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Background: Sleep disturbance is common following hospital admission both for COVID-19 and other causes. The clinical associations of this for recovery after hospital admission are poorly understood despite sleep disturbance contributing to morbidity in other scenarios. We aimed to investigate the prevalence and nature of sleep disturbance after discharge following hospital admission for COVID-19 and to assess whether this was associated with dyspnoea., Methods: CircCOVID was a prospective multicentre cohort substudy designed to investigate the effects of circadian disruption and sleep disturbance on recovery after COVID-19 in a cohort of participants aged 18 years or older, admitted to hospital for COVID-19 in the UK, and discharged between March, 2020, and October, 2021. Participants were recruited from the Post-hospitalisation COVID-19 study (PHOSP-COVID). Follow-up data were collected at two timepoints: an early time point 2-7 months after hospital discharge and a later time point 10-14 months after hospital discharge. Sleep quality was assessed subjectively using the Pittsburgh Sleep Quality Index questionnaire and a numerical rating scale. Sleep quality was also assessed with an accelerometer worn on the wrist (actigraphy) for 14 days. Participants were also clinically phenotyped, including assessment of symptoms (ie, anxiety [Generalised Anxiety Disorder 7-item scale questionnaire], muscle function [SARC-F questionnaire], dyspnoea [Dyspnoea-12 questionnaire] and measurement of lung function), at the early timepoint after discharge. Actigraphy results were also compared to a matched UK Biobank cohort (non-hospitalised individuals and recently hospitalised individuals). Multivariable linear regression was used to define associations of sleep disturbance with the primary outcome of breathlessness and the other clinical symptoms. PHOSP-COVID is registered on the ISRCTN Registry (ISRCTN10980107)., Findings: 2320 of 2468 participants in the PHOSP-COVID study attended an early timepoint research visit a median of 5 months (IQR 4-6) following discharge from 83 hospitals in the UK. Data for sleep quality were assessed by subjective measures (the Pittsburgh Sleep Quality Index questionnaire and the numerical rating scale) for 638 participants at the early time point. Sleep quality was also assessed using device-based measures (actigraphy) a median of 7 months (IQR 5-8 months) after discharge from hospital for 729 participants. After discharge from hospital, the majority (396 [62%] of 638) of participants who had been admitted to hospital for COVID-19 reported poor sleep quality in response to the Pittsburgh Sleep Quality Index questionnaire. A comparable proportion (338 [53%] of 638) of participants felt their sleep quality had deteriorated following discharge after COVID-19 admission, as assessed by the numerical rating scale. Device-based measurements were compared to an age-matched, sex-matched, BMI-matched, and time from discharge-matched UK Biobank cohort who had recently been admitted to hospital. Compared to the recently hospitalised matched UK Biobank cohort, participants in our study slept on average 65 min (95% CI 59 to 71) longer, had a lower sleep regularity index (-19%; 95% CI -20 to -16), and a lower sleep efficiency (3·83 percentage points; 95% CI 3·40 to 4·26). Similar results were obtained when comparisons were made with the non-hospitalised UK Biobank cohort. Overall sleep quality (unadjusted effect estimate 3·94; 95% CI 2·78 to 5·10), deterioration in sleep quality following hospital admission (3·00; 1·82 to 4·28), and sleep regularity (4·38; 2·10 to 6·65) were associated with higher dyspnoea scores. Poor sleep quality, deterioration in sleep quality, and sleep regularity were also associated with impaired lung function, as assessed by forced vital capacity. Depending on the sleep metric, anxiety mediated 18-39% of the effect of sleep disturbance on dyspnoea, while muscle weakness mediated 27-41% of this effect., Interpretation: Sleep disturbance following hospital admission for COVID-19 is associated with dyspnoea, anxiety, and muscle weakness. Due to the association with multiple symptoms, targeting sleep disturbance might be beneficial in treating the post-COVID-19 condition., Funding: UK Research and Innovation, National Institute for Health Research, and Engineering and Physical Sciences Research Council., Competing Interests: Declaration of interests IDS declares a statistical editor honoraria role with Thorax. TP declares support from the National Institute for Health Research (NIHR) Leicester Biomedical Research Centre (BRC) to complete the work. ALH declares an editor-in-chief role for Computer Physics Communications. RA declares speaker fees and travel support from Boehringer Ingelheim. CEB declares their institute was awarded a grant from the UK Research and Innovation (UKRI)/NIHR and institutional support from NIHR Nottingham BRC to complete this work; the author reports grants from Nottingham Hospitals Charity and Nottingham University Hospitals Research and Innovation Department. TC declares support from the NIHR South London and Maudsley NHS Foundation Trust, King's College London BRC to complete the work; the author reports grants from Guy's and St Thomas' Charity, NIHR, and UKRI; the author has published self-help books on chronic fatigue for which she receives royalties; the author has received ad-hoc payments for workshops carried out in long-term conditions; the author declares travel and accommodation support; the author is part of the scientific committee of the British Association for Behavioural and Cognitive Psychotherapies (BABCP) and she is on the expert advisory panel for COVID-19 Rapid Guidelines. JDC declares grants from AstraZeneca, Novartis, Boehringer Ingelheim, Genentech, Gilead Sciences, Insmed, GlaxoSmithKline, and Grifols; the author reports consulting fees from AstraZeneca, Insmed, Boehringer Ingelheim, Janssen, Antabio, Chiesi, Novartis, Pfizer, Zambon, GlaxoSmithKline, and Grifols. GD declares support from the NIHR Imperial BRC, Royal Brompton and Harefield NGS Foundation Trust, Royal Brompton & Harefield Hospitals Charity, Imperial College Healthcare NHS Trust, and the Medical Research Council (MRC) to complete this work; the author reports grants from Genentech, AstraZeneca, British Lung Foundation (BLF) Early Cohort, GlaxoSmithKline, Novartis, Chiesi, and Boehringer Ingelheim; the author has a published chapter in a textbook for which he receives payment; the author declares a role in the advisory boards for AstraZeneca and Novartis and as honorarium as deputy editor of the American Journal of Respiratory and Critical Care Medicine (AJRCCM). L-PH declares grants from NIHR Oxford BRC. MGJ declares grants from the Royal Society, MRC, BLF, Boehringer Ingelheim, and the Asthma, Allergy and Inflammatory Research Charity. BR declares support from the British Heart Foundation (BHF) Oxford Centre of Research Excellence (CRE) to complete this work. SLR-J declares support for her institute from UKRI to complete the work; the author reports grants from UKRI, The European and Developing Countries Clinical Trials Partnership (EDCTP), MRC, Rosetrees Trust, and the Global Challenges Research Fund (GCRF); the author reports an honorarium for chapter contribution from the Federation of European Academies of Medicine; the author is Data and Safety Monitoring Board (DSMB) Chair for a Bexsero trial funded by Wellcome Trust; the author declares an editor role for AIDS journal. AVR declares support from NIHR Leicester BRC to complete the work. MS declares support for his institute from MRC/Department of Health and Social Care (DHSC) to complete the work. ASi declares support for her institute from UKRI/NIHR to complete the work. DGW declares an advanced Fellowship grant from NIHR; the author receives an honorarium from bioMérieux to present. TY declares support from the NIHR Leicester BRC to complete the work. RGJ declares grants from AstraZeneca, Biogen, Galecto, GlaxoSmithKline, Nordic Biosciences, RedX, Pliant; the author received consulting fees from AstraZeneca, Brainomix, Bristol Myers Squibb, Chiesi, Cohbar, Daewoong, GlaxoSmithKline, Veracyte, Resolution Therapeutics, and Pliant; the author has received payments from Boehringer Ingelheim, Chiesi, Roche, patientMpower, and AstraZeneca; the author was paid for expert testimony by Pinsent Masons LLP; the author has participated on a DSMB for Boehringer Ingelheim, Galapagos, and Vicore; the author has held a leadership role at NuMedii and is President of Action for Pulmonary Fibrosis. SJS declares grants from NIHR, Wellcome Doctoral Training Programme (DTP), the Human Tissue Authority, NIHR DHSC/UKRI COVID-19 Rapid Response Initiative, NIHR Global Research Group, Actegy Limited, and as an NIHR Senior Investigator; the author has presented for GlaxoSmithKline, Ministry of Justice, CIPLA, and Sherbourne Gibbs; the author is on the National Institute for Health and Care Excellence (NICE) Expert Advisor Panel for Long COVID and was on the Wales Long COVID Advisory Board; the author is the American Thoracic Society (ATS) Pulmonary Rehabilitation Assembly Chair, Clinical Lead Royal Society of Physicians (RSP) Pulmonary Rehabilitation Accreditation Scheme, and Clinical Lead Nation Asthma and COPD Audit Programme (NACAP) for Pulmonary Rehabilitation. WD-CM declares grants for his institution from NIHR, National Health Service (NHS) Accelerated Access Collaborative, and BLF; the author is the honorary President of the Association for Respiratory Technology and Physiology but receives no payment. CEBr declares support from UKRI/DHSC and NIHR Leicester BRC to complete the work; the author reports grants from GlaxoSmithKline, AstraZeneca, Sanofi, CI, Chiesi, Novartis, Roche, Genentech, Mologic, and 4DPharma; the author received consulting fees paid to his institution from GlaxoSmithKline, AstraZeneca, Sanofi, BI, Chiesi, Novartis, Roche, Genentech, Mologic, 4DPharma, and TEVA. LVW declares support from UKRI, GlaxoSmithKline/Asthma + Lung UK, and NIHR to complete this work; the author receives grants from Orion Pharma, GlaxoSmithKline, Genentech, and AstraZeneca; the author received consulting fees paid to her institution from Galapagos and Boehringer Ingelheim; the author received support for attending a meeting from Genentech. JCP received consulting fees from Istesso and The Limbic; the author participated on a DSMB for Vicore. AART declares a fellowship grant from BHF and a grant from NIHR to his institution; the author received an honorarium for lectures from Janssen-Cilag Ltd; the author received support for attending meetings from Janssen-Cilag Ltd. AH declares support from UKRI, NIHR, and NIHR Manchester BRC to complete the work; the author is Chair NIHR Translational Research Collaboration (unpaid). PLM declares a grant for his institution from AstraZeneca; the author received consulting fees from Hoffmann-La Roche, Boehringer Ingelheim, AstraZeneca, Trevi, and Qureight; the author received speaker fees from Boehringer Ingelheim and Hoffmann-La Roche. RAE declares support from UKRI/MRC to complete the work; the author reports a grant from NIHR/Wolfson Foundation; the author received consulting fees from AstraZeneca for Long COVID; the author received a speaker fee from Boehringer Ingelheim for a lecture on Long COVID; the author received support to attend BTS conference virtually from Chiesi; the author is the European Respiratory Society Group 01.02 Pulmonary Rehabilitation Secretary (unpaid). JFB declares support to his institute from an MRC Transition Fellowship, Asthma + Lung UK, NIHR Manchester BRC, and UKRI; the author reports grants paid to his institution from the Small Business Research Initiative Home Spirometer and the National Institute of Academic Anaesthesia; the author has received support for attending meetings from TEVA and Therakos; the author is a committee member of the Royal Society of Medicine (RSM). All other authors declare no competing interests., (Copyright © 2023 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)

Background: Immunocompromised patients may be at higher risk of mortality if hospitalised with Coronavirus Disease 2019 (COVID-19) compared with immunocompetent patients. However, previous studies have been contradictory. We aimed to determine whether immunocompromised patients were at greater risk of in-hospital death and how this risk changed over the pandemic., Methods and Findings: We included patients > = 19 years with symptomatic community-acquired COVID-19 recruited to the ISARIC WHO Clinical Characterisation Protocol UK prospective cohort study. We defined immunocompromise as immunosuppressant medication preadmission, cancer treatment, organ transplant, HIV, or congenital immunodeficiency. We used logistic regression to compare the risk of death in both groups, adjusting for age, sex, deprivation, ethnicity, vaccination, and comorbidities. We used Bayesian logistic regression to explore mortality over time. Between 17 January 2020 and 28 February 2022, we recruited 156,552 eligible patients, of whom 21,954 (14%) were immunocompromised. In total, 29% (n = 6,499) of immunocompromised and 21% (n = 28,608) of immunocompetent patients died in hospital. The odds of in-hospital mortality were elevated for immunocompromised patients (adjusted OR 1.44, 95% CI [1.39, 1.50], p < 0.001). Not all immunocompromising conditions had the same risk, for example, patients on active cancer treatment were less likely to have their care escalated to intensive care (adjusted OR 0.77, 95% CI [0.7, 0.85], p < 0.001) or ventilation (adjusted OR 0.65, 95% CI [0.56, 0.76], p < 0.001). However, cancer patients were more likely to die (adjusted OR 2.0, 95% CI [1.87, 2.15], p < 0.001). Analyses were adjusted for age, sex, socioeconomic deprivation, comorbidities, and vaccination status. As the pandemic progressed, in-hospital mortality reduced more slowly for immunocompromised patients than for immunocompetent patients. This was particularly evident with increasing age: the probability of the reduction in hospital mortality being less for immunocompromised patients aged 50 to 69 years was 88% for men and 83% for women, and for those >80 years was 99% for men and 98% for women. The study is limited by a lack of detailed drug data prior to admission, including steroid doses, meaning that we may have incorrectly categorised some immunocompromised patients as immunocompetent., Conclusions: Immunocompromised patients remain at elevated risk of death from COVID-19. Targeted measures such as additional vaccine doses, monoclonal antibodies, and nonpharmaceutical preventive interventions should be continually encouraged for this patient group., Trial Registration: ISRCTN 66726260., Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: LT declares a lecture fee paid to his institution from Eisai ltd. CP reports research grants from Pfizer, Daiichi Sankyo and Seagen, consulting fees from Pfizer, Roche, Daiichi Sankyo, Novartis, Exact sciences, Gilead, SeaGen and Eli Lilly, and payment for lectures from Pfizer, Novartis and Eisai ltd. PO declares fees from Affnivax, Oxford Immunotech, Nestle, Pfizer and Janessen for consulting or chairing a symposium, paid to Imperial College. MGS is chair of the infectious disease advisory board for Integrum Scientific, director of MedEx solutions ltd, participated in the DSMB for Pfizer COVID-19 vaccine trials, and was donated an investigational medicinal product by Chiesi Farmaceutici S.p.A. MGS and PJMO sat on HMG UK New Emerging Respiratory Virus Threats Advisory Group (NERVTAG). MGS sat on HMG UK Scientific Advisory Group for Emergencies (SAGE), COVID-19 Response from March 2020 to March 2022., (Copyright: © 2023 Turtle et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Introduction: The COVID-19 pandemic has led to over 100 million cases worldwide. The UK has had over 4 million cases, 400 000 hospital admissions and 100 000 deaths. Many patients with COVID-19 suffer long-term symptoms, predominantly breathlessness and fatigue whether hospitalised or not. Early data suggest potentially severe long-term consequence of COVID-19 is development of long COVID-19-related interstitial lung disease (LC-ILD)., Methods and Analysis: The UK Interstitial Lung Disease Consortium (UKILD) will undertake longitudinal observational studies of patients with suspected ILD following COVID-19. The primary objective is to determine ILD prevalence at 12 months following infection and whether clinically severe infection correlates with severity of ILD. Secondary objectives will determine the clinical, genetic, epigenetic and biochemical factors that determine the trajectory of recovery or progression of ILD. Data will be obtained through linkage to the Post-Hospitalisation COVID platform study and community studies. Additional substudies will conduct deep phenotyping. The Xenon MRI investigation of Alveolar dysfunction Substudy will conduct longitudinal xenon alveolar gas transfer and proton perfusion MRI. The POST COVID-19 interstitial lung DiseasE substudy will conduct clinically indicated bronchoalveolar lavage with matched whole blood sampling. Assessments include exploratory single cell RNA and lung microbiomics analysis, gene expression and epigenetic assessment., Ethics and Dissemination: All contributing studies have been granted appropriate ethical approvals. Results from this study will be disseminated through peer-reviewed journals., Conclusion: This study will ensure the extent and consequences of LC-ILD are established and enable strategies to mitigate progression of LC-ILD., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2021. Re-use permitted under CC BY. Published by BMJ.)

Background: Microbiological characterisation of co-infections and secondary infections in patients with COVID-19 is lacking, and antimicrobial use is high. We aimed to describe microbiologically confirmed co-infections and secondary infections, and antimicrobial use, in patients admitted to hospital with COVID-19., Methods: The International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC) WHO Clinical Characterisation Protocol UK (CCP-UK) study is an ongoing, prospective cohort study recruiting inpatients from 260 hospitals in England, Scotland, and Wales, conducted by the ISARIC Coronavirus Clinical Characterisation Consortium. Patients with a confirmed or clinician-defined high likelihood of SARS-CoV-2 infection were eligible for inclusion in the ISARIC WHO CCP-UK study. For this specific study, we excluded patients with a recorded negative SARS-CoV-2 test result and those without a recorded outcome at 28 days after admission. Demographic, clinical, laboratory, therapeutic, and outcome data were collected using a prespecified case report form. Organisms considered clinically insignificant were excluded., Findings: We analysed data from 48 902 patients admitted to hospital between Feb 6 and June 8, 2020. The median patient age was 74 years (IQR 59-84) and 20 786 (42·6%) of 48 765 patients were female. Microbiological investigations were recorded for 8649 (17·7%) of 48 902 patients, with clinically significant COVID-19-related respiratory or bloodstream culture results recorded for 1107 patients. 762 (70·6%) of 1080 infections were secondary, occurring more than 2 days after hospital admission. Staphylococcus aureus and Haemophilus influenzae were the most common pathogens causing respiratory co-infections (diagnosed ≤2 days after admission), with Enterobacteriaceae and S aureus most common in secondary respiratory infections. Bloodstream infections were most frequently caused by Escherichia coli and S aureus . Among patients with available data, 13 390 (37·0%) of 36 145 had received antimicrobials in the community for this illness episode before hospital admission and 39 258 (85·2%) of 46 061 patients with inpatient antimicrobial data received one or more antimicrobials at some point during their admission (highest for patients in critical care). We identified frequent use of broad-spectrum agents and use of carbapenems rather than carbapenem-sparing alternatives., Interpretation: In patients admitted to hospital with COVID-19, microbiologically confirmed bacterial infections are rare, and more likely to be secondary infections. Gram-negative organisms and S aureus are the predominant pathogens. The frequency and nature of antimicrobial use are concerning, but tractable targets for stewardship interventions exist., Funding: National Institute for Health Research (NIHR), UK Medical Research Council, Wellcome Trust, UK Department for International Development, Bill & Melinda Gates Foundation, EU Platform for European Preparedness Against (Re-)emerging Epidemics, NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool, and NIHR HPRU in Respiratory Infections at Imperial College London., Competing Interests: All authors declare support from the NIHR, the Medical Research Council (MRC), the NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool, the NIHR HPRU in Respiratory Infections at Imperial College London, the NIHR Biomedical Research Centre (BRC) at Imperial College London, and the NIHR Clinical Research Network, for the submitted work. ABD reports grants from the UK Department of Health and Social Care (DHSC), during the conduct of the study, and grants from Wellcome Trust, outside the submitted work. PJMO reports personal fees from consultancies (GlaxoSmithKline, Janssen, Bavarian Nordic, Pfizer, and Cepheid) and from the European Respiratory Society, grants from MRC, MRC Global Challenge Research Fund, the EU, NIHR BRC, MRC–GlaxoSmithKline, Wellcome Trust, NIHR (HPRU in Respiratory Infection), and is an NIHR senior investigator outside the submitted work. PJMO's role as President of the British Society for Immunology was unpaid but travel and accommodation at some meetings was provided by the Society. JKB reports grants from MRC. MGS reports grants from DHSC, NIHR UK, MRC, HPRU in Emerging and Zoonotic Infections, and University of Liverpool, during the conduct of the study, and is chair of the scientific advisory board and a minority share holder at Integrum Scientific, outside the submitted work., (© 2021 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license.)

The demographics and comorbidities of patients with community acquired pneumonia (CAP) vary enormously but stratified treatment is difficult because aetiological studies have failed to comprehensively identify the pathogens. Our aim was to describe the bacterial microbiota of CAP and relate these to clinical characteristics in order to inform future trials of treatment stratified by co-morbidity. CAP patients were prospectively recruited at two UK hospitals. We used 16S rRNA gene sequencing to identify the dominant bacteria in sputum and compositional data analysis to determine associations with patient characteristics. We analysed sputum samples from 77 patients and found a Streptococcus sp. and a Haemophilus sp. were the most relatively abundant pathogens. The Haemophilus sp. was more likely to be dominant in patients with pre-existing lung disease, and its relative abundance was associated with qPCR levels of Haemophilus influenzae. The most abundant Streptococcus sp. was associated with qPCR levels of Streptococcus pneumoniae but dominance could not be predicted from clinical characteristics. These data suggest chronic lung disease influences the microbiota of sputum in patients with CAP. This finding could inform a trial of stratifying empirical CAP antibiotics to target Haemophilus spp. in addition to Streptococcus spp. in those with chronic lung disease.

Our aims were to address three fundamental questions relating to the symptoms of community-acquired pneumonia (CAP): Do patients completely recover from pneumonia symptoms? How long does this recovery take? Which factors influence symptomatic recovery?We prospectively recruited patients at two hospitals in Liverpool, UK, into a longitudinal, observational cohort study and modelled symptom recovery from CAP. We excluded patients with cancer, immunosuppression or advanced dementia, and those who were intubated or palliated from admission. We derived a statistical model to describe symptom patterns.We recruited 169 (52% male) adults. Multivariable analysis demonstrated that the time taken to recover to baseline was determined by the initial severity of symptoms. Severity of symptoms was associated with comorbidity and was inversely related to age. The pattern of symptom recovery was exponential and most patients' symptoms returned to baseline by 10 days.These results will inform the advice given to patients regarding the resolution of their symptoms. The recovery model described here will facilitate the use of symptom recovery as an outcome measure in future clinical trials., Competing Interests: Conflict of interest: None declared., (Copyright ©ERS 2017.)