Epidemiological assessment of schistosomiasis: hotspots, morbidity, and transmission

There are currently over 250 million humans infected with schistosomiasis, over 90% of which reside within sub-Saharan Africa. The World Health Organization (WHO) aims to eliminate schistosomiasis as a public health problem (EPHP) in all 78 currently endemic countries, and achieve interruption of transmission (IoT) in selected African regions, by 2030. Achieving these targets requires targeted research to refine intervention strategies. My thesis evaluates several aspects of the WHO guidelines, critically assessing definitions and thresholds, transmission dynamics and exploring alternative methodologies. Chapter one includes a general introduction into schistosomiasis, WHO goals and targets, highlighting knowledge gaps and setting the scene for all the different aspects of the thesis. In chapter two, I evaluated the validity of the WHO’s heavy infection intensity threshold (≥400 eggs per gram [EPG]) as a morbidity indicator for S. mansoni and the reliance on infection intensity as a proxy for morbidity. I examined infection intensity and morbidity in individuals from Bugoto, Uganda, using egg-based Kato- Katz and point-of-care circulating cathodic antigen (POC-CCA) tests for diagnosis, and ultrasound (Niamey protocol) for morbidity quantification. While school-aged children (SAC) had the highest infection intensities, pre-SAC had a significantly higher proportion of positive portal vein dilation (PVD), left parasternal line (PSL) enlargement, and anaemia compared to all other age groups. Infection intensity only predicted fibrosis and anaemia at burdens far above the WHO’s threshold, and malaria was strongly associated with PVD and anaemia. These findings suggest that the current WHO standard of simply using the prevalence of individuals with heavy infection intensities within a community is an unreliable morbidity proxy, highlighting the need for refined metrics that account for broader health impacts, age differences and co-infections. In chapter three, I examined the operational designation of persistent hotspots, as introduced in the WHO’s most recent Roadmap for Neglected Tropical Diseases. The definition identifies areas where transmission persists above the 10% baseline prevalence despite ongoing control or elimination interventions, a distinction that has implications for determining which communities receive biannual treatment. Using a systematic-style review methodology, I outlined the historical use of the term hotspot and observed a substantial increase in its use after 2016, with the Schistosomiasis Consortium for Operational Research and Evaluation being most influential in the use of the term. Next, using studies that had identified hotspots, I assessed the four criteria outlined in the WHO draft definition. The most restrictive criteria for designation of a hotspots by WHO definition was achieving ≥75% coverage alongside a 1/3 reduction in prevalence. Using these results, in combination with novel data obtained from interviews with key stakeholders and program managers, I proposed a revised framework for defining persistent hotspots, advocating for greater regional flexibility in prevalence reduction thresholds and distinguishing between biological and operational hotspots which may not meet coverage targets. In chapter four, I examined the relationship between human mobility and S. mansoni transmission, focusing on the impact of habitual travel to and from a persistently hyper-endemic region and one that has reached elimination thresholds. Understanding these dynamics is critical for achieving and maintaining WHO elimination targets, particularly in low-prevalence regions where overlooked transmission drivers and surveillance gaps may hinder progress to control. Using parasite diagnostics and travel questionnaires from individuals living ~5 km from Lake Victoria, Uganda, I developed a causal model of infection, constructing a directed acyclic graph (DAG) to identify key confounders, determinants, and mediators. Bayesian linear models estimated infection probability as a function of travel frequency, water exposure, and duration in water. Results showed that frequent travellers had a higher infection risk and that the activity that they did when at the Lake was also an important driver of infection. In settings approaching elimination thresholds, such mobility may undermine control efforts if not adequately captured by existing surveillance systems. In chapter five, I evaluated the potential of Nanopore adaptive sampling to selectively enrich S. mansoni DNA from miracidia preserved on Whatman FTA® cards for whole-genome sequencing (WGS). While unwashed miracidia on FTA cards are generally suitable for targeted gene amplification or microsatellite analyses, WGS typically requires additional pre-washing to reduce contamination, particularly from faecal material. This study aimed to determine whether adaptive sampling could minimise the need for labour-intensive pre-washing while maximising DNA recovery from long-term archived samples. Using Nanopore sequencing, I compared washed and unwashed miracidia samples, assessing contamination levels with Kraken2 and sequencing depth through read mapping. While washed samples contained more S. mansoni DNA, adaptive sampling failed to generate sufficient reads for effective WGS, likely due to high genomic repeat content causing the rejecEon of valid S. mansoni reads. These findings suggest that while washing improves purity, adaptive sampling alone is insufficient, and further optimisation or alternative enrichment strategies will be necessary to improve sequencing efficiency and data quality. In chapter six, my general discussion, I addressed the common themes and topics of interest from within and across each of the chapters and outlined ideas for further research. Through a series of studies, I questioned the reliability of egg burden as a morbidity proxy, assessed the effectiveness of the persistent hotspot designation, explored the role of human mobility in sustaining transmission, and evaluated the potential of adaptive sampling for parasite genotyping. These findings provide evidence which can contribute to recommendations to refine intervention strategies and improve surveillance accuracy for Schistosoma spp. research, supporting more effective disease control and elimination efforts to ultimately improve health outcomes for affected populations.