Wellcome Open Research

ObjectivesTo determine the sensitivity and specificity of RT-PCR testing of upper respiratory tract (URT) samples from hospitalised patients with COVID-19, compared to the gold standard of a clinical diagnosis. MethodsAll URT RT-PCR testing for SARS-CoV-2 in NHS Lothian, Scotland, United Kingdom between the 7th of February and 19th April 2020 (inclusive) was reviewed, and hospitalised patients were identified. All URT RT-PCR tests were analysed for each patient to determine the sequence of nega...

Clinical assessment of possible infection with SARS-CoV-2, the novel coronavirus responsible for the outbreak of COVID-19 respiratory illness, has been a major activity of infectious diseases services in the UK and elsewhere since the first report of cases in December 2019. We report our case series of 68 patients, reviewed by Infectious Diseases Consultants at a Regional Infectious Diseases Unit in the UK. We prospectively evaluated our service between the 29th Jan 2020 and 24th Feb 2020. Demo...

BackgroundLaboratory diagnosis of SARS-CoV-2 infection (the cause of COVID-19) uses PCR to detect viral RNA (vRNA) in respiratory samples. SARS-CoV-2 RNA has also been detected in other sample types, but there is limited understanding of the clinical or laboratory significance of its detection in blood. MethodsWe undertook a systematic literature review to assimilate the evidence for the frequency of vRNA in blood, and to identify associated clinical characteristics. We performed RT-PCR in seru...

ImportanceA strategy for preventing further spread of the ongoing COVID-19 epidemic is to detect infections and isolate infected individuals without the need of extensive bio-specimen testing. ObjectivesHere we investigate the prevalence of loss of smell and taste among COVID-19 diagnosed individuals and we identify the combination of symptoms, besides loss of smell and taste, most likely to correspond to a positive COVID-19 diagnosis in non-severe cases. DesignCommunity survey. Setting and P...

BackgroundDiagnostic testing forms a major part of the UKs response to the current COVID-19 pandemic with tests offered to people with a continuous cough, high temperature or anosmia. Testing capacity must be sufficient during the winter respiratory season when levels of cough and fever are high due to non-COVID-19 causes. This study aims to make predictions about the contribution of baseline cough or fever to future testing demand in the UK. MethodsIn this analysis of the Bug Watch prospective...

BackgroundNutritional status has been compromised by ongoing war and restrictions on food deliveries in the Gaza Strip. We developed a mathematical model that outputs retrospective estimates and scenario-based projections of acute malnutrition prevalence among children given caloric intake and other factors. We present here the model and its application to the crisis in Gaza. MethodsWe extended an existing mechanistic model for weight change as a function of energy balance, calibrating it to re...

We assessed the validity of coded health care data to identify cases of haemophagocytic lymphohistiocytosis (HLH). Hospital Episode Statistics (HES) identified 127 cases within five hospital Trusts 2013-2018 using ICD-10 codes D76.1, D76.2 and D76.3. Hospital records were reviewed to validate diagnoses. 73/74 patients with confirmed/probable HLH were coded D76.1 or D76.2 (positive predictive value 89.0% [95% CI 80.2-94.9%]). For cases considered not HLH, 44/53 were coded D76.3 (negative predicti...

BackgroundWe set out to characterise chronic Hepatitis B (CHB) in the primary care population in England and investigate risk factors for progression to hepatocellular carcinoma (HCC). MethodsWe identified 8039 individuals with CHB in individuals aged [≥]18 years between 1999-2019 in the English primary care database QResearch. HCC risk factors were investigated using Cox proportional hazards modelling. FindingsMost of those living with CHB were males (60%) of non-White ethnicity (>70%), an...

Reports of COVID-19 prevalence through national statistics, community surveys and targeted testing at places of work or study have guided national and institutional responses to the pandemic. The University of Edinburgh established a mass testing programme, TestEd, for detection of COVID-19 in asymptomatic staff and students who are studying or working on campus. The study has tested more than 100,000 samples with more than 170 confirmed positive results. Since the introduction of a change in po...

BackgroundOver the course of the pandemic, testing policies for SARS-CoV-2 have varied considerably in England, particularly in the five months up to 1 April 2022 when free community testing ended. We described the trends and demographics of COVID-19 cases during this period. MethodsCOVID-19 cases reported between 15 November 2021 and 30 April 2022 were extracted and aggregated by testing pillar: Pillar 1 for those tested within the NHS, private or public health laboratories, and Pillar 2 for c...

ObjectiveNucleos/tide analogue (NA) drugs are used for the long-term treatment of chronic hepatitis B virus (HBV) infection. In a landscape of changing clinical recommendations, we set out to quantify the prescription of NA drugs to date, and to determine the impact of relaxing treatment eligibility criteria in a unique large real-world dataset. DesignWe assimilated longitudinal data from adults with chronic HBV infection from six centres in England through the UK National Institute for Health ...

FluSurvey is a participatory surveillance system used to monitor trends in influenza and other respiratory viruses through weekly symptom surveys among the UK population. We aimed to characterise the wider impact of "influenza-like illnesses" (ILI) among FluSurvey participants and assess correlations of ILI with other established influenza surveillance systems. We included data reported by FluSurvey participants over the 2023-24 and 2024-25 winter seasons. Using weekly symptoms surveys, we deri...

This study investigates the contribution of population age structure to mortality from Covid-19 in the UK by geographical units. We project death rates at various spatial scales by applying data on age-specific fatality rates to the areas population by age and sex. Our analysis shows a significant variation in the projected death rates between the constituent countries of the UK, between its regions and within regions. First, Scotland and Wales have higher projected fatality levels from Covid-19...

BackgroundThe progression and severity of the COVID 19 pandemic have been measured based on the daily and total numbers of cases, hospitalisations and deaths. We focused on the nature of hospitalisations from 2020 to 2022. MethodsWe analysed the role played by SARS-CoV-2 in the pandemic in the UK; we lodged FOI requests to Public Health Wales (PHW), Scotland (PHS), and Northern Ireland (PHA NI), the UK Health Security Agency (UKHSA) and NHS England. We asked for all-cause hospital admission mon...

IntroductionBetter understanding of hepatitis B virus (HBV) biomarkers is needed. We evaluated Hepatitis B core related antigen (HBcrAg), in the United Kingdom (UK) and South Africa (SA). MethodsWe undertook a cross-sectional retrospective observational study of adults with chronic HBV infection from the UK (n=142) and SA (n=211). We recorded clinical and laboratory parameters and quantified HBcrAg. We report HBcrAg distribution, relationship with other biomarkers, and performance in risk strat...

BackgroundUnderstanding of the true asymptomatic rate of infection of SARS-CoV-2 is currently limited, as is understanding of the population-based seroprevalence after the first wave of COVID-19 within the UK. The majority of data thus far come from hospitalised patients, with little focus on general population cases, or their symptoms. MethodsWe undertook enzyme linked immunosorbent assay characterisation of IgM and IgG responses against SARS-CoV-2 spike glycoprotein and nucleocapsid protein o...

BackgroundThe progression and geographical distribution of SARS coronavirus 2 (SARS-CoV-2) infection in the UK and elsewhere is unknown because typically only symptomatic individuals are diagnosed. We performed a serological study of blood donors in Scotland between the 17th of March and the 18th of May to detect neutralising antibodies to SARS-CoV-2 as a marker of past infection and epidemic progression. AimTo determine if sera from blood bank donors can be used to track the emergence and prog...

Human metapneumovirus is a common upper respiratory tract infection, routinely monitored as part of laboratory respiratory virus surveillance in England. Given the recent international interest in trends of hMPV, we describe the current and historical trends of hMPV in England overall and by age group using activity threshold methods.

IntroductionSeveral viral respiratory infections - notably influenza - are associated with secondary bacterial infection and additional pathology. The extent to which this applies for COVID-19 is unknown. Accordingly, we aimed to define the bacteria causing secondary pneumonias in COVID-19 ICU patients using the FilmArray Pneumonia Panel, and to determine this tests potential in COVID-19 management. MethodsCOVID-19 ICU patients with clinically-suspected secondary infection at 5 UK hospitals wer...

RationaleManagement of the COVID-19 pandemic is hampered by long delays associated with centralised laboratory PCR testing. In hospitals this leads to poor patient flow and nosocomial transmission and rapid, accurate diagnostic tests are urgently required. The FebriDx is a point-of-care test that detects an antiviral host response protein in finger prick blood within 10 minutes, but its accuracy for the detection of COVID-19 is unknown. ObjectivesTo evaluate the diagnostic accuracy of FebriDx i...