Oliver Stirrup

• PhD
• Research Associate at University College London

Background Long-term-care facilities (LTCFs) were heavily affected by COVID-19 early in the pandemic, but the impact of the virus has reduced over time with vaccination campaigns and build-up of immunity from prior infection. Objectives To evaluate the mortality and hospital admissions associated with SARS-CoV-2 in LTCFs in England over the course...

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused severe disease in unvaccinated long-term care facility (LTCF) residents. Initial booster vaccination following primary vaccination is known to provide strong short-term protection, but data are limited on duration of protection and the protective effect of further boos...

Active-control trials, where an experimental treatment is compared with an established treatment, are performed when the inclusion of a placebo control group is deemed to be unethical. For time-to-event outcomes, the primary estimand is usually the rate ratio, or the closely-related hazard ratio, comparing the experimental group with the control gr...

Objectives: The COG-UK hospital-onset COVID-19 infection (HOCI) trial evaluated the impact of SARS-CoV-2 whole genome sequencing (WGS) on acute infection, prevention, and control (IPC) investigation of nosocomial transmission within hospitals. We estimated the cost implications of using the information from the sequencing reporting tool (SRT), use...

Purpose: The aim of this study was to conduct a process evaluation of a whole-genome sequence report form (SRF) used to reduce nosocomial SARS-CoV-2 through changing infection prevention and control (IPC) behaviours within the COVID-19 pandemic. Methods: We used a three-staged design. Firstly, we described and theorized the purported content of...

Background Ulcerative colitis (UC) and Crohn’s disease (CD) can be associated with severe comorbidities, namely opportunistic infections and malignancies. We present the first systematic review and meta-analysis evaluating the burden of anal human papillomavirus disease in patients with UC and CD. Methods PubMed, Web of Science and Scopus were sea...

We evaluated the effectiveness of 1-3 booster vaccinations against SARS-CoV-2 related mortality among a cohort of 13407 older residents of long-term care facilities (LTCFs) participating in the VIVALDI study in England in 2022. Cox regression was used to estimate relative hazards of SARS-CoV-2 related death following booster vaccination relative to...

Third-dose coronavirus disease 2019 vaccines are being deployed widely but their efficacy has not been assessed adequately in vulnerable older people who exhibit suboptimal responses after primary vaccination series. This observational study, which was carried out by the VIVALDI study based in England, looked at spike-specific immune responses in 3...

Background Successive SARS-CoV-2 variants have caused severe disease in long-term care facility (LTCF) residents. Primary vaccination provides strong short-term protection, but data are limited on duration of protection following booster vaccines, particularly against the Omicron variant. We investigated effectiveness of booster vaccination against...

Background Post-acute COVID-19 sequelae refers to a variety of health complications involving different organ systems that have been described among individuals after acute phase of illness. Data from unselected population groups with long-time follow up is needed to comprehensively describe the full spectrum of post-acute COVID-19 complications....

Background: Barriers to rapid return of sequencing results can affect the utility of sequence data for infection prevention and control decisions. Aim: To undertake a mixed-methods analysis to identify challenges sites faced in achieving a rapid turnaround time (TAT) in the COG-UK Hospital-Onset COVID-19 Infection (COG-UK HOCI) study. Methods:...

Background Accelerated partner therapy has shown promise in improving contact tracing. We aimed to evaluate the effectiveness of accelerated partner therapy in addition to usual contact tracing compared with usual practice alone in heterosexual people with chlamydia, using a biological primary outcome measure. Methods We did a crossover cluster-ra...

Objectives We report the results of a mixed-methods process evaluation that aimed to provide insight on the Afya conditional cash transfer (CCT) intervention fidelity and acceptability. Intervention, setting and participants The Afya CCT intervention aimed to retain women in the continuum of maternal healthcare including antenatal care (ANC), deli...

Background: Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings. Methods: We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data-c...

Background: Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings. Methods: We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data co...

Purpose: To conduct a process evaluation of a whole genome sequence report form (SRF) used to reduce nosocomial SARS-CoV-2 through changing infection prevention and control (IPC) behaviours. Here using qualitative behavioural analyses we report how the SRF worked. Methods: Prior to a multisite non-randomised trial of its effectiveness, the SRF was...

Background Successive SARS-CoV-2 variants have caused severe disease in long-term care facility (LTCF) residents. Primary vaccination provides strong short-term protection, but data are limited on duration of protection following booster vaccines, particularly against the Omicron variant. We investigated effectiveness of booster vaccination against...

Structured summary Background Whole genome sequencing (WGS) for managing healthcare associated infections (HCAIs) has developed considerably through experiences with SARS-CoV-2. We interviewed various healthcare professionals (HCPs) with direct experience of using WGS in hospitals (within the COG-UK Hospital Onset COVID-19 Infection (HOCI) study)...

Background The SARS-CoV-2 omicron variant (B.1.1.529) is highly transmissible, but disease severity appears to be reduced compared with previous variants such as alpha and delta. We investigated the risk of severe outcomes following infection in residents of long-term care facilities. Methods We did a prospective cohort study in residents of long-...

Third dose COVID-19 vaccines are being deployed widely but their efficacy has not been assessed adequately in vulnerable elderly people who exhibit suboptimal responses after primary series vaccination. We studied spike-specific immune responses in 341 staff and residents in long-term care facilities (LTCF) who received an mRNA vaccine following du...

General population studies have shown strong humoral response following SARS-CoV-2 vaccination with subsequent waning of anti-spike antibody levels. Vaccine-induced immune responses are often attenuated in frail and older populations, but published data are scarce. We measured SARS-CoV-2 anti-spike antibody levels in Long-Term Care Facility residen...

Objectives Nosocomial transmission of SARS-CoV-2 has been a significant cause of mortality in National Health Service (NHS) hospitals during the COVID-19 pandemic. The COG-UK Consortium Hospital-Onset COVID-19 Infections (COG-UK HOCI) study aims to evaluate whether the use of rapid whole-genome sequencing of SARS-CoV-2, supported by a novel probabi...

There is limited evidence on the cost and cost-effectiveness of cash transfer programmes to improve maternal and child health in Kenya and other sub-Saharan African countries. This article presents the economic evaluation results of the Afya trial, assessing the costs, cost-effectiveness and equity impact of a demand-side financing intervention tha...

Introduction Viral sequencing of SARS-CoV-2 has been used for outbreak investigation, but there is limited evidence supporting routine use for infection prevention and control (IPC) within hospital settings. Methods We conducted a prospective non-randomised trial of sequencing at 14 acute UK hospital trusts. Sites each had a 4-week baseline data-c...

Background General population studies have shown strong humoral response following SARS-CoV-2 vaccination with subsequent waning of anti-spike antibody levels. Vaccine-induced immune responses are often attenuated in frail and older populations such as Long-Term Care Facility (LTCF) residents but published data are scarce. Methods VIVALDI is a pro...

Background Recently there has been a rapid, global increase in SARS-CoV-2 infections associated with the Omicron variant (B.1.1.529). Although severity of Omicron cases may be reduced, the scale of infection suggests hospital admissions and deaths may be substantial. Definitive conclusions about disease severity require evidence from populations wi...

Objectives Given high maternal and child mortality rates, we assessed the impact of conditional cash transfers (CCTs) to retain women in the continuum of care (antenatal care (ANC), delivery at facility, postnatal care (PNC) and child immunisation). Design We conducted an unblinded 1:1 cluster-randomised controlled trial. Setting 48 health facili...

Objectives The averted infections ratio (AIR) is a novel measure for quantifying the preservation-of-effect in active-control non-inferiority clinical trials with a time-to-event outcome. In the main formulation, the AIR requires an estimate of the counterfactual placebo incidence rate. We describe two approaches for calculating confidence limits f...

Objectives: The aim of this study was to evaluate whether infection occurred pre or postmigration and the associated diagnosis delay in migrants diagnosed with HIV in the UK. Design: We analyzed a cohort of individuals diagnosed with HIV in the UK in 2014-2016 born in Africa or elsewhere in Europe. Inclusion criteria were arrival within 15 years...

Objectives Integrase strand transfer inhibitors (INSTIs) are commonplace in modern antiretroviral therapy (ART). Increased weight gain with their use is increasingly scrutinized. We evaluated weight changes in treatment‐naïve adults with HIV‐1 attending a UK centre who started regimens including raltegravir or dolutegravir. Methods A retrospective...

Objectives : Recently emerging SARS-CoV-2 variants have been associated with an increased rate of transmission within the community. We sought to determine whether this also resulted in increased transmission within hospitals. Methods : We collected viral sequences and epidemiological data of patients with community and healthcare associated SARS-...

Background SARS-CoV-2 lineage B.1.1.7 has been associated with an increased rate of transmission and disease severity among subjects testing positive in the community. Its impact on hospitalised patients is less well documented. Methods We collected viral sequences and clinical data of patients admitted with SARS-CoV-2 and hospital-onset COVID-19...

Objective: To assess accelerated partner therapy (APT) as a contact tracing intervention for people with chlamydia. Design: Cross-over cluster-randomised controlled trial. Setting: 17 sexual health clinics (clusters) in the United Kingdom, 2018-2019. Participants: Heterosexual people aged over 16 years with a positive Chlamydia trachomatis test res...

Objectives Analysis of nosocomial transmission in the early stages of the pandemic at a large multi-site healthcare institution. Nosocomial incidence is linked with infection control interventions.. Methods Viral genome sequence and epidemiological data were analysed for 574 consecutive SARS-CoV-2 PCR-positive patients including 86 nosocomial case...

Background Accelerated partner therapy (APT) is a partner notification (PN) method whereby healthcare professionals assess sex partners by telephone, then send or give the index patient antibiotics and self-sampling kits for their sex partner(s). We determined the effect of APT on proportions of: index patients who test positive for chlamydia at 12...

Background Accelerated partner therapy (APT) is a partner notification (PN) method whereby healthcare professionals assess sex partners by telephone, then send or give the index patient antibiotics and self-sampling kits for their sex partner(s). APT was implemented within a cluster cross-over randomised control trial in 17 sexual health clinics in...

Background Accelerated partner therapy (APT) is a partner notification (PN) method whereby healthcare professionals assess sex partners by telephone, then send or give the index patient antibiotics and self-sampling kits for them. We described characteristics and outcomes of people choosing APT in an RCT. Methods We did a cross-over cluster-random...

Background: Rapid identification and investigation of healthcare-associated infections (HCAIs) is important for suppression of SARS-CoV-2, but the infection source for hospital onset COVID-19 infections (HOCIs) cannot always be readily identified based only on epidemiological data. Viral sequencing data provides additional information regarding pot...

Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage B.1.1.7 has been associated with an increased rate of transmission and disease severity among subjects testing positive in the community. Its impact on hospitalised patients is less well documented. Methods We collected viral sequences and clinical data of patients admi...

Introduction: anal condylomas are associated with human papillomavirus (HPV) infection and are a risk factor for anal squamous cell carcinoma (SCC). Objective: to conduct a meta-analysis evaluating the prevalence of anal high-risk-HPV, high-grade squamous intraepithelial lesions (HSIL) and SCC in patients with condylomas. The standardised incide...

Introduction: Randomized trials of new agents for HIV pre-exposure prophylaxis (PrEP) compare against emtricitabine and tenofovir disoproxil fumarate (F/TDF), without a placebo group. We used the well-characterized adherence-efficacy relationship for F/TDF to back-calculate the (non-PrEP) counterfactual background HIV incidence (bHIV) in a randomi...

Objectives: Patients requiring haemodialysis are at increased risk of serious illness with SARS-CoV-2 infection. To improve the understanding of transmission risks in six Scottish renal dialysis units, we utilised the rapid whole-genome sequencing data generated by the COG-UK consortium. Methods: We combined geographical, temporal and genomic se...

Introduction Nosocomial transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a significant cause of mortality in National Health Service (NHS) hospitals during the coronavirus disease 2019 (COVID-19) pandemic. The aim of this study is to evaluate the impact of rapid whole genome sequencing of SARS-CoV-2, supported b...

Introduction: Nosocomial transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a significant cause of mortality in National Health Service (NHS) hospitals during the coronavirus disease 2019 (COVID-19) pandemic. The aim of this study is to evaluate the impact of rapid whole genome sequencing of SARS-CoV-2, supported...

Objectives: Patients requiring haemodialysis are at increased risk of serious illness with SARS-CoV-2 infection. To improve the understanding of transmission risks in six Scottish renal dialysis units, we utilised the rapid whole-genome sequencing data generated by the COG-UK consortium. Methods: We combined geographical, temporal and genomic seque...

Intervention programme theory enhances the development, evaluation, optimisation and translation of complex interventions. It clearly specifies the ways intervention context and content combine to produce intervention outcomes. We report the development of initial programme theory for a SARS-CoV-2 genome sequence-report tool (SRT). The SRT translat...

Objective: To construct chorionicity-specific birthweight reference charts for dichorionic diamniotic (DCDA) and monchorionic diamniotic (MCDA) twin pregnancies incorporating estimated fetal weight (EFW) data in order to adjust for the relationship between suboptimal growth and premature delivery. An additional aim of this study was to determine i...

Background RRandomized trials of new PrEP agents compare to oral emtricitabine+tenofovir disoproxil fumarate (F/TDF) and do not have a placebo arm. We used the well-characterized adherence-efficacy relationship for F/TDF from iPrEX OLE, to back-calculate the (non-PrEP) background HIV incidence (bHIV) in the F/TDF arm of DISCOVER and estimate compar...

Objectives Rectal swab specimens, either alone or pooled with first-void urine (FVU) and pharyngeal swab specimens, are used to test for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) infection in men who have sex with men (MSM). Following introduction of human papillomavirus (HPV) vaccination for MSM attending UK sexual health services...

OBJECTIVES: Rectal swab specimens, either alone or pooled with first-void urine (FVU) and pharyngeal swab specimens, are used to test for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) infection in men who have sex with men (MSM). Following introduction of human papillomavirus (HPV) vaccination for MSM attending UK sexual health services...

Background Rapid identification and investigation of healthcare-associated infections (HCAIs) is important for suppression of SARS-CoV-2, but the infection source for hospital onset COVID-19 infections (HOCIs) cannot always be readily identified based only on epidemiological data. Viral sequencing data provides additional information regarding pote...

Trials of candidate agents for HIV pre-exposure prophylaxis (PrEP) might randomly assign participants to be given a new PrEP agent or oral coformulated tenofovir disoproxil fumarate plus emtricitabine. This design presents unique challenges in interpretation. First, with two active arms, HIV incidence might be low. Second, the effectiveness of teno...

The number of solid organ transplant recipients (SOTR), and their life expectancy, is increasing, with higher risk for long‐term complications from immunosuppression. We carried out a systematic review describing the burden of anal squamous cell carcinoma (SCC), and its surrogates, in SOTR. We conducted mixed effect model‐based meta‐analyses evalua...

Men who have sex with men (MSM) who experience problematic chemsex are at high risk of acquiring HIV due to combined drug use and sexual behaviours. Pre-exposure prophylaxis (PrEP) could substantially reduce the risk of HIV transmission in this group of men. The aim of this study was to examine the biopsychosocial characteristics associated with Pr...

Objectives: The aim of the study was to investigate whether lamivudine (3TC) or emtricitabine (FTC) use following detection of M184V/I is associated with better virological outcomes. Methods: We identified people with viruses harbouring the M184V/I mutation in UK multicentre data sets who had treatment change/initiation within 1 year. We analyse...

Rationale: Development of diagnostic tools with improved predictive value for tuberculosis (TB) is a global research priority. Objectives: We evaluated whether implementing higher diagnostic thresholds than currently recommended for QuantiFERON Gold-in-Tube (QFT-GIT), T-SPOT.TB and the tuberculin skin test (TST) might improve prediction of incid...

Objectives The aim of this study was to investigate associations between baseline characteristics and CD4 cell count response on first-line antiretroviral therapy and risk of virological failure (VF) with or without drug resistance. Methods We conducted an analysis of UK Collaborative HIV Cohort data linked to the UK HIV Drug Resistance Database....

Objective: Excessive weight gain has been reported with integrase strand transfer inhibitors (INSTIs). We evaluated weight changes in virologically-suppressed adults with HIV who switched from non-INSTI regimens to raltegravir- or dolutegravir-containing antiretroviral therapy. Design: Retrospective single-centre cohort. Methods: Adults who sw...

Background Anorectal swab specimens, either alone, or pooled with first catch urine (FCU) and pharyngeal swab specimens, are used to test for STIs in MSM. The residual sample, after routine testing, may be used to monitor human papillomavirus (HPV) prevalence in this population, but the sensitivity of HPV detection in such specimens is unknown. Me...

Objectives: Evaluate long-term rates of virological failure and treatment interruption for people living with HIV (PLWHIV) with viral suppression on first-line efavirenz + tenofovir disoproxil fumarate + emtricitabine/lamivudine (EFV + TDF + FTC/3TC), and compare these according to patient characteristics. Methods: PLWHIV enrolled in the Collabo...

Anal squamous intraepithelial lesions (ASIL) or anal intraepithelial neoplasia (AIN) are precancerous lesions. microRNAs (miRNAs) have been implicated in cervical carcinogenesis, but have never been assessed in anal precancerous lesions. Our aim was to evaluate the expression of miR-16, miR-20a, miR-150 and miR-155 in several grades of ASIL obtaine...

ABSTRACT Background There is increasing evidence for the importance of haemodynamic monitoring in pregnancy. Device‐specific reference ranges are required in order to correctly intepret hemodynamic indices in healthy and pathological pregnancies. Methods This was a prospective cohort study of healthy singleton pregnancies. Haemodynamic measuremen...

Background Minimisation of the delay to diagnosis is critical to achieving optimal outcomes for HIV patients and to limiting the potential for further onward infections. However, investigation of diagnosis delay is hampered by the fact that in most newly diagnosed patients the exact timing of infection cannot be determined and so inferences must be...

Tenofovir disoproxil fumarate combined with emtricitabine is a highly effective oral pre-exposure prophylaxis (PrEP) agent for preventing the acquisition of HIV. This effectiveness has consequences for the design and analysis of trials assessing experimental PrEP regimens, which now generally include an active-control tenofovir disoproxil fumarate...

Background: Information on the performance of anal cytology in women who are high-risk for human papillomavirus-related lesions and the factors that might influence it are largely lacking. Aims: Evaluate the performance of anal cytology in women with lower anogenital tract neoplasia. Methods: retrospective study including all new referrals of women...

Background: The prevalence of HIV-1 resistance to antiretroviral therapies (ART) has declined in high-income countries over recent years, but drug resistance remains a substantial concern in many low and middle-income countries. The Q151M and T69 insertion (T69i) resistance mutations in the viral reverse transcriptase gene can reduce susceptibilit...

Background: Information on the performance of anal cytology in women who are high-risk for human papillomavirus-related lesions and the factors that might influence it are largely lacking. Aims: Evaluate the performance of anal cytology in women with lower anogenital tract neoplasia. Methods: retrospective study including all new referrals of...

Objectives: To investigate factors that predict speed of recovery and long-term CD4 cell count in HIV-1 seroconverters initiating combination antiretroviral therapy (cART), and to quantify the influence of very early treatment initiation. We make use of all pre-treatment CD4 counts, because analyses using only a single observation at initiation ma...

Objectives: The main aim of this study was to construct reference ranges of the maternal central hemodynamic parameters during pregnancy. The second aim was to determine the maternal and pregnancy characteristics, which influence these hemodynamic parameters. Methods: This was a prospective cohort study of low-risk pregnant women attending for r...

For the analysis of longitudinal biomedical data in which the timing of observations in each patient is irregular and in which there is substantial loss to follow-up, it is important that statistical models adequately describe both the patterns of variation within the data and any relationships between the variable of interest and time, clinical ch...

Background There has been some debate in the literature as to whether baseline values of a measurement of interest at treatment initiation should be treated as an outcome variable as part of a model for longitudinal change or instead used as a predictive variable with respect to the response to treatment. We develop a new approach that involves a c...

Introduction: This study investigates patterns of intertwin size discordance in dichorionic diamniotic (DCDA) and monochorionic diamniotic (MCDA) twin pregnancies. Material and methods: Ultrasound measurements of twin pregnancies, from 14 weeks to term, were collected by 9 hospitals over a 10-year period. This analysis considers the modelled and...

Longitudinal data are widely analysed using linear mixed models, with 'random slopes' models particularly common. However, when modelling, for example, longitudinal pre-treatment CD4 cell counts in HIV-positive patients, the incorporation of non-stationary stochastic processes such as Brownian motion has been shown to lead to a more biologically pl...

Objective To generate reference charts for expected fetal growth in dichorionic diamniotic (DCDA) and monochorionic diamniotic (MCDA) twin pregnancies and to compare these with those from singleton pregnancies.Methods This was a retrospective study of biometric measurements from serial ultrasound examinations of twin pregnancies in the second and t...