Predicted properties of CD1d proteins coded by different mRNA transcripts in human respiratory epithelial cells.

<p>V1–6: CD1D spliced variants; NS: Non-spliced.</p

Expression of six CD1D alternatively spliced CD1D variants in human respiratory epithelial cells.

<p>Panel A: Schematic illustration of primer pairs “C/C”, “D/D”, and “D/E” annealing sites on CD1D mRNA, and corresponding full-length product sizes. Panel B: RT-PCR on primary bronchial epithelial cells detected a 305-bp band. Same primers amplified the expected full-length (572-bp) product plus a shorter amplicon (305-bp) both in oligo dT– and CD1D specific primer–reverse transcribed cDNA from Beas2B. Direct nucleotide sequencing of the smaller band (lower panel) identified a CD1D variant lacking α1 exon (“V1”). Panel C: Primer pairs “D/D” and “D/E” detected five other CD1D variants (“V2–6”) in Beas2B. Panel D: Direct nucleotide sequencing of “V4–6” revealed the splicing junction in these variants.</p

Human respiratory epithelial cells express CD1d protein.

<p>Panel A: Flow cytometry analysis of CD1d expression on Beas2B and A549 epithelial cell lines, using three anti-human CD1d mAbs – clones 42, 51.1.3, and NOR3.2. Panel B: CD1b staining on Beas2B cells and CD1b-expressing monocyte-derived dendritic cells (DC). Panel C: Flow cytometry analysis of CD1d expression on primary human lung epithelial cells (top panel) and normal human bronchial epithelial (NHBE; bottom panel) cells.</p

Admission drugs, Radiologist Reports of Presenting chest radiograph (CXR) and absolute blood leukocyte counts at the point of sampling of PBMC used for phenotyping.

<p>Admission drugs, Radiologist Reports of Presenting chest radiograph (CXR) and absolute blood leukocyte counts at the point of sampling of PBMC used for phenotyping.</p

Longitudinal changes in organ function from onset of symptoms (Day 1).

<p>Biochemical and haematological indices were captured every two days throughout disease course for Patient 1 (column A), Patient 2 (column B) and Patient 3 (column C). Relevant clinical and therapeutic interventions are shown on the urea and creatinine serial graph for each patient. Normal levels are Urea – 2.5–7.5 mmol/l; Creatinine - 40–139 umol/l; Hb - 12.0–17.5 g/dl; lymphocytes – 1.5–3.5×10^∧9/l; monocytes 0.2–0.8×10^∧9/l; neutrophils 2.5–7.5×10^∧9/l; ALT- 0–50U/l; albumin - 32–45 g/l; CRP - 0–10 mg/l.</p

Viral RNA in Samples from Patients 1–3.

<p>Note. – Neg  =  Negative</p

Radiographic images at presentation for Patient 1–3.

<p>Cut (mediastinal window) from mid thoracic region of the CT pulmonary angiogram of Patient 1 showing bilateral widespread nodular consolidation (A). The CTPA was reported as showing extensive inflammatory change in both lungs with solid consolidation of both lower lobes and right middle lobe; with widespread patchy infiltration in both upper lobes. CXR for Patient 2 (B) on day of intubation showed bilateral mid and lower zone consolidations, and possible left pleural fluid collection; and for Patient 3 (C) – extensive right lower lobe consolidation and patchy consolidation in left lower lobe; enlarged cardiothoracic ratio and evidence of pulmonary edema.</p

Constructing custom-made radiotranscriptomic signatures of vascular inflammation from routine CT angiograms: a prospective outcomes validation study in COVID-19.

BackgroundDirect evaluation of vascular inflammation in patients with COVID-19 would facilitate more efficient trials of new treatments and identify patients at risk of long-term complications who might respond to treatment. We aimed to develop a novel artificial intelligence (AI)-assisted image analysis platform that quantifies cytokine-driven vascular inflammation from routine CT angiograms, and sought to validate its prognostic value in COVID-19.MethodsFor this prospective outcomes validation study, we developed a radiotranscriptomic platform that uses RNA sequencing data from human internal mammary artery biopsies to develop novel radiomic signatures of vascular inflammation from CT angiography images. We then used this platform to train a radiotranscriptomic signature (C19-RS), derived from the perivascular space around the aorta and the internal mammary artery, to best describe cytokine-driven vascular inflammation. The prognostic value of C19-RS was validated externally in 435 patients (331 from study arm 3 and 104 from study arm 4) admitted to hospital with or without COVID-19, undergoing clinically indicated pulmonary CT angiography, in three UK National Health Service (NHS) trusts (Oxford, Leicester, and Bath). We evaluated the diagnostic and prognostic value of C19-RS for death in hospital due to COVID-19, did sensitivity analyses based on dexamethasone treatment, and investigated the correlation of C19-RS with systemic transcriptomic changes.FindingsPatients with COVID-19 had higher C19-RS than those without (adjusted odds ratio [OR] 2·97 [95% CI 1·43-6·27], p=0·0038), and those infected with the B.1.1.7 (alpha) SARS-CoV-2 variant had higher C19-RS values than those infected with the wild-type SARS-CoV-2 variant (adjusted OR 1·89 [95% CI 1·17-3·20] per SD, p=0·012). C19-RS had prognostic value for in-hospital mortality in COVID-19 in two testing cohorts (high [≥6·99] vs low [InterpretationRadiotranscriptomic analysis of CT angiography scans introduces a potentially powerful new platform for the development of non-invasive imaging biomarkers. Application of this platform in routine CT pulmonary angiography scans done in patients with COVID-19 produced the radiotranscriptomic signature C19-RS, a marker of cytokine-driven inflammation driving systemic activation of coagulation and responsible for adverse clinical outcomes, which predicts in-hospital mortality and might allow targeted therapy.FundingEngineering and Physical Sciences Research Council, British Heart Foundation, Oxford BHF Centre of Research Excellence, Innovate UK, NIHR Oxford Biomedical Research Centre, Wellcome Trust, Onassis Foundation

Device-assessed sleep and physical activity in individuals recovering from a hospital admission for COVID-19: a multicentre study

Background The number of individuals recovering from severe COVID-19 is increasing rapidly. However, little is known about physical behaviours that make up the 24-h cycle within these individuals. This study aimed to describe physical behaviours following hospital admission for COVID-19 at eight months post-discharge including associations with acute illness severity and ongoing symptoms. Methods One thousand seventy-seven patients with COVID-19 discharged from hospital between March and November 2020 were recruited. Using a 14-day wear protocol, wrist-worn accelerometers were sent to participants after a five-month follow-up assessment. Acute illness severity was assessed by the WHO clinical progression scale, and the severity of ongoing symptoms was assessed using four previously reported data-driven clinical recovery clusters. Two existing control populations of office workers and individuals with type 2 diabetes were comparators. Results Valid accelerometer data from 253 women and 462 men were included. Women engaged in a mean ± SD of 14.9 ± 14.7 min/day of moderate-to-vigorous physical activity (MVPA), with 12.1 ± 1.7 h/day spent inactive and 7.2 ± 1.1 h/day asleep. The values for men were 21.0 ± 22.3 and 12.6 ± 1.7 h /day and 6.9 ± 1.1 h/day, respectively. Over 60% of women and men did not have any days containing a 30-min bout of MVPA. Variability in sleep timing was approximately 2 h in men and women. More severe acute illness was associated with lower total activity and MVPA in recovery. The very severe recovery cluster was associated with fewer days/week containing continuous bouts of MVPA, longer total sleep time, and higher variability in sleep timing. Patients post-hospitalisation with COVID-19 had lower levels of physical activity, greater sleep variability, and lower sleep efficiency than a similarly aged cohort of office workers or those with type 2 diabetes. Conclusions Those recovering from a hospital admission for COVID-19 have low levels of physical activity and disrupted patterns of sleep several months after discharge. Our comparative cohorts indicate that the long-term impact of COVID-19 on physical behaviours is significant.</p

The effect of COVID rehabilitation for ongoing symptoms post hospitalisation with COVID-19 (PHOSP-R): protocol for a randomised parallel group controlled trial on behalf of the PHOSP consortium

Introduction: Many adults hospitalised with COVID-19 have persistent symptoms such as fatigue, breathlessness and brain fog that limit day-to-day activities. These symptoms can last over 2 years. Whilst there is limited controlled studies on interventions that can support those with ongoing symptoms, there has been some promise in rehabilitation interventions in improving function and symptoms either using face-to-face or digital methods, but evidence remains limited and these studies often lack a control group.  Methods and analysis: This is a nested single-blind, parallel group, randomised control trial with embedded qualitative evaluation comparing rehabilitation (face-to-face or digital) to usual care and conducted within the PHOSP-COVID study. The aim of this study is to determine the effectiveness of rehabilitation interventions on exercise capacity, quality of life and symptoms such as breathlessness and fatigue. The primary outcome is the Incremental Shuttle Walking Test following the eight week intervention phase. Secondary outcomes include measures of function, strength and subjective assessment of symptoms. Blood inflammatory markers and muscle biopsies are an exploratory outcome. The interventions last eight weeks and combine symptom-titrated exercise therapy, symptom management and education delivered either in a face-to-face setting or through a digital platform (www.yourcovidrecovery.nhs.uk). The proposed sample size is 159 participants, and data will be intention-to-treat analyses comparing rehabilitation (face-to-face or digital) to usual care.  Ethics and dissemination: Ethical approval was gained as part of the PHOSP-COVID study by Yorkshire and the Humber Leeds West Research NHS Ethics Committee, and the study was prospectively registered on the ISRCTN trial registry (ISRCTN13293865). Results will be disseminated to stakeholders, including patients and members of the public, and published in appropriate journals.  Article summary Strengths and limitations of this study • This protocol utilises two interventions to support those with ongoing symptoms of COVID-19 • This is a two-centre parallel-group randomised controlled trial • The protocol has been supported by patient and public involvement groups who identified treatments of symptoms and activity limitation as a top priority</p