Publications
385 results found
Whitaker M, Davies B, Atchison C, et al., 2023, SARS-CoV-2 rapid antibody test results and subsequent risk of hospitalisation and death in 361,801 people, Nature Communications, Vol: 14, ISSN: 2041-1723
The value of SARS-CoV-2 lateral flow immunoassay (LFIA) tests for estimating individual disease risk is unclear. The REACT-2 study in England, UK, obtained self-administered SARS-CoV-2 LFIA test results from 361,801 adults in January-May 2021. Here, we link to routine data on subsequent hospitalisation (to September 2021), and death (to December 2021). Among those who had received one or more vaccines, a negative LFIA is associated with increased risk of hospitalisation with COVID-19 (HR: 2.73 [95% confidence interval: 1.15,6.48]), death (all-cause) (HR: 1.59, 95% CI:1.07, 2.37), and death with COVID-19 as underlying cause (20.6 [1.83,232]). For people designated at high risk from COVID-19, who had received one or more vaccines, there is an additional risk of all-cause mortality of 1.9 per 1000 for those testing antibody negative compared to positive. However, the LFIA does not provide substantial predictive information over and above that which is available from detailed sociodemographic and health-related variables. Nonetheless, this simple test provides a marker which could be a valuable addition to understanding population and individual-level risk.
Teodorowski P, Gleason K, Gregory J, et al., 2023, Participatory evaluation of the process of co-producing resources for the public on data science and artificial intelligence, Research Involvement and Engagement, Vol: 9, Pages: 1-12, ISSN: 2056-7529
Background: The growth of data science and artificial intelligence offers novel healthcareapplications and research possibilities. Patients should be able to make informed choicesabout using healthcare. Therefore, they must be provided with lay information about newtechnology. A team consisting of academic researchers, health professionals, and publiccontributors collaboratively co-designed and co-developed the new resource offering thatinformation. In this paper, we evaluate this novel approach to co-production.Methods: We used participatory evaluation to understand the co-production process. Thisconsisted of creative approaches and reflexivity over three stages. Firstly, everyone had anopportunity to participate in three online training sessions. The first one focused on the aimsof evaluation, the second on photovoice (that included practical training on using photos asmetaphors), and the third on being reflective (recognising one’s biases and perspectivesduring analysis). During the second stage, using photovoice, everyone took photos thatsymbolised their experiences of being involved in the project. This included a session with aprofessional photographer. At the last stage, we met in person and, using data collected fromphotovoice, built the mandala as a representation of a joint experience of the project. Thisstage was supported by professional artists who summarised the mandala in the illustration.Results: The mandala is the artistic presentation of the findings from the evaluation. It is ashared journey between everyone involved. We divided it into six related layers. Starting frominside layers present the following experiences 1) public contributors had space to buildconfidence in a new topic, 2) relationships between individuals and within the project, 3)working remotely during the COVID-19 pandemic, 4) motivation that influenced people tobecome involved in this particular piece of work, 5) requirements that co-production needs tobe inclusive and acce
Pearce FA, Lim SH, Bythell M, et al., 2023, Antibody prevalence after three or more COVID-19 vaccine doses in individuals who are immunosuppressed in the UK: a cross-sectional study from MELODY, The Lancet Rheumatology, Vol: 5, Pages: e461-e473, ISSN: 2665-9913
BackgroundIn the UK, additional COVID-19 vaccine booster doses and treatments are offered to people who are immunosuppressed to protect against severe COVID-19, but how best to choose the individuals that receive these vaccine booster doses and treatments is unclear. We investigated the association between seropositivity to SARS-CoV-2 spike protein with demographic, disease, and treatment-related characteristics after at least three COVID-19 vaccines in three cohorts of people who are immunosuppressed.MethodsIn a cross-sectional study using UK national disease registries, we identified, contacted, and recruited recipients of solid organ transplants, participants with rare autoimmune rheumatic diseases, and participants with lymphoid malignancies who were 18 years or older, resident in the UK, and who had received at least three doses of a COVID-19 vaccine. The study was open to recruitment from Dec 7, 2021, to June 26, 2022. Participants received a lateral flow immunoassay test for SARS-CoV-2 spike antibodies to complete at home, and an online questionnaire. Multivariable logistic regression was used to estimate the mutually adjusted odds of seropositivity against each characteristic.FindingsBetween Feb 14 and June 26, 2022, we screened 101 972 people (98 725 invited, 3247 self-enrolled) and recruited 28 411 (27·9%) to the study. 23 036 (81·1%) recruited individuals provided serological data. Of these, 9927 (43·1%) were recipients of solid organ transplants, 6516 (28·3%) had rare autoimmune rheumatic diseases, and 6593 (28·6%) had lymphoid malignancies. 10 485 (45·5%) participants were men and 12 535 (54·4%) were women (gender was not reported for 16 [<0·1%] participants), and 21661 (94·0%) participants were of White ethnicity. The median age of participants with solid organ transplants was 60 years (SD 50–67), with rare autoimmune rheumatic diseases was
Coukan F, Murray K-K, Papageorgiou V, et al., 2023, Barriers and facilitators to HIV Pre-Exposure Prophylaxis (PrEP) in Specialist Sexual Health Services in the United Kingdom: A systematic review using the PrEP Care Continuum., HIV Med, Vol: 24, Pages: 893-913
OBJECTIVES: HIV pre-exposure prophylaxis (PrEP) delivery in the UK is inequitable; over 95% of PrEP users were men who have sex with men (MSM) despite making up less than 50% of new HIV diagnoses. We conducted a systematic review to identify modifiable barriers and facilitators to PrEP delivery in the UK among underserved populations. METHODS: We searched bibliographic/conference databases using the terms HIV, PrEP, barriers, facilitators, underserved populations, and UK. Modifiable factors were mapped along the PrEP Care Continuum (PCC) to identify targets for interventions. RESULTS: In total, 44 studies were eligible: 29 quantitative, 12 qualitative and three mixed-methods studies. Over half (n = 24 [54.5%]) exclusively recruited MSM, whereas 11 were in mixed populations (all included MSM as a sub-population) and the other nine were in other underserved populations (gender and ethnicity minorities, women, and people who inject drugs). Of the 15 modifiable factors identified, two-thirds were at the PrEP contemplation and PrEParation steps of the PCC. The most reported barriers were lack of PrEP awareness (n = 16), knowledge (n = 19), willingness (n = 16), and access to a PrEP provider (n = 16), whereas the more reported facilitators were prior HIV testing (n = 8), agency and self-care (n = 8). All but three identified factors were at the patient rather than provider or structural level. CONCLUSIONS: This review highlights that the bulk of the scientific literature focuses on MSM and on patient-level factors. Future research needs to ensure underserved populations are included and prioritized (e.g. ethnicity and gender minorities, people who inject drugs) and provider and structural factors are investigated.
Eales O, de Oliveira Martins L, Page A, et al., 2023, Dynamics and scale of the SARS-CoV-2 variant Omicron epidemic in England, Nature Communications, Vol: 13, ISSN: 2041-1723
The SARS-CoV-2 pandemic has been characterised by the regular emergence of genomic variants. With natural and vaccine-induced population immunity at high levels, evolutionary pressure favours variants better able to evade SARS-CoV-2 neutralising antibodies. The Omicron variant (first detected in November 2021) exhibited a high degree of immune evasion, leading to increased infection rates worldwide. However, estimates of the magnitude of this Omicron wave have often relied on routine testing data, which are prone to several biases. Using data from the REal-time Assessment of Community Transmission-1 (REACT-1) study, a series of cross-sectional surveys assessing prevalence of SARS-CoV-2 infection in England, we estimated the dynamics of England’s Omicron wave (from 9 September 2021 to 1 March 2022). We estimate an initial peak in national Omicron prevalence of 6.89% (5.34%, 10.61%) during January 2022, followed by a resurgence in SARS-CoV-2 infections as the more transmissible Omicron sub-lineage, BA.2 replaced BA.1 and BA.1.1. Assuming the emergence of further distinct variants, intermittent epidemics of similar magnitudes may become the ‘new normal’.
Atchison C, Whitaker M, Donnelly C, et al., 2023, Characteristics and predictors of persistent symptoms post COVID-19 in children and young people: a large community cross-sectional study in England, Archives of Disease in Childhood, Vol: 108, ISSN: 0003-9888
Objective: To estimate the prevalence of, and associated risk factors for, persistent symptoms post-COVID-19 among children aged 5–17 years in England.Design: Serial cross-sectional study.Setting: Rounds 10–19 (March 2021 to March 2022) of the REal-time Assessment of Community Transmission-1 study (monthly cross-sectional surveys of random samples of the population in England).Study population: Children aged 5–17 years in the community.Predictors: Age, sex, ethnicity, presence of a pre-existing health condition, index of multiple deprivation, COVID-19 vaccination status and dominant UK circulating SARS-CoV-2 variant at time of symptom onset.Main outcome measures: Prevalence of persistent symptoms, reported as those lasting ≥3 months post-COVID-19.Results: Overall, 4.4% (95% CI 3.7 to 5.1) of 3173 5–11 year-olds and 13.3% (95% CI 12.5 to 14.1) of 6886 12–17 year-olds with prior symptomatic infection reported at least one symptom lasting ≥3 months post-COVID-19, of whom 13.5% (95% CI 8.4 to 20.9) and 10.9% (95% CI 9.0 to 13.2), respectively, reported their ability to carry out day-to-day activities was reduced ‘a lot’ due to their symptoms. The most common symptoms among participants with persistent symptoms were persistent coughing (27.4%) and headaches (25.4%) in children aged 5–11 years and loss or change of sense of smell (52.2%) and taste (40.7%) in participants aged 12–17 years. Higher age and having a pre-existing health condition were associated with higher odds of reporting persistent symptoms.Conclusions: One in 23 5–11 year-olds and one in eight 12–17 year-olds post-COVID-19 report persistent symptoms lasting ≥3 months, of which one in nine report a large impact on performing day-to-day activities.
Eales O, Haw D, Wang H, et al., 2023, Dynamics of SARS-CoV-2 infection hospitalisation and infection fatality ratios over 23 months in England, PLoS Biology, Vol: 21, Pages: 1-21, ISSN: 1544-9173
The relationship between prevalence of infection and severe outcomes such as hospitalisation and death changed over the course of the COVID-19 pandemic. Reliable estimates of the infection fatality ratio (IFR) and infection hospitalisation ratio (IHR) along with the time-delay between infection and hospitalisation/death can inform forecasts of the numbers/timing of severe outcomes and allow healthcare services to better prepare for periods of increased demand. The REal-time Assessment of Community Transmission-1 (REACT-1) study estimated swab positivity for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection in England approximately monthly from May 2020 to March 2022. Here, we analyse the changing relationship between prevalence of swab positivity and the IFR and IHR over this period in England, using publicly available data for the daily number of deaths and hospitalisations, REACT-1 swab positivity data, time-delay models, and Bayesian P-spline models. We analyse data for all age groups together, as well as in 2 subgroups: those aged 65 and over and those aged 64 and under. Additionally, we analysed the relationship between swab positivity and daily case numbers to estimate the case ascertainment rate of England's mass testing programme. During 2020, we estimated the IFR to be 0.67% and the IHR to be 2.6%. By late 2021/early 2022, the IFR and IHR had both decreased to 0.097% and 0.76%, respectively. The average case ascertainment rate over the entire duration of the study was estimated to be 36.1%, but there was some significant variation in continuous estimates of the case ascertainment rate. Continuous estimates of the IFR and IHR of the virus were observed to increase during the periods of Alpha and Delta's emergence. During periods of vaccination rollout, and the emergence of the Omicron variant, the IFR and IHR decreased. During 2020, we estimated a time-lag of 19 days between hospitalisation and swab positivity, and 26 days between deaths
Routen A, O'Mahoney L, Aiyegbusi OL, et al., 2023, Patient and public involvement within epidemiological studies of long COVID in the UK., Nat Med, Vol: 29, Pages: 771-773
Papageorgiou V, Hamza H, Anderson J, et al., 2023, Co-production in HIV research: reflections from a study on building relationships, conducting qualitative research and developing skills remotely, AIDS Impact
Elliott P, Ward H, Riley S, 2023, Population monitoring of SARS-CoV-2 infections via random sampling during the COVID-19 pandemic., American Journal of Public Health, Pages: e1-e3, ISSN: 0090-0036
Elliott P, Whitaker M, Tang D, et al., 2023, Design and implementation of a national SARS-CoV-2 monitoring programme in England: REACT-1 Study, American Journal of Public Health, ISSN: 0090-0036
Data System. The REal-time Assessment of Community Transmission-1 (REACT-1) Study was funded by the Department of Health and Social Care in England to provide reliable and timely estimates of prevalence of SARS-CoV-2 infection by time, person and place.Data Collection/Processing. The data were obtained by writing to named individuals aged 5 years and above in random cross-sections of the population of England, using the National Health Service (NHS) list of patients registered with a general practitioner (>99% coverage) as sampling frame. Data were collected 2-3 weekly approximately every month across 19distinct rounds of data collection from May 1, 2020 to March 31, 2022.Data Analysis/Dissemination. The data and study materials are widely disseminated via the study website, preprints, publications in peer-reviewed journals and the media. Data tabulations suitably anonymised to protect participant confidentiality are available on request to the study’s Data Access Committee.Implications. The study provided inter alia real-time data on SARS-CoV-2 prevalence over time, by area, and by socio-demographic variables; estimates of vaccine effectiveness; symptom profiles and detected emergence of new variants based on viral genome sequencing.
Day S, Gleason K, Lury C, et al., 2023, 'In the picture': perspectives on living and working with cancer, Medical Humanities, Vol: 49, Pages: 83-92, ISSN: 1468-215X
We explored working and living with cancer at a large research-intensive National Health Service hospital breast cancer service and adjoining non-governmental organisation (NGO). The project had three elements that were largely autonomous in practice but conceptually integrated through a focus on personalised cancer medicine. Di Sherlock held conversations with staff and patients from which she produced a collection of poems, Written Portraits. At the same time, we conducted interviews and observation in the hospital, and hosted a public series of science cafés in the NGO. The trajectory of this project was not predetermined, but we found that the poetry residency provided a context for viewing participation in experimental cancer care and vice versa. Taking themes from the poetry practice, we show how they revealed categories of relevance to participants and illuminated others that circulated in the hospital and NGO. Reciprocally, turning to findings from long-term ethnographic research with patients, we show that their observations were not only representations but also tools for navigating life in waiting with cancer. The categories that we discovered and assembled about living and working with cancer do not readily combine into an encompassing picture, we argue, but instead provide alternating perspectives. Through analysis of different forms of research participation, we hope to contribute to an understanding of how categories are made, recognised and inhabited through situated comparisons. In personalised medicine, category-making is enabled if not dependent on increasingly intensive computation and so the practices seem far removed from mundane processes of interaction. Yet, we emphasise connections with everyday practices, in which people categorise themselves and others routinely according to what they like and resemble.
Atchison C, Moshe M, Brown J, et al., 2023, Validity of self-testing at home with rapid SARS-CoV-2 antibody detection by lateral flow immunoassay, Clinical Infectious Diseases, Vol: 76, Pages: 658-666, ISSN: 1058-4838
Background: We explore severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody lateral flow immunoassay (LFIA) performance under field conditions compared to laboratory-based ELISA and live virus neutralisation. Methods: In July 2021, 3758 participants performed, at home, a self-administered LFIA on finger-prick blood, reported and submitted a photograph of the result, and provided a self-collected capillary blood sample for assessment of IgG antibodies using the Roche Elecsys® Anti-SARS-CoV-2 assay. We compared the self-reported LFIA result to the quantitative Roche assay and checked the reading of the LFIA result with an automated image analysis (ALFA). In a subsample of 250 participants, we compared the results to live virus neutralisation. Results: Almost all participants (3593/3758, 95.6%) had been vaccinated or reported prior infection. Overall, 2777/3758 (73.9%) were positive on self-reported LFIA, 2811/3457 (81.3%) positive by LFIA when ALFA-reported, and 3622/3758 (96.4%) positive on Roche (using the manufacturer reference standard threshold for positivity of 0.8 U ml−1). Live virus neutralisation was detected in 169 of 250 randomly selected samples (67.6%); 133/169 were positive with self-reported LFIA (sensitivity 78.7%; 95% CI 71.8, 84.6), 142/155 (91.6%; 86.1, 95.5) with ALFA, and 169 (100%; 97.8, 100.0) with Roche. There were 81 samples with no detectable virus neutralisation; 47/81 were negative with self-reported LFIA (specificity 58.0%; 95% CI 46.5, 68.9), 34/75 (45.3%; 33.8, 57.3) with ALFA, and 0/81 (0%; 0.0, 4.5) with Roche. Conclusions: Self-administered LFIA is less sensitive than a quantitative antibody test, but the positivity in LFIA correlates better than the quantitative ELISA with virus neutralisation.
Eales O, Page AJ, Tang SN, et al., 2023, The use of representative community samples to assess SARS-CoV-2 lineage competition: Alpha outcompetes Beta and wild-type in England from January to March 2021., Microbial Genomics, Vol: 9, Pages: 1-14, ISSN: 2057-5858
Genomic surveillance for SARS-CoV-2 lineages informs our understanding of possible future changes in transmissibility and vaccine efficacy and will be a high priority for public health for the foreseeable future. However, small changes in the frequency of one lineage over another are often difficult to interpret because surveillance samples are obtained using a variety of methods all of which are known to contain biases. As a case study, using an approach which is largely free of biases, we here describe lineage dynamics and phylogenetic relationships of the Alpha and Beta variant in England during the first 3 months of 2021 using sequences obtained from a random community sample who provided a throat and nose swab for rt-PCR as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. Overall, diversity decreased during the first quarter of 2021, with the Alpha variant (first identified in Kent) becoming predominant, driven by a reproduction number 0.3 higher than for the prior wild-type. During January, positive samples were more likely to be Alpha in those aged 18 to 54 years old. Although individuals infected with the Alpha variant were no more likely to report one or more classic COVID-19 symptoms compared to those infected with wild-type, they were more likely to be antibody-positive 6 weeks after infection. Further, viral load was higher in those infected with the Alpha variant as measured by cycle threshold (Ct) values. The presence of infections with non-imported Beta variant (first identified in South Africa) during January, but not during February or March, suggests initial establishment in the community followed by fade-out. However, this occurred during a period of stringent social distancing. These results highlight how sequence data from representative community surveys such as REACT-1 can augment routine genomic surveillance during periods of lineage diversity.
Cooper E, Lound A, Atchison CJ, et al., 2023, Awareness and perceptions of Long COVID among people in the REACT programme: early insights from a pilot interview study, PLoS One, Vol: 18, ISSN: 1932-6203
BACKGROUND: Long COVID is a patient-made term describing new or persistent symptoms experienced following SARS-CoV-2 infection. The Real-time Assessment of Community Transmission-Long COVID (REACT-LC) study aims to understand variation in experiences following infection, and to identify biological, social, and environmental factors associated with Long COVID. We undertook a pilot interview study to inform the design, recruitment approach, and topic guide for the REACT-LC qualitative study. We sought to gain initial insights into the experience and attribution of new or persistent symptoms and the awareness or perceived applicability of the term Long COVID. METHODS: People were invited to REACT-LC assessment centres if they had taken part in REACT, a random community-based prevalence study, and had a documented history of SARS-CoV-2 infection. We invited people from REACT-LC assessment centres who had reported experiencing persistent symptoms for more than 12 weeks to take part in an interview. We conducted face to face and online semi-structured interviews which were transcribed and analysed using Thematic Analysis. RESULTS: We interviewed 13 participants (6 female, 7 male, median age 31). Participants reported a wide variation in both new and persistent symptoms which were often fluctuating or unpredictable in nature. Some participants were confident about the link between their persistent symptoms and COVID-19; however, others were unclear about the underlying cause of symptoms or felt that the impact of public health measures (such as lockdowns) played a role. We found differences in awareness and perceived applicability of the term Long COVID. CONCLUSION: This pilot has informed the design, recruitment approach and topic guide for our qualitative study. It offers preliminary insights into the varied experiences of people living with persistent symptoms including differences in symptom attribution and perceived applicability of the term Long COVID. This variation
Day S, Lury C, Ward H, 2023, Personalization: a new political arithmetic?, DISTINKTION-JOURNAL OF SOCIAL THEORY, ISSN: 1600-910X
O'Mahoney LL, Routen A, Gillies C, et al., 2023, The prevalence and long-term health effects of Long Covid among hospitalised and non-hospitalised populations: A systematic review and meta-analysis, EClinicalMedicine, Vol: 55, ISSN: 2589-5370
BACKGROUND: The aim of this study was to systematically synthesise the global evidence on the prevalence of persistent symptoms in a general post COVID-19 population. METHODS: A systematic literature search was conducted using multiple electronic databases (MEDLINE and The Cochrane Library, Scopus, CINAHL, and medRxiv) until January 2022. Studies with at least 100 people with confirmed or self-reported COVID-19 symptoms at ≥28 days following infection onset were included. Patient-reported outcome measures and clinical investigations were both assessed. Results were analysed descriptively, and meta-analyses were conducted to derive prevalence estimates. This study was pre-registered (PROSPERO-ID: CRD42021238247). FINDINGS: 194 studies totalling 735,006 participants were included, with five studies conducted in those <18 years of age. Most studies were conducted in Europe (n = 106) or Asia (n = 49), and the time to follow-up ranged from ≥28 days to 387 days. 122 studies reported data on hospitalised patients, 18 on non-hospitalised, and 54 on hospitalised and non-hospitalised combined (mixed). On average, at least 45% of COVID-19 survivors, regardless of hospitalisation status, went on to experience at least one unresolved symptom (mean follow-up 126 days). Fatigue was frequently reported across hospitalised (28.4%; 95% CI 24.7%-32.5%), non-hospitalised (34.8%; 95% CI 17.6%-57.2%), and mixed (25.2%; 95% CI 17.7%-34.6%) cohorts. Amongst the hospitalised cohort, abnormal CT patterns/x-rays were frequently reported (45.3%; 95% CI 35.3%-55.7%), alongside ground glass opacification (41.1%; 95% CI 25.7%-58.5%), and impaired diffusion capacity for carbon monoxide (31.7%; 95% CI 25.8%-3.2%). INTERPRETATION: Our work shows that 45% of COVID-19 survivors, regardless of hospitalisation status, were experiencing a range of unresolved symptoms at ∼ 4 months. Current understanding is limited by heterogeneous study design, follow-up durations, and me
Day S, Lury C, Ward H, 2023, Introduction. Political arithmetic: old and new, Distinktion, Vol: 24, Pages: 157-166, ISSN: 1600-910X
The articles in this Special Issue arose from a workshop in June 2021 (https://peoplelikeyou.ac.uk/activities/people-like-you-a-new-political-arithmetic/) which considered whether we might understand the enormous variety of calculations we encounter today as a political arithmetic. Our proposal was that the term provides a powerful way to understand the political nature of calculations of economic and social value. In this introduction we showcase how contributors address the proposal in studies of personalisation, competitive test formats, algorithmic profiling, YouTube personalities and the significance of information as an increasingly important medium of ‘the social. We suggest that, together, these developments are transforming relations between the individual and society today in ways that both intensify inequalities and provide the basis for new forms of individual and collective identity.
Jefferson E, Cole C, Mumtaz S, et al., 2022, A Hybrid Architecture (CO-CONNECT) to Facilitate Rapid Discovery and Access to Data Across the United Kingdom in Response to the COVID-19 Pandemic: Development Study., J Med Internet Res, Vol: 24
BACKGROUND: COVID-19 data have been generated across the United Kingdom as a by-product of clinical care and public health provision, as well as numerous bespoke and repurposed research endeavors. Analysis of these data has underpinned the United Kingdom's response to the pandemic, and informed public health policies and clinical guidelines. However, these data are held by different organizations, and this fragmented landscape has presented challenges for public health agencies and researchers as they struggle to find relevant data to access and interrogate the data they need to inform the pandemic response at pace. OBJECTIVE: We aimed to transform UK COVID-19 diagnostic data sets to be findable, accessible, interoperable, and reusable (FAIR). METHODS: A federated infrastructure model (COVID - Curated and Open Analysis and Research Platform [CO-CONNECT]) was rapidly built to enable the automated and reproducible mapping of health data partners' pseudonymized data to the Observational Medical Outcomes Partnership Common Data Model without the need for any data to leave the data controllers' secure environments, and to support federated cohort discovery queries and meta-analysis. RESULTS: A total of 56 data sets from 19 organizations are being connected to the federated network. The data include research cohorts and COVID-19 data collected through routine health care provision linked to longitudinal health care records and demographics. The infrastructure is live, supporting aggregate-level querying of data across the United Kingdom. CONCLUSIONS: CO-CONNECT was developed by a multidisciplinary team. It enables rapid COVID-19 data discovery and instantaneous meta-analysis across data sources, and it is researching streamlined data extraction for use in a Trusted Research Environment for research and public health analysis. CO-CONNECT has the potential to make UK health data more interconnected and better able to answer national-level research questions while maintainin
Piggin M, Smith E, Mankone P, et al., 2022, The role of public involvement in the design of the first SARS-CoV-2 human challenge study during an evolving pandemic, Epidemics: the journal of infectious disease dynamics, Vol: 41, Pages: 1-6, ISSN: 1755-4365
High quality health care research must involve patients and the public. This ensures research is important, relevant and acceptable to those it is designed to benefit. The world’s first human challenge study with SARS-CoV-2 undertook detailed public involvement to inform study design despite the urgency to review and establish the study. The work was integral to the UK Research Ethics Committee review and approval of the study. Discussion with individuals from ethnic minorities within the UK population supported decision-making around the study exclusion criteria. Public review of study materials for consent processes led to the addition of new information, comparisons and visual aids to help volunteers consider the practicalities and risks involved in participating. A discussion exploring the acceptability of a human challenge study with SARS-CoV-2 taking place in the UK, given the current context of the pandemic, identified overall support for the study. Public concern for the wellbeing of trial participants, as a consequence of isolation, was identified. We outline our approach to public involvement and its impact on study design.
Eales O, Wang H, Haw D, et al., 2022, Trends in SARS-CoV-2 infection prevalence during England’s roadmap out of lockdown, January to July 2021, PLoS Computational Biology, Vol: 18, Pages: 1-16, ISSN: 1553-734X
Background:Following rapidly rising COVID-19 case numbers, England entered a national lockdown on 6 January 2021, with staged relaxations of restrictions from 8 March 2021 onwards.Aim:We characterise how the lockdown and subsequent easing of restrictions affected trends in SARS-CoV-2 infection prevalence.Methods:On average, risk of infection is proportional to infection prevalence. The REal-time Assessment of Community Transmission-1 (REACT-1) study is a repeat cross-sectional study of over 98,000 people every round (rounds approximately monthly) that estimates infection prevalence in England. We used Bayesian P-splines to estimate prevalence and the time-varying reproduction number (Rt) nationally, regionally and by age group from round 8 (beginning 6 January 2021) to round 13 (ending 12 July 2021) of REACT-1. As a comparator, a separate segmented-exponential model was used to quantify the impact on Rt of each relaxation of restrictions.Results:Following an initial plateau of 1.54% until mid-January, infection prevalence decreased until 13 May when it reached a minimum of 0.09%, before increasing until the end of the study to 0.76%. Following the first easing of restrictions, which included schools reopening, the reproduction number Rt increased by 82% (55%, 108%), but then decreased by 61% (82%, 53%) at the second easing of restrictions, which was timed to match the Easter school holidays. Following further relaxations of restrictions, the observed Rt increased steadily, though the increase due to these restrictions being relaxed was offset by the effects of vaccination and also affected by the rapid rise of Delta. There was a high degree of synchrony in the temporal patterns of prevalence between regions and age groups.Conclusion:High-resolution prevalence data fitted to P-splines allowed us to show that the lockdown was effective at reducing risk of infection with school holidays/closures playing a significant part.
Papageorgiou V, Bruton P, Johnson H, et al., 2022, Supporting material for co-researchers
This pack has been designed to be used alongside the Peer Research Training Resource (https://doi.org/10.25561/94819) and includes:• Skills, experience, and training reviews for Advisory Group Members and Peer Researchers• Zoom Interviews: Guide for Peer Researchers• Useful COVID-19 resources for people living with HIVThe pack is suitable for academics and public involvement practitioners who are involving people with lived experience as co-researchers in research. The material presented here was developed for a participatory research study on COVID-19 experiences among people living with HIV where interviews were conducted online.
Whitaker M, Elliott J, Bodinier B, et al., 2022, Variant-specific symptoms of COVID-19 in a study of 1,542,510 adults in England, Nature Communications, Vol: 13, Pages: 1-10, ISSN: 2041-1723
Infection with SARS-CoV-2 virus is associated with a wide range of symptoms. The REal-time Assessment of Community Transmission -1 (REACT-1) study monitored the spread and clinical manifestation of SARS-CoV-2 among random samples of the population in England from 1 May 2020 to 31 March 2022. We show changing symptom profiles associated with the different variants over that period, with lower reporting of loss of sense of smell or taste for Omicron compared to previous variants, and higher reporting of cold-like and influenza-like symptoms, controlling for vaccination status. Contrary to the perception that recent variants have become successively milder, Omicron BA.2 was associated with reporting more symptoms, with greater disruption to daily activities, than BA.1. With restrictions lifted and routine testing limited in many countries, monitoring the changing symptom profiles associated with SARS-CoV-2 infection and effects on daily activities will become increasingly important.
Eales O, Haw D, Wang H, et al., 2022, Quantifying changes in the IFR and IHR over 23 months of the SARS-CoV-2 pandemic in England
<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>The relationship between prevalence of infection and severe outcomes such as hospitalisation and death changed over the course of the COVID-19 pandemic. The REal-time Assessment of Community Transmission-1 (REACT-1) study estimated swab positivity in England approximately monthly from May 2020 to 31 March 2022. This period covers widespread circulation of the original strain, the emergence of the Alpha, Delta and Omicron variants and the rollout of England’s mass vaccination campaign.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>Here, we explore this changing relationship between prevalence of swab positivity and the infection fatality rate (IFR) and infection hospitalisation rate (IHR) over 23 months of the pandemic in England, using publicly available data for the daily number of deaths and hospitalisations, REACT-1 swab positivity data, time-delay models and Bayesian P-spline models. We analyse data for all age groups together, as well as in two sub-groups: those aged 65 and over and those aged 64 and under.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>During 2020, we estimated the IFR to be 0.67% and the IHR to be 2.6%. By late-2021/early-2022 the IFR and IHR had both decreased to 0.097% and 0.76% respectively. Continuous estimates of the IFR and IHR of the virus were observed to increase during the periods of Alpha and Delta’s emergence. During periods of vaccination rollout, and the emergence of the Omicron variant, the IFR and IHR of the virus decreased. During 2020, we estimated a time-lag of 19 days between hospitalisation and swab positivity, and 26 days between deaths and swab positivity. By late-2021/early-2022 these time-lags had decreased to 7 days for hospitalisations, and 18 days for deaths.</jats:
Chadeau-Hyam M, Tang D, Eales O, et al., 2022, Omicron SARS-CoV-2 epidemic in England during February 2022: A series of cross-sectional community surveys, The Lancet Regional Health Europe, Vol: 21, Pages: 1-11, ISSN: 2666-7762
BackgroundThe Omicron wave of COVID-19 in England peaked in January 2022 resulting from the rapid transmission of the Omicron BA.1 variant. We investigate the spread and dynamics of the SARS-CoV-2 epidemic in the population of England during February 2022, by region, age and main SARS-CoV-2 sub-lineage.MethodsIn the REal-time Assessment of Community Transmission-1 (REACT-1) study we obtained data from a random sample of 94,950 participants with valid throat and nose swab results by RT-PCR during round 18 (8 February to 1 March 2022).FindingsWe estimated a weighted mean SARS-CoV-2 prevalence of 2.88% (95% credible interval [CrI] 2.76–3.00), with a within-round effective reproduction number (R) overall of 0.94 (0·91–0.96). While within-round weighted prevalence fell among children (aged 5 to 17 years) and adults aged 18 to 54 years, we observed a level or increasing weighted prevalence among those aged 55 years and older with an R of 1.04 (1.00–1.09). Among 1,616 positive samples with sublineages determined, one (0.1% [0.0–0.3]) corresponded to XE BA.1/BA.2 recombinant and the remainder were Omicron: N=1047, 64.8% (62.4–67.2) were BA.1; N=568, 35.2% (32.8–37.6) were BA.2. We estimated an R additive advantage for BA.2 (vs BA.1) of 0.38 (0.34–0.41). The highest proportion of BA.2 among positives was found in London.InterpretationIn February 2022, infection prevalence in England remained high with level or increasing rates of infection in older people and an uptick in hospitalisations. Ongoing surveillance of both survey and hospitalisations data is required.FundingDepartment of Health and Social Care, England.
Eales O, Ainslie KEC, Walters CE, et al., 2022, Appropriately smoothing prevalence data to inform estimates of growth rate and reproduction number, Epidemics: the journal of infectious disease dynamics, Vol: 40, ISSN: 1755-4365
The time-varying reproduction number () can change rapidly over the course of a pandemic due to changing restrictions, behaviours, and levels of population immunity. Many methods exist that allow the estimation of from case data. However, these are not easily adapted to point prevalence data nor can they infer across periods of missing data. We developed a Bayesian P-spline model suitable for fitting to a wide range of epidemic time-series, including point-prevalence data. We demonstrate the utility of the model by fitting to periodic daily SARS-CoV-2 swab-positivity data in England from the first 7 rounds (May 2020–December 2020) of the REal-time Assessment of Community Transmission-1 (REACT-1) study. Estimates of over the period of two subsequent rounds (6–8 weeks) and single rounds (2–3 weeks) inferred using the Bayesian P-spline model were broadly consistent with estimates from a simple exponential model, with overlapping credible intervals. However, there were sometimes substantial differences in point estimates. The Bayesian P-spline model was further able to infer changes in over shorter periods tracking a temporary increase above one during late-May 2020, a gradual increase in over the summer of 2020 as restrictions were eased, and a reduction in during England’s second national lockdown followed by an increase as the Alpha variant surged. The model is robust against both under-fitting and over-fitting and is able to interpolate between periods of available data; it is a particularly versatile model when growth rate can change over small timescales, as in the current SARS-CoV-2 pandemic. This work highlights the importance of pairing robust methods with representative samples to track pandemics.
Delisle TG, D'Souza N, Tan J, et al., 2022, Introduction of an integrated primary care faecal immunochemical test referral pathway for patients with suspected colorectal cancer symptoms, COLORECTAL DISEASE, Vol: 24, Pages: 1526-1534, ISSN: 1462-8910
Papageorgiou V, Crittendon E, Coukan F, et al., 2022, Impact of daily, oral pre-exposure prophylaxis on the risk of bacterial sexually transmitted infections among cisgender women: a systematic review and narrative synthesis [version 2; peer review: 2 approved], Wellcome Open Research, Vol: 7, Pages: 1-21, ISSN: 2398-502X
Background: There are concerns that the use of pre-exposure prophylaxis (PrEP) may result in an increased incidence of sexually transmitted infections (STIs). Evidence for this is mixed and has mostly been based on reviews focussed on gay and bisexual men and transgender women, while none have summarised evidence in cisgender women.Methods: We conducted a systematic review to explore whether daily, oral PrEP use is associated with changes in bacterial STI occurrence (diagnoses or self-reported) and/or risk among HIV seronegative cisgender women (ciswomen). The quality of evidence was assessed using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) tool.Results: We included 11 full text articles in a narrative synthesis, with the studies published between 2012 and 2021. The studies were mostly based in Africa (n=7, 63.6%) and reported on 3168 ciswomen using PrEP aged 16–56 years. Studies had marked differences in variables, including measurements and definitions (e.g., STI type) and limited data available looking specifically at ciswomen, principally in studies with both male and female participants. The limited evidence suggests that PrEP use is not associated with increased STI rates in ciswomen generally; however, adolescent girls and young women in Sub Saharan Africa have a higher prevalence of bacterial STIs prior to PrEP initiation, compared to adult ciswomen and female sex workers.Conclusions: We suggest future PrEP research make efforts to include ciswomen as study participants and report stratified results by gender identity to provide adequate data to inform guidelines for PrEP implementation.PROSPERO registration: CRD42019130438
Elliott P, Eales O, Bodinier B, et al., 2022, Dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022 in England, Nature Communications, Vol: 13, ISSN: 2041-1723
Rapid transmission of the SARS-CoV-2 Omicron variant has led to record-breaking case incidence rates around the world. Since May 2020, the REal-time Assessment of Community Transmission-1 (REACT-1) study tracked the spread of SARS-CoV-2 infection in England through RT-PCR of self-administered throat and nose swabs from randomly-selected participants aged 5 years and over. In January 2022, we found an overall weighted prevalence of 4.41% (n=102,174), three-fold higher than in November to December 2021; we sequenced 2,374 (99.2%) Omicron infections (19 BA.2), and only 19 (0.79%) Delta, with a growth rate advantage for BA.2 compared to BA.1 or BA.1.1. Prevalence was decreasing overall (reproduction number R=0.95, 95% credible interval [CrI], 0.93, 0.97), but increasing in children aged 5 to 17 years (R=1.13, 95% CrI, 1.09, 1.18). In England during January 2022, we observed unprecedented levels of SARS-CoV-2 infection, especially among children, driven by almost complete replacement of Delta by Omicron.
Papageorgiou V, Bruton P, Dsouza K, et al., 2022, Experiences of the COVID-19 epidemic: a participatory qualitative study with people living and/or working with HIV in the UK, 24th International AIDS Conference
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