Publications

@article{Phillips2023-qi,

title = {Air filtration mitigates aerosol levels both during and after 

 endoscopy procedures},

author = {Frank Phillips and Jane Crowley and Samantha Warburton and Karren Staniforth and Adolfo Parra-Blanco and George S D Gordon},

year  = {2023},

date = {2023-04-01},

journal = {DEN Open},

volume = {3},

number = {1},

pages = {e231},

publisher = {Wiley},

abstract = {Objectives: Upper gastrointestinal endoscopies are 

 aerosol-generating procedures, increasing the risk of spreading 

 airborne pathogens. We aim to quantify the mitigation of 

 airborne particles via improved ventilation, specifically 

 laminar flow theatres and portable high-efficiency particulate 

 air (HEPA) filters, during and after upper gastrointestinal 

 endoscopies. Methods: This observational study included patients 

 undergoing routine upper gastrointestinal endoscopy in a 

 standard endoscopy room with 15-17 air changes per hour, a 

 standard endoscopy room with a portable HEPA filtration unit, 

 and a laminar flow theatre with 300 air changes per hour. A 

 particle counter (diameter range 0.3 μm-25 μm) took 

 measurements 10 cm from the mouth. Three analyses were 

 performed: whole procedure particle counts, event-based counts, 

 and air clearance estimation using post-procedure counts. 

 Results: Compared to a standard endoscopy room, for whole 

 procedures we observe a 28.5x reduction in particle counts in 

 laminar flow (p 5 μm for oral extubation (12.2x, p \< 0.01), 

 reduction in particles \<5 μm for coughing/gagging (6.9x, p \< 

 0.05), and reduction for all sizes in anesthetic throat spray 

 (8.4x, p \< 0.01) but no significant effect of HEPA filtration. 

 However, we find that in the fallow period between procedures 

 HEPA filtration reduces particle clearance times by 40%. 

 Conclusions: Laminar flow theatres are highly effective at 

 dispersing aerosols immediately after production and should be 

 considered for high-risk cases where patients are actively 

 infectious or the supply of personal protective equipment is 

 limited. Portable HEPA filers can safely reduce the fallow time 

 between procedures by 40%.},

keywords = {aerosols, air conditioning, COVID-19, endoscopy, infection   control},

pubstate = {published},

tppubtype = {article}

}

@article{Blake2022-qn,

title = {A qualitative evaluation of the barriers and enablers for 

 implementation of an asymptomatic SARS-CoV-2 testing service 

 at the university of Nottingham: A multi-site higher education 

 setting in England},

author = {Holly Blake and Sarah Somerset and Ikra Mahmood and Neelam Mahmood and Jessica Corner and Jonathan K Ball and Chris Denning},

year  = {2022},

date = {2022-10-01},

journal = {Int. J. Environ. Res. Public Health},

volume = {19},

number = {20},

pages = {13140},

publisher = {MDPI AG},

abstract = {Asymptomatic testing for SARS-CoV-2 RNA has been used to prevent 

 and manage COVID-19 outbreaks in university settings, but few 

 studies have explored their implementation. The aim of the study 

 was to evaluate how an accredited asymptomatic SARS-CoV-2 

 testing service (ATS) was implemented at the University of 

 Nottingham, a multi-campus university in England, to identify 

 barriers and enablers of implementation and to draw out lessons 

 for implementing pandemic response initiatives in higher 

 education settings. A qualitative interview study was conducted 

 with 25 ATS personnel between May and July 2022. Interviews were 

 conducted online, audio-recorded, and transcribed. Participants 

 were asked about their experience of the ATS, barriers and 

 enablers of implementation. Transcripts were thematically 

 analysed. There were four overarching themes: (1) social 

 responsibility and innovation, (2) when, how and why people 

 accessed testing, (3) impact of the ATS on the spread of 

 COVID-19, and (4) lessons learned for the future. In 

 establishing the service, the institution was seen to be valuing 

 its community and socially responsible. The service was viewed 

 to be broadly successful as a COVID-19 mitigation approach. 

 Challenges to service implementation were the rapidly changing 

 pandemic situation and government advice, delays in service 

 accreditation and rollout to staff, ambivalence towards testing 

 and isolating in the target population, and an inability to 

 provide follow-up support for positive cases within the service. 

 Facilitators included service visibility, reduction in 

 organisational bureaucracy and red tape, inclusive leadership, 

 collaborative working with regular feedback on service status, 

 flexibility in service delivery approaches and simplicity of 

 saliva testing. The ATS instilled a perception of early 'return 

 to normality' and impacted positively on staff feelings of 

 safety and wellbeing, with wider benefits for healthcare 

 services and local communities. In conclusion, we identified 

 common themes that have facilitated or hindered the 

 implementation of a SARS-CoV-2 testing service at a university 

 in England. Lessons learned from ATS implementation will inform 

 future pandemic response interventions in higher education 

 settings.},

keywords = {COVID-19, health protection, health testing, pandemic, qualitative, SARS-CoV-2},

pubstate = {published},

tppubtype = {article}

}

@article{Crooks2022-ng,

title = {Predicting need for escalation of care or death from repeated 

 daily clinical observations and laboratory results in patients 

 with severe acute respiratory syndrome Coronavirus 2},

author = {Colin J Crooks and Joe West and Andrew Fogarty and Joanne R Morling and Matthew J Grainge and Sherif Gonem and Mark Simmonds and Andrea Race and Irene Juurlink and Steve Briggs and Simon Cruickshank and Susan Hammond-Pears and Timothy R Card},

year  = {2022},

date = {2022-10-01},

journal = {Am. J. Epidemiol.},

volume = {191},

number = {11},

pages = {1944\textendash1953},

publisher = {Oxford University Press (OUP)},

abstract = {We compared the performance of prognostic tools for severe acute 

 respiratory syndrome coronavirus 2 (SARS-CoV-2) using parameters 

 fitted either at the time of hospital admission or across all 

 time points of an admission. This cohort study used clinical 

 data to model the dynamic change in prognosis of SARS-CoV-2 at a 

 single hospital center in the United Kingdom, including all 

 patients admitted from February 1, 2020, to December 31, 2020, 

 and then followed up for 60 days for intensive care unit (ICU) 

 admission, death, or discharge from the hospital. We 

 incorporated clinical observations and blood tests into 2 

 time-varying Cox proportional hazards models predicting daily 

 24- to 48-hour risk of admission to the ICU for those eligible 

 for escalation of care or death for those ineligible for 

 escalation. In developing the model, 491 patients were eligible 

 for ICU escalation and 769 were ineligible for escalation. Our 

 model had good discrimination of daily risk of ICU admission in the validation cohort (n = 1,141; C statistic: C = 0.91, 95% 

 confidence interval: 0.89, 0.94) and our score performed better 

 than other scores (National Early Warning Score 2, International 

 Severe Acute Respiratory and Emerging Infection Comprehensive 

 Clinical Characterisation Collaboration score) calculated using 

 only parameters measured on admission, but it overestimated the risk of escalation (calibration slope = 0.7). A bespoke daily 

 SARS-CoV-2 escalation risk prediction score can predict the need 

 for clinical escalation better than a generic early warning 

 score or a single estimation of risk calculated at admission.},

keywords = {coronavirus disease 2019, COVID-19, critical care, mortality, SARS-CoV-2, severe acute respiratory syndrome coronavirus 2, survival analysis},

pubstate = {published},

tppubtype = {article}

}

@article{Blake2022-sv,

title = {Workforce experiences of a rapidly established SARS-CoV-2 

 asymptomatic testing service in a higher education setting: A 

 qualitative study},

author = {Holly Blake and Sarah Somerset and Ikra Mahmood and Neelam Mahmood and Jessica Corner and Jonathan K Ball and Chris Denning},

year  = {2022},

date = {2022-09-01},

journal = {Int. J. Environ. Res. Public Health},

volume = {19},

number = {19},

pages = {12464},

publisher = {MDPI AG},

abstract = {The aim of the study was to explore workforce experiences of the 

 rapid implementation of a SARS-CoV-2 asymptomatic testing 

 service (ATS) in a higher education setting during the COVID-19 

 pandemic. The setting was a multi-campus university in the UK, 

 which hosted a testing service for employees and students over 

 two years. Qualitative semi-structured videoconference 

 interviews were conducted. We contacted 58 participants and 25 

 were interviewed (43% response rate). Data were analysed 

 thematically. The analysis produced four overarching themes: (1) 

 feelings relating to their involvement in the service, (2) 

 perceptions of teamwork, (3) perceptions of ATS leadership, (4) 

 valuing the opportunity for career development. Agile and 

 inclusive leadership style created psychological safety and team 

 cohesion, which facilitated participants in the implementation 

 of a rapid mitigation service, at pace and scale. Specific 

 features of the ATS (shared vision, collaboration, networking, 

 skills acquisition) instilled self-confidence, value and 

 belonging, meaningfully impacting on professional development 

 and career opportunities. This is the first qualitative study to 

 explore the experiences of university employees engaged in the 

 rapid deployment of a service as part of a pandemic outbreak and 

 mitigation strategy within a higher education setting. Despite 

 pressures and challenges of the task, professional growth and 

 advancement were universal. This has implications for workforce 

 engagement and creating workplaces across the sector that are 

 well-prepared to respond to future pandemics and other 

 disruptive events.},

keywords = {careers, COVID-19, employability, higher education, SARS-CoV-2, universities, workforce},

pubstate = {published},

tppubtype = {article}

}

@article{Blake2022-nv,

title = {Mixed-methods process evaluation of a residence-based 

 SARS-CoV-2 testing participation pilot on a UK university 

 campus during the COVID-19 pandemic},

author = {H Blake and S Carlisle and L Fothergill and J Hassard and A Favier and J Corner and J K Ball and C Denning},

year  = {2022},

date = {2022-08-01},

journal = {BMC Public Health},

volume = {22},

number = {1},

pages = {1470},

publisher = {Springer Science and Business Media LLC},

abstract = {BACKGROUND: Regular testing for Severe Acute Respiratory 

 Syndrome Coronavirus 2 (SARS-CoV-2) is an important strategy for 

 controlling virus outbreaks on university campuses during the 

 COVID-19 pandemic but testing participation rates can be low. 

 The Residence-Based Testing Participation Pilot (RB-TPP) was a 

 novel intervention implemented at two student residences on a 

 large UK university campus over 4 weeks. The aim of the pilot 

 was to increase the frequency of asymptomatic SARS-CoV-2 saliva 

 testing onsite. This process evaluation aimed to determine 

 whether RB-TPP was implemented as planned and identify 

 implementation barriers and facilitators. METHODS: A 

 mixed-methods process evaluation was conducted alongside the 

 RB-TPP. Evaluation participants were students (opting in, or out 

 of RB-TPP) and staff with a role in service provision or student 

 support. Monitoring data were collected from the intervention 

 delivery team and meeting records. Data were collected from students via online survey (n = 152) and seven focus groups (n = 30), and from staff via individual interviews (n = 13). 

 Quantitative data were analysed descriptively and qualitative 

 data thematically. Barriers and facilitators to implementation 

 were mapped to the 'Capability, Opportunity, 

 Motivation-Behaviour' (COM-B) behaviour change framework. 

 RESULTS: Four hundred sixty-four students opted to participate 

 in RB-TPP (98% of students living onsite). RB-TPP was 

 implemented broadly as planned but relaxed social distancing was 

 terminated early due to concerns relating to national escalation 

 of the COVID-19 Delta variant, albeit testing continued. Most 

 students (97.9%) perceived the period of relaxed social 

 distancing within residences positively. The majority engaged in 

 asymptomatic testing (88%); 46% (52% of testers) were fully 

 compliant with pre-determined testing frequency. Implementation 

 was facilitated by convenience and efficiency of testing, and 

 reduction in the negative impacts of isolation through 

 opportunities for students to socialise. Main barriers to 

 implementation were perceived mixed-messages about the rules, 

 ambivalent attitudes, and lack of adherence to COVID-19 

 protective measures in the minority. CONCLUSIONS: This process 

 evaluation identifies factors that help or hinder the success of 

 university residence-based outbreak prevention and management 

 strategies. RB-TPP led to increased rates of SARS-CoV-2 testing 

 participation among students in university residences. Perceived 

 normalisation of university life significantly enhanced student 

 mental wellbeing. The complexity and challenge generated by 

 multiple lines of communication and rapid adaptions to a 

 changing pandemic context was evident. TRIAL REGISTRATION 

 NUMBER: UKAS 307727-02-01; Pre-results. CLINICALTRIALS: gov 

 Identifier: NCT05045989 ; post-results (first posted, 16/09/21). 

 ETHICAL APPROVAL: Faculty of Medicine \& Health Sciences 

 Research Ethics Committee, University of Nottingham (Ref: FMHS 

 96-0920).},

keywords = {Complex interventions, COVID-19, Implementation, Mixed-methods, Process evaluation, Public health, SARS-CoV-2, universities},

pubstate = {published},

tppubtype = {article}

}

@article{Tarantini2022-zb,

title = {Direct RT-qPCR assay for the detection of SARS-CoV-2 in 

 saliva samples},

author = {Francesco Saverio Tarantini and Siyu Wu and Harry Jenkins and Ana Tellechea Lopez and Hannah Tomlin and Ralph Hyde and Katarzyna Lis-Slimak and Jamie Louise Thompson and Sara Pijuan-Galit\'{o} and Danielle Scales and Kazuyo Kaneko and Jayasree Dey and Emily Park and Jack Hill and I-Ning Lee and Lara Doolan and Asta Arendt-Tranholm and Chris Denning and Claire Seedhouse and Andrew V Benest},

year  = {2022},

date = {2022-03-01},

journal = {Methods Protoc.},

volume = {5},

number = {2},

pages = {25},

publisher = {MDPI AG},

abstract = {Since mid-2020 there have been complexities and difficulties in 

 the standardisation and administration of nasopharyngeal swabs. 

 Coupled with the variable and/or poor accuracy of lateral flow 

 devices, this has led to increased societal 'testing fatigue' 

 and reduced confidence in test results. Consequently, 

 asymptomatic individuals have developed reluctance towards 

 repeat testing, which remains the best way to monitor COVID-19 

 cases in the wider population. On the other hand, saliva-based 

 PCR, a non-invasive, highly sensitive, and accurate test 

 suitable for everyone, is gaining momentum as a straightforward 

 and reliable means of detecting SARS-CoV-2 in symptomatic and 

 asymptomatic individuals. Here, we provide an itemised list of 

 the equipment and reagents involved in the process of sample 

 submission, inactivation and analysis, as well as a detailed 

 description of how each of these steps is performed.},

keywords = {COVID-19, qPCR, saliva},

pubstate = {published},

tppubtype = {article}

}

@article{Yan2021-bf,

title = {Serum glucose, lactate dehydrogenase and hypertension are 

 mediators of the effect of body mass index on severity of 

 COVID-19},

author = {Huadong Yan and Amrita Vijay and Fanrong Jiang and Nanhong Zheng and Yaoren Hu and Honghua Ye and Benjamin Ollivere and Ting Cai and Ana M Valdes and Guruprasad P Aithal},

year  = {2021},

date = {2021-04-01},

journal = {Endocrinol. Diabetes Metab.},

volume = {4},

number = {2},

pages = {e00215},

publisher = {Wiley},

abstract = {Background: COVID-19 has a broad clinical spectrum. We 

 investigated the role of serum markers measured on admission on 

 severity as assessed at discharge and investigated those which 

 relate to the effect of BMI on severity. Methods: Clinical and 

 laboratory data from 610 COVID-19 cases hospitalized in the 

 province of Zheijang, China were investigated as risk factors 

 for severe COVID-19 (assessed by respiratory distress) compared 

 to mild or common forms using logistic regression methods. 

 Biochemical markers were correlated with severity using spearman 

 correlations, and a ROC analysis was used to determine the 

 individual contribution of each of the biochemical markers on 

 severity. We carried out formal mediation analyses to 

 investigate the extent of the effect of body mass index (BMI) on 

 COVID-19 severity mediated by hypertension, glycemia, Lactose 

 Dehydrogenase (LDH) at the time of hospitalization and 

 C-Reactive Protein levels (CRP), in units of standard 

 deviations. Results: The individual markers measured on 

 admission contributing most strongly to prediction of COVID-19 

 severity as assessed at discharge were LDH, CRP and glucose. The 

 proportion of the effect of BMI on severity of COVID-19 mediated 

 by CRP, glycemia or hypertension, we find that glucose mediated 

 79% (p \< .0001), LDH mediated 78% (p \< .0001), hypertension 

 mediated 66% (p \< .0001); however, only 44% (p \< .005) was 

 mediated by systemic inflammation (CRP). Conclusion: Our data 

 indicate that a larger proportion of the effect of BMI on 

 severity of COVID-19 is mediated by glycemia and LDH levels 

 whereas less than half of it is mediated by systemic 

 inflammation.},

keywords = {biochemical markers, BMI, COVID-19, disease severity},

pubstate = {published},

tppubtype = {article}

}

@article{Thompson2021-wc,

title = {Comparative effects of viral-transport-medium heat inactivation 

 upon downstream SARS-CoV-2 detection in patient samples},

author = {Jamie L Thompson and Angela Downie Ruiz Velasco and Alice Cardall and Rebecca Tarbox and Jaineeta Richardson and Gemma Clarke and Michelle Lister and Hannah C Howson-Wells and Vicki M Fleming and Manjinder Khakh and Tim Sloan and Nichola Duckworth and Sarah Walsh and Chris Denning and C Patrick McClure and Andrew V Benest and Claire H Seedhouse},

year  = {2021},

date = {2021-03-01},

journal = {J. Med. Microbiol.},

volume = {70},

number = {3},

publisher = {Microbiology Society},

abstract = {Introduction. The COVID-19 pandemic, which began in 2020 is 

 testing economic resilience and surge capacity of healthcare 

 providers worldwide. At the time of writing, positive detection 

 of the SARS-CoV-2 virus remains the only method for diagnosing 

 COVID-19 infection. Rapid upscaling of national SARS-CoV-2 

 genome testing presented challenges: (1) Unpredictable supply 

 chains of reagents and kits for virus inactivation, RNA 

 extraction and PCR-detection of viral genomes. (2) Rapid time to 

 result of \<24 h is required in order to facilitate timely 

 infection control measures.Hypothesis. Extraction-free sample 

 processing would impact commercially available SARS-CoV-2 genome 

 detection methods.Aim. We evaluated whether alternative 

 commercially available kits provided sensitivity and accuracy of 

 SARS-CoV-2 genome detection comparable to those used by regional 

 National Healthcare Services (NHS).Methodology. We tested 

 several detection methods and tested whether detection was 

 altered by heat inactivation, an approach for rapid one-step 

 viral inactivation and RNA extraction without chemicals or 

 kits.Results. Using purified RNA, we found the CerTest VIASURE 

 kit to be comparable to the Altona RealStar system currently in 

 use, and further showed that both diagnostic kits performed 

 similarly in the BioRad CFX96 and Roche LightCycler 480 II 

 machines. Additionally, both kits were comparable to a third 

 alternative using a combination of Quantabio qScript one-step 

 Quantitative Reverse Transcription Polymerase Chain Reaction 

 (qRT-PCR) mix and Centre for Disease Control and Prevention 

 (CDC)-accredited N1 and N2 primer/probes when looking 

 specifically at borderline samples. Importantly, when using the 

 kits in an extraction-free protocol, following heat 

 inactivation, we saw differing results, with the combined 

 Quantabio-CDC assay showing superior accuracy and sensitivity. 

 In particular, detection using the CDC N2 probe following the 

 extraction-free protocol was highly correlated to results 

 generated with the same probe following RNA extraction and reported clinically (n=127; R2=0.9259).Conclusion. Our results 

 demonstrate that sample treatment can greatly affect the 

 downstream performance of SARS-CoV-2 diagnostic kits, with 

 varying impact depending on the kit. We also showed that 

 one-step heat-inactivation methods could reduce time from swab 

 receipt to outcome of test result. Combined, these findings 

 present alternatives to the protocols in use and can serve to 

 alleviate any arising supply-chain issues at different points in 

 the workflow, whilst accelerating testing, and reducing cost and 

 environmental impact.},

keywords = {COVID-19, RT-qPCR testing, SARS-CoV-2, viral transport media},

pubstate = {published},

tppubtype = {article}

}

@article{Yan2020-vl,

title = {Role of drugs used for chronic disease management on 

 susceptibility and severity of COVID-19: A large case-control 

 study},

author = {Huadong Yan and Ana M Valdes and Amrita Vijay and Shanbo Wang and Lili Liang and Shiqing Yang and Hongxia Wang and Xiaoyan Tan and Jingyuan Du and Susu Jin and Kecheng Huang and Fanrong Jiang and Shun Zhang and Nanhong Zheng and Yaoren Hu and Ting Cai and Guruprasad P Aithal},

year  = {2020},

date = {2020-12-01},

journal = {Clin. Pharmacol. Ther.},

volume = {108},

number = {6},

pages = {1185\textendash1194},

publisher = {Wiley},

abstract = {This study aimed to investigate whether specific medications 

 used in the treatment chronic diseases affected either the 

 development and/ or severity of coronavirus disease 2019 

 (COVID-19) in a cohort of 610 COVID-19 cases and 48,667 

 population-based controls from Zhejiang, China. Using a cohort 

 of 578 COVID-19 cases and 48,667 population-based controls from 

 Zhejiang, China, we tested the role of usage of cardiovascular, 

 antidiabetic, and other medications on risk and severity of 

 COVID-19. Analyses were adjusted for age, sex, and body mass 

 index and for presence of relevant comorbidities. Individuals 

 with hypertension taking calcium channel blockers had significantly increased risk (odds ratio (OR) = 1.73, 95% 

 confidence interval (CI) 1.2-2.3) of manifesting symptoms of 

 COVID-19, whereas those taking angiotensin receptor blockers and diuretics had significantly lower disease risk (OR = 0.22, 95% CI 0.15-0.30 and OR = 0.30, 95% CI 0.19-0.58, respectively). 

 Among those with type 2 diabetes, dipeptidyl peptidase-4 inhibitors (OR = 6.02, 95% CI 2.3-15.5) and insulin (OR = 2.71, 

 95% CI 1.6-5.5) were more and glucosidase inhibitors were less prevalent (OR = 0.11, 95% CI 0.1-0.3) among with patients with 

 COVID-19. Drugs used in the treatment of hypertension and 

 diabetes influence the risk of development of COVID-19, but, not 

 its severity.},

keywords = {#Joint first authors, Antidiabetic medications, Antihypertensive medications, Calcium channel   blockers, Corticosteroids, COVID-19, Risk, Severity},

pubstate = {published},

tppubtype = {article}

}