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Journal articleKucharski A, Cori A, 2024,
Inference of epidemic dynamics in the COVID-19 era and beyond
, Epidemics: the journal of infectious disease dynamics, Vol: 48, ISSN: 1755-4365The COVID-19 pandemic demonstrated the key role that epidemiology and modelling play in analysing infectious threats and supporting decision making in real-time. Motivated by the unprecedented volume and breadth of data generated during the pandemic, we review modern opportunities for analysis to address questions that emerge during a major modern epidemic. Following the broad chronology of insights required — from understanding initial dynamics to retrospective evaluation of interventions, we describe the theoretical foundations of each approach and the underlying intuition. Through a series of case studies, we illustrate real life applications, and discuss implications for future work.
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Journal articleYang Q, Park SW, Saad-Roy CM, et al., 2024,
Assessing population-level target product profiles of universal human influenza A vaccines
, EPIDEMICS, Vol: 48, ISSN: 1755-4365 -
Journal articleKruger M, van Elsland SL, Davidson A, et al., 2024,
Outcome of retinoblastoma after implementation of national retinoblastoma treatment guidelines in South Africa
, JCO Global Oncology, Vol: 10, ISSN: 2687-8941PurposeRetinoblastoma, a curable childhood cancer, has been identified as a tracer cancer in the WHO Global Initiative for Childhood Cancer. To document the outcomes of children with retinoblastoma in South Africa, treated as per the first prospective standard national treatment guidelines for childhood cancer in South Africa.Patients and MethodsAll children diagnosed with retinoblastoma between 2012 and 2016 in five South African pediatric oncology units were treated with a standard treatment on the basis of the International Society of Pediatric Oncology-Pediatric Oncology in Developing Countries guidelines for high-income settings. Treatment included focal therapy with/without chemotherapy, or enucleation with/without chemotherapy, and orbital radiotherapy, depending on enucleated eye histology. The end point was survival at 24 months, using Kaplan-Meier curves with log-rank (Mantel-Cox) and chi-square (χ2) tests with respective P values reported.ResultsA total of 178 children were included in the study; 68% presented with unilateral disease. The median age was 27 months (range 0-118 months) with a male:female ratio of 1:0.75. The overall survival was 79% at 24 months with significant association with stage at diagnosis (P < .001) and older age over 2 years as opposed to younger than 2 years (P < .001). Causes of death were disease progression/relapses in 90% (34 of 38) and unknown in 2% (1 of 38), whereas treatment abandonment was 1.7% (3 of 178).ConclusionEfficacy with national treatment guidelines was confirmed, and feasibility of implementing standard national childhood cancer treatment guidelines was documented, involving multidisciplinary teams in South Africa. Outcome was significantly associated with stage at diagnosis and age.
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Journal articleUzzell CB, Gray E, Rigby J, et al., 2024,
Environmental surveillance for Salmonella Typhi in rivers and wastewater from an informal sewage network in Blantyre, Malawi
, PLoS Neglected Tropical Diseases, Vol: 18, ISSN: 1935-2727Environmental surveillance for Salmonella Typhi may provide information on the community-level dynamics of typhoid fever in resource poor regions experiencing high disease burden. Many knowledge gaps concerning the feasibility of ES remain, especially in areas lacking formal sewage systems. We implemented protocols for S. Typhi ES, including site selection and catchment population estimation, sample concentration and testing using qPCR for S. Typhi specific gene targets. Between May 2021 and May 2022, we collected grab samples and Moore swabs from 43 sites in Blantyre, Malawi. Catchment characteristics, water quality, and human faecal contamination (qPCR for Bacteroides HF183) were also recorded. Their association with S. Typhi detection was investigated using a logistic mixed-effects regression analysis. Prevalence of S. Typhi in ES samples was 2.1% (1.1–4.0%) and 3.9% (1.9–7.9%) for grab and Moore swab samples, respectively. HF183 was associated S. Typhi positivity, with a unit increase in log genome copies/microlitre increasing the odds of detection of S. Typhi by 1.56 (95% CI: 1.29–1.89) and 1.33 (1.10–1.61) in Moore swabs and grab samples, respectively. The location and timing of S. Typhi detection through ES was not associated with the incidence of typhoid fever reported in associated catchment populations. During this period of relatively low typhoid fever incidence, wastewater surveillance continued to detect S. Typhi in human sewage and wastewater suggesting that ES using natural river systems can be a sensitive indicator of transmission.
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Journal articleCucunubá ZM, Gutiérrez-Romero SA, Ramírez J-D, et al., 2024,
The epidemiology of Chagas disease in the Americas
, The Lancet Regional Health - Americas, Vol: 37, ISSN: 2667-193XChagas disease is a complex parasitic zoonosis that still threatens public health across the Americas. Initiatives to control Trypanosoma cruzi transmission via blood transfusion and non-native triatomine-bug vectors have yielded crucial advances; native vectors, however, actively bridge wild and domestic/peri-domestic transmission cycles throughout the region, and tens of thousands of people become infected each year. Oral-transmission outbreaks, urbanisation, and vertical transmission are additional/emerging issues calling for innovative strategic thinking. While critical for advocacy and sustained public health action, assessing Chagas disease burden remains difficult; the often-asymptomatic nature of T. cruzi infection, healthcare access limitations, pervasive underreporting, and other methodological hurdles inherent to reliably measuring incidence, prevalence, and disease progression all contribute to the difficulty. Whether and how parasite, vector, and host genetic makeups affect transmission dynamics and epidemiology is also unclear. Continued high-quality research and long-term, adaptive strategies combining vector control surveillance with enhanced case detection and integral patient care remain critical to effectively address the ethical and societal challenge of Chagas disease control.
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Journal articleHill V, Cleemput S, Pereira JS, et al., 2024,
A new lineage nomenclature to aid genomic surveillance of dengue virus
, PLOS BIOLOGY, Vol: 22, ISSN: 1544-9173 -
Journal articleImada S, Khawaled S, Shin H, et al., 2024,
Short-term post-fast refeeding enhances intestinal stemness via polyamines.
, Nature, Vol: 633, Pages: 895-904For over a century, fasting regimens have improved health, lifespan and tissue regeneration in diverse organisms, including humans1-6. However, how fasting and post-fast refeeding affect adult stem cells and tumour formation has yet to be explored in depth. Here we demonstrate that post-fast refeeding increases intestinal stem cell (ISC) proliferation and tumour formation; post-fast refeeding augments the regenerative capacity of Lgr5+ ISCs, and loss of the tumour suppressor gene Apc in post-fast-refed ISCs leads to a higher tumour incidence in the small intestine and colon than in the fasted or ad libitum-fed states, demonstrating that post-fast refeeding is a distinct state. Mechanistically, we discovered that robust mTORC1 induction in post-fast-refed ISCs increases protein synthesis via polyamine metabolism to drive these changes, as inhibition of mTORC1, polyamine metabolite production or protein synthesis abrogates the regenerative or tumorigenic effects of post-fast refeeding. Given our findings, fast-refeeding cycles must be carefully considered and tested when planning diet-based strategies for regeneration without increasing cancer risk, as post-fast refeeding leads to a burst in stem-cell-driven regeneration and tumorigenicity.
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Journal articleValente de Almeida S, Hauck K, Njenga S, et al., 2024,
Value for money of medicine sampling and quality testing: evidence from Indonesia
, BMJ Global Health, Vol: 9, ISSN: 2059-7908Background Substandard and falsified medicines (SFMs) are a public health concern of global importance. Postmarket surveillance in the form of medicine sampling and quality testing can prevent and detect SFM, however, there is remarkably scarce evidence about the cost and value for money of these activities: how much do they cost and how effective are they in detecting SFM?Methods Between February and October 2022, Systematic Tracking of At Risk Medicines (STARmeds) collected and analysed for quality 1274 samples of 5 medicines from physical and online retail outlets in 7 Indonesian districts. We collated data on the resources consumed by STARmeds, related to all stages of medicines sampling and quality testing including design, fieldwork and laboratory analysis. We used activity-based costing principles to calculate the financial and economic cost of medicine quality surveillance from the perspective of a hypothetical medicines’ regulator. We calculated the cost per day and per week of fieldwork, per sample collected and per substandard sample. We used bootstrapping to capture uncertainty in the number of samples collected, by seller location type (urban, rural and online).Results The total cost of sampling and testing medicines from the market was US$712 964 (current 2022 values). Laboratory costs represented the largest share (70%), followed by other direct costs (12%) and indirect costs (7%). On average, it costs STARmeds US$479 (95% CI US$462 to US$516) to collect one medicine sample and US$5990 (95% CI US$5601 to US$6258) to identify one substandard sample.Conclusion Our findings bring urgently needed and novel information on the cost and value for money of medicine quality surveillance. These may support planning and budgeting of the Indonesian pharmaceutical regulator, but also of regulators and researchers elsewhere, particularly in low-income and middle-income settings, as well as international organisations with health regulation and quality of care
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Journal articleMcquaid CF, Menzies NA, Houben RMGJ, et al., 2024,
Improving the contribution of mathematical modelling evidence to guidelines and policy: Experiences from tuberculosis
, EPIDEMICS, Vol: 48, ISSN: 1755-4365 -
Journal articleStevens O, Sabin K, Anderson RL, et al., 2024,
Population size, HIV prevalence, and antiretroviral therapy coverage among key populations in sub-Saharan Africa: collation and synthesis of survey data, 2010–23
, The Lancet Global Health, Vol: 12, Pages: e1400-e1412, ISSN: 2214-109XBackgroundKey population HIV programmes in sub-Saharan Africa require epidemiological information to ensure equitable and universal access to effective services. We aimed to consolidate and harmonise survey data among female sex workers, men who have sex with men, people who inject drugs, and transgender people to estimate key population size, HIV prevalence, and antiretroviral therapy (ART) coverage for countries in mainland sub-Saharan Africa.MethodsKey population size estimates, HIV prevalence, and ART coverage data from 39 sub-Saharan Africa countries between 2010 and 2023 were collated from existing databases and verified against source documents. We used Bayesian mixed-effects spatial regression to model urban key population size estimates as a proportion of the gender-matched, year-matched, and area-matched population aged 15–49 years. We modelled subnational key population HIV prevalence and ART coverage with age-matched, gender-matched, year-matched, and province-matched total population estimates as predictors.FindingsWe extracted 2065 key population size data points, 1183 HIV prevalence data points, and 259 ART coverage data points. Across national urban populations, a median of 1·65% (IQR 1·35–1·91) of adult cisgender women were female sex workers, 0·89% (0·77–0·95) were men who have sex with men, 0·32% (0·31–0·34) were men who injected drugs, and 0·10% (0·06–0·12) were women who were transgender. HIV prevalence among key populations was, on average, four to six times higher than matched total population prevalence, and ART coverage was correlated with, but lower than, the total population ART coverage with wide heterogeneity in relative ART coverage across studies. Across sub-Saharan Africa, key populations were estimated as comprising 1·2% (95% credible interval 0·9–1·6) of the total population aged 15–49 ye
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