold increase in median sgRNA abundance. We demonstrate that ORF9b protein levels are increased 6-fold in B.1.1.7 compared to a B lineage virus in vitro. We hypothesise that increased ORF9b in B.1.1.7 is a direct consequence of a triple nucleotide mutation in nucleocapsid (28280:GAT > CAT, D3L) creating a transcription regulatory-like sequence complementary to a region 3' of the genomic leader. These findings provide a unique insight into the biology of B.1.1.7 and support monitoring of sgRNA profiles to evaluate emerging potential variants of concern.

Published
2022
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4. Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves

Author

Lindsey, Benjamin B, Villabona-Arenas, Ch Julián, Campbell, Finlay, Keeley, Alexander J, Parker, Matthew D, Shah, Dhruv R, Parsons, Helena, Zhang, Peijun, Kakkar, Nishchay, Gallis, Marta, Foulkes, Benjamin H, Wolverson, Paige, Louka, Stavroula F, Christou, Stella, State, Amy, Johnson, Katie, Raza, Mohammad, Hsu, Sharon, Jombart, Thibaut, Cori, Anne, Group, Sheffield COVID-19 Genomics, COVID-19 Genomics UK (COG-UK) Consortium, CMMID COVID-19 Working Group, Evans, Cariad M, Partridge, David G, Atkins, Katherine E, Hué, Stéphane, De Silva, Thushan I, Lindsey, Benjamin B [0000-0003-4227-2592], Villabona-Arenas, Ch Julián [0000-0001-9928-3968], Keeley, Alexander J [0000-0001-9386-1157], Parker, Matthew D [0000-0003-2999-3870], Shah, Dhruv R [0000-0002-6198-8273], Foulkes, Benjamin H [0000-0001-8532-3295], Wolverson, Paige [0000-0003-2709-0686], Hsu, Sharon [0000-0003-2356-9155], Partridge, David G [0000-0002-0417-2016], Atkins, Katherine E [0000-0001-5250-0558], Hué, Stéphane [0000-0002-8580-6905], de Silva, Thushan I [0000-0002-6498-9212], and Apollo - University of Cambridge Repository

Subjects
Cross Infection, Molecular Epidemiology, Multidisciplinary, SARS-CoV-2, Health Personnel, Science, COVID-19, General Physics and Astronomy, Bayes Theorem, Genome, Viral, Genomics, General Chemistry, Hospitals, United Kingdom, General Biochemistry, Genetics and Molecular Biology, Disease Outbreaks, Cohort Studies, Humans, Pandemics
Abstract

Hospital outbreaks of COVID19 result in considerable mortality and disruption to healthcare services and yet little is known about transmission within this setting. We characterise within hospital transmission by combining viral genomic and epidemiological data using Bayesian modelling amongst 2181 patients and healthcare workers from a large UK NHS Trust. Transmission events were compared between Wave 1 (1st March to 25th July 2020) and Wave 2 (30th November 2020 to 24th January 2021). We show that staff-to-staff transmissions reduced from 31.6% to 12.9% of all infections. Patient-to-patient transmissions increased from 27.1% to 52.1%. 40%-50% of hospital-onset patient cases resulted in onward transmission compared to 4% of community-acquired cases. Control measures introduced during the pandemic likely reduced transmissions between healthcare workers but were insufficient to prevent increasing numbers of patient-to-patient transmissions. As hospital-acquired cases drive most onward transmission, earlier identification of nosocomial cases will be required to break hospital transmission chains.

Published
2022

5. Publisher Correction: Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves.

Author

Lindsey, Benjamin B., Villabona-Arenas, Ch. Julián, Campbell, Finlay, Keeley, Alexander J., Parker, Matthew D., Shah, Dhruv R., Parsons, Helena, Zhang, Peijun, Kakkar, Nishchay, Gallis, Marta, Foulkes, Benjamin H., Wolverson, Paige, Louka, Stavroula F., Christou, Stella, State, Amy, Johnson, Katie, Raza, Mohammad, Hsu, Sharon, Jombart, Thibaut, and Cori, Anne

Subjects
SARS-CoV-2, COVID-19
Abstract

In the main text and References, the phrase "Identifying within-hospitalSARS-CoV-2 transmission" was missing a space between "hospital" and "SARS-CoV-2", which has been corrected to "Identifying within-hospital SARS-CoV-2 transmission". In the main text, there were two uses of the phrase "hospital-acquiredSARS-CoV-2 infections" which were also missing a space between "acquired" and "SARS-CoV-2", which have been corrected to "hospital-acquired SARS-CoV-2 infections". [Extracted from the article]

Published
2022
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