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.

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.

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.

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.

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

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.

Measurement of Vital Signs by Lifelight Software in Comparison to Standard of Care Multisite Development (VISION-MD): Protocol for an Observational Study.

BACKGROUND: Measuring vital signs (VS) is an important aspect of clinical care but is time-consuming and requires multiple pieces of equipment and trained staff. Interest in the contactless measurement of VS has grown since the COVID-19 pandemic, including in nonclinical situations. Lifelight is an app being developed as a medical device for the contactless measurement of VS using remote photoplethysmography (rPPG) via the camera on smart devices. The VISION-D (Measurement of Vital Signs by Lifelight Software in Comparison to the Standard of Care-Development) and VISION-V (Validation) studies demonstrated the accuracy of Lifelight compared with standard-of-care measurement of blood pressure, pulse rate, and respiratory rate, supporting the certification of Lifelight as a class I Conformité Européenne (CE) medical device. OBJECTIVE: To support further development of the Lifelight app, the observational VISION Multisite Development (VISION-MD) study is collecting high-quality data from a broad range of patients, including those with VS measurements outside the normal healthy range and patients who are critically ill. METHODS: The study is recruiting adults (aged ≥16 years) who are inpatients (some critically ill), outpatients, and healthy volunteers, aiming to cover a broad range of normal and clinically relevant VS values; there are no exclusion criteria. High-resolution 60-second videos of the face are recorded by the Lifelight app while simultaneously measuring VS using standard-of-care methods (automated sphygmomanometer for blood pressure; finger clip sensor for pulse rate and oxygen saturation; manual counting of respiratory rate). Feedback from patients and nurses who use Lifelight is collected via a questionnaire. Data to estimate the cost-effectiveness of Lifelight compared with standard-of-care VS measurement are also being collected. A new method for rPPG signal processing is currently being developed, based on the identification of small areas of high-quality signals in each individual. Anticipated recruitment is 1950 participants, with the expectation that data from approximately 1700 will be used for software development. Data from 250 participants will be retained to test the performance of Lifelight against predefined performance targets. RESULTS: Recruitment began in May 2021 but was hindered by the restrictions instigated during the COVID-19 pandemic. The development of data processing methodology is in progress. The data for analysis will become available from September 2022, and the algorithms will be refined continuously to improve clinical accuracy. The performance of Lifelight compared with that of the standard-of-care measurement of VS will then be tested. Recruitment will resume if further data are required. The analyses are expected to be completed in early 2023. CONCLUSIONS: This study will support the refinement of data collection and processing toward the development of a robust app that is suitable for routine clinical use. TRIAL REGISTRATION: ClinicalTrials.gov NCT04763746; https://clinicaltrials.gov/ct2/show/NCT04763746. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/41533.

Measurement of Vital Signs Using Lifelight Remote Photoplethysmography: Results of the VISION-D and VISION-V Observational Studies.

BACKGROUND: The detection of early changes in vital signs (VSs) enables timely intervention; however, the measurement of VSs requires hands-on technical expertise and is often time-consuming. The contactless measurement of VSs is beneficial to prevent infection, such as during the COVID-19 pandemic. Lifelight is a novel software being developed to measure VSs by remote photoplethysmography based on video captures of the face via the integral camera on mobile phones and tablets. We report two early studies in the development of Lifelight. OBJECTIVE: The objective of the Vital Sign Comparison Between Lifelight and Standard of Care: Development (VISION-D) study (NCT04763746) was to measure respiratory rate (RR), pulse rate (PR), and blood pressure (BP) simultaneously by using the current standard of care manual methods and the Lifelight software to iteratively refine the software algorithms. The objective of the Vital Sign Comparison Between Lifelight and Standard of Care: Validation (VISION-V) study (NCT03998098) was to validate the use of Lifelight software to accurately measure VSs. METHODS: BP, PR, and RR were measured simultaneously using Lifelight, a sphygmomanometer (BP and PR), and the manual counting of RR. Accuracy performance targets for each VS were defined from a systematic literature review of the performance of state-of-the-art VSs technologies. RESULTS: The VISION-D data set (17,233 measurements from 8585 participants) met the accuracy targets for RR (mean error 0.3, SD 3.6 vs target mean error 2.3, SD 5.0; n=7462), PR (mean error 0.3, SD 4.0 vs mean error 2.2, SD 9.2; n=10,214), and diastolic BP (mean error -0.4, SD 8.5 vs mean error 5.5, SD 8.9; n=8951); for systolic BP, the mean error target was met but not the SD (mean error 3.5, SD 16.8 vs mean error 6.7, SD 15.3; n=9233). Fitzpatrick skin type did not affect accuracy. The VISION-V data set (679 measurements from 127 participants) met all the standards: mean error -0.1, SD 3.4 for RR; mean error 1.4, SD 3.8 for PR; mean error 2.8, SD 14.5 for systolic BP; and mean error -0.3, SD 7.0 for diastolic BP. CONCLUSIONS: At this early stage in development, Lifelight demonstrates sufficient accuracy in the measurement of VSs to support certification for a Level 1 Conformité Européenne mark. As the use of Lifelight does not require specific training or equipment, the software is potentially useful for the contactless measurement of VSs by nonclinical staff in residential and home care settings. Work is continuing to enhance data collection and processing to achieve the robustness and accuracy required for routine clinical use. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR2-10.2196/14326.

The VICTORY (Investigation of Inflammacheck to Measure Exhaled Breath Condensate Hydrogen Peroxide in Respiratory Conditions) Study: Protocol for a Cross-sectional Observational Study.

BACKGROUND: More than 7% of the world's population is living with a chronic respiratory condition. In the United Kingdom, lung disease affects approximately 1 in 5 people, resulting in over 700,000 hospital admissions each year. People with respiratory conditions have several symptoms and can require multiple health care visits and investigations before a diagnosis is made. The tests available can be difficult to perform, especially if a person is symptomatic, leading to poor quality results. A new, easy-to-perform, point-of-care test that can be performed in any health care setting and that can differentiate between various respiratory conditions would have a significant, beneficial impact on the ability to diagnose respiratory diseases. OBJECTIVE: The objective of this study is to use a new handheld device (Inflammacheck) in different respiratory conditions to measure the exhaled breath condensate hydrogen peroxide (EBC H2O2) and compare these results with those of healthy controls and with each other. This study also aims to determine whether the device can measure other parameters, including breath humidity, breath temperature, breath flow dynamics, and end tidal carbon dioxide. METHODS: We will perform a single-visit, cross-sectional observational study of EBC H2O2 levels, as measured by Inflammacheck, in people with respiratory disease and volunteers with no known lung disease. Participants with a confirmed diagnosis of asthma, chronic obstructive pulmonary disease, lung cancer, bronchiectasis, pneumonia, breathing pattern disorder, and interstitial lung disease as well as volunteers with no history of lung disease will be asked to breathe into the Inflammacheck device to record their breath sample. RESULTS: The results from this study will be available in 2022, in anticipation of COVID-19-related delays. CONCLUSIONS: This study will investigate the EBC H2O2, as well as other exhaled breath parameters, for use as a future diagnostic tool.

Impact of the coronavirus pandemic on the patterns of vital signs recording and staff compliance with expected monitoring schedules on general wards.

INTRODUCTION: Coronavirus disease 2019 (COVID-19) placed increased burdens on National Health Service hospitals and necessitated significant adjustments to their structures and processes. This research investigated if and how these changes affected the patterns of vital sign recording and staff compliance with expected monitoring schedules on general wards. METHODS: We compared the pattern of vital signs and early warning score (EWS) data collected from admissions to a single hospital during the initial phase of the COVID-19 pandemic with those in three control periods from 2018, 2019 and 2020. Main outcome measures were weekly and monthly hospital admissions; daily and hourly patterns of recorded vital signs and EWS values; time to next observation and; proportions of 'on time', 'late' and 'missed' vital signs observations sets. RESULTS: There were large falls in admissions at the beginning of the COVID-19 era. Admissions were older, more unwell on admission and throughout their stay, more often required supplementary oxygen, spent longer in hospital and had a higher in-hospital mortality compared to one or more of the control periods. More daily observation sets were performed during the COVID-19 era than in the control periods. However, there was no clear evidence that COVID-19 affected the pattern of vital signs collection across the 24-h period or the week. CONCLUSIONS: The increased burdens of the COVID-19 pandemic, and the alterations in healthcare structures and processes necessary to respond to it, did not adversely affect the hospitals' ability to monitor patients under its care and to comply with expected monitoring schedules.

The performance of the National Early Warning Score and National Early Warning Score 2 in hospitalised patients infected by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

INTRODUCTION: Since the introduction of the UK's National Early Warning Score (NEWS) and its modification, NEWS2, coronavirus disease 2019 (COVID-19), has caused a worldwide pandemic. NEWS and NEWS2 have good predictive abilities in patients with other infections and sepsis, however there is little evidence of their performance in COVID-19. METHODS: Using receiver-operating characteristics analyses, we used the area under the receiver operating characteristic (AUROC) curve to evaluate the performance of NEWS or NEWS2 to discriminate the combined outcome of either death or intensive care unit (ICU) admission within 24 h of a vital sign set in five cohorts (COVID-19 POSITIVE, n = 405; COVID-19 NOT DETECTED, n = 1716; COVID-19 NOT TESTED, n = 2686; CONTROL 2018, n = 6273; CONTROL 2019, n = 6523). RESULTS: The AUROC values for NEWS or NEWS2 for the combined outcome were: COVID-19 POSITIVE, 0.882 (0.868-0.895); COVID-19 NOT DETECTED, 0.875 (0.861-0.89); COVID-19 NOT TESTED, 0.876 (0.85-0.902); CONTROL 2018, 0.894 (0.884-0.904); CONTROL 2019, 0.842 (0.829-0.855). CONCLUSIONS: The finding that NEWS or NEWS2 performance was good and similar in all five cohorts (range = 0.842-0.894) suggests that amendments to NEWS or NEWS2, such as the addition of new covariates or the need to change the weighting of existing parameters, are unnecessary when evaluating patients with COVID-19. Our results support the national and international recommendations for the use of NEWS or NEWS2 for the assessment of acute-illness severity in patients with COVID-19.

COVID-19: A collision of complement, coagulation and inflammatory pathways.

COVID-19 is frequently accompanied by a hypercoagulable inflammatory state with microangiopathic pulmonary changes that can precede the diffuse alveolar damage characteristic of typical acute respiratory distress syndrome (ARDS) seen in other severe pathogenic infections. Parallels with systemic inflammatory disorders such as atypical hemolytic uremic syndrome (aHUS) have implicated the complement pathway in the pathogenesis of COVID-19, and particularly the anaphylatoxins C3a and C5a released from cleavage of C3 and C5, respectively. C5a is a potent cell signalling protein that activates a cytokine storm-a hyper-inflammatory phenomenon-within hours of infection and the innate immune response. However, excess C5a can result in a pro-inflammatory environment orchestrated through a plethora of mechanisms that propagate lung injury, lymphocyte exhaustion, and an immune paresis. Furthermore, disruption of the homeostatic interactions between complement and extrinsic and intrinsic coagulation pathways contributes to a net pro-coagulant state in the microvasculature of critical organs. Fatal COVID-19 has been associated with a systemic inflammatory response accompanied by a pro-coagulant state and organ damage, particularly microvascular thrombi in the lungs and kidneys. Pathologic studies report strong evidence of complement activation. C5 blockade reduces inflammatory cytokines and their manifestations in animal studies, and has shown benefits in patients with aHUS, prompting investigation of this approach in the treatment of COVID-19. This review describes the role of the complement pathway and particularly C5a and its aberrations in highly pathogenic virus infections, and therefore its potential as a therapeutic target in COVID-19.