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.

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.