Adrienne Epstein

Malaria transmission in southwestern Uganda is low, but persists despite control efforts. Identifying whether infections are locally sustained or imported by travelers is critical for guiding interventions. We integrated epidemiologic surveillance with parasite genomics to characterize imported malaria episodes at three health facilities in southwestern Uganda. Between January 2023 and June 2024, we enrolled microscopy-confirmed malaria cases at three health facilities, Maziba and Muko (very low transmission) and Kamwezi (low-to-moderate transmission), administered travel history questionnaires, and collected dried blood spots for genotyping. 348 Plasmodium falciparum infections were genotyped using MAD ⁴ HatTeR, a multiplex amplicon sequencing panel targeting 165 diversity markers and 38 drug resistance loci. Complexity of infection and pairwise relatedness were estimated using MOIRE and Dcifer, respectively. Plasmotrack, a transmission network framework, was used to infer transmission networks and importation rates. Amongst malaria cases, travel was common in Maziba (87%) and Muko (96%) but infrequent in Kamwezi (12%). Most travel in Maziba and Muko was from high-transmission regions in northern and eastern Uganda. Parasites in Maziba and Muko exhibited higher within-host diversity and lower within-site relatedness compared to those in Kamwezi, with the proportion of significant related infection pairs substantially lower in Maziba (0.59%) and Muko (0.17%) than in Kamwezi (6.36%). Transmission network inference identified most infections in Maziba and Muko as imported, with the majority of inferred secondary transmission linked to recent travelers. In contrast, Kamwezi showed multiple highly related clusters, indicating sustained local transmission. Validated markers of artemisinin resistance (K13 P441L and R561H) were more prevalent in Kamwezi. Malaria in Maziba and Muko was driven largely by importation from other parts of Uganda, while local transmission predominated in Kamwezi. Tailored interventions addressing travel-associated risks and local transmission, supported by travel histories and genetic data will be valuable to advance malaria elimination in this region.

A common barrier to insecticide-treated net (ITN) use, the backbone of malaria prevention, is heat discomfort. Using multilevel regression models, we quantified the association between temperature and ITN use reported in Demographic and Health and Malaria Indicator Surveys from 2011-2022 across 28 countries in sub-Saharan Africa. Marginal predicted probability of use was unimodal with nighttime temperature and decreased above a threshold daytime temperature. For women (n=731,947), temperatures above specified thresholds were associated with lower use, with adjusted odds ratios [aOR] 0.91 for daytime (95% confidence interval [CI] 0.88-0.94) and 0.87 for nighttime (95% CI 0.85-0.91). For children under 5 (n=524,926), corresponding aOR were 0.87 (95% CI 0.84-0.91) and 0.86 (95% CI 0.83-0.90). Considering a counterfactual in which temperatures never exceeded these thresholds, we estimated 25.8 million (95% CI 14.4-38.2 million) cases of malaria attributable to heat-associated non-use. These results demonstrate the importance of considering climate-behavior interactions for malaria control.

The invasive urban malaria vector Anopheles stephensi threatens 126 million city dwellers in Africa. Controlling An. stephensi requires greater understanding of its origin, invasion dynamics, and insecticide resistance mechanisms. Analysis of 645 whole genomes sampled across Africa, the Middle East, and Asia supports an invasion scenario in which an initial South Asian introduction established a bridgehead population in Djibouti, which seeded distinct invasion fronts in Sudan, Ethiopia/Kenya, and Yemen. These incursions show contrasting rates and routes of spread shaped by landscape topology. Insecticide resistance is predominantly mediated by metabolic detoxification genes, with resistance haplotypes and copy-number amplifications introduced from South Asia. These findings, alongside a companion genomic resource, enable genomic surveillance of An. stephensi spread and resistance to aid control strategies.

Background: Malaria transmission in southwestern Uganda is low, but persists despite ongoing control efforts. Identifying whether infections are locally sustained or imported by travelers is critical for guiding interventions. We integrated epidemiologic surveillance with parasite genomics to characterize imported malaria episodes at three health facilities in southwestern Uganda. Methods: Between January 2023 and June 2024, we enrolled microscopy-confirmed malaria cases at three health facilities, Maziba and Muko (very low transmission) and Kamwezi (low-to-moderate transmission), administered travel history questionnaires, and collected dried blood spots for genotyping. Plasmodium falciparum infections were genotyped using MAD ⁴ HatTeR, a highly sensitive multiplex amplicon sequencing panel targeting 165 diversity markers and 38 drug resistance loci. Complexity of infection and pairwise relatedness were estimated using MOIRE and Dcifer, respectively. Plasmotrack, a Bayesian transmission network framework, was used to infer network structure, transmission directionality, reproduction numbers, and importation rates. Results: Amongst malaria cases, recent overnight travel was common in Maziba (87%) and Muko (96%) but infrequent in Kamwezi (12%). Most travel in cases from Maziba and Muko was from high-transmission regions in northern and eastern Uganda. Parasites in Maziba and Muko cases exhibited higher within-host diversity and lower within-site relatedness compared to those in Kamwezi cases. Transmission network inference identified most infections in Maziba and Muko as imported, with the majority of inferred secondary transmission linked to recent travelers. In contrast, Kamwezi showed multiple highly related clusters, indicating sustained local transmission. Validated and candidate markers of artemisinin partial resistance (K13 P441L and R561H) were more prevalent in Kamwezi. Conclusion: Malaria in Maziba and Muko was driven largely by importation from other parts of Uganda, while local transmission played a larger role in Kamwezi . Tailored interventions addressing travel-associated risks and local transmission, supported by travel histories and parasite genetic data will be valuable to advance malaria elimination in this region.

Background: Parasite importation remains a challenge to malaria elimination. The extent to which human travel contributes to sustained transmission in low-to-moderate burden areas is poorly understood. Methods: We conducted a 14-month longitudinal cohort study in Southwest Uganda. A total of 1918 individuals from 400 households were followed bimonthly. Travel histories and household characteristics were collected through surveys. Symptomatic and asymptomatic Plasmodium falciparum infections were captured through health facility surveillance and household reports (for symptomatic cases) and qPCR (for asymptomatic infections). Multilevel logistic regression models estimated associations between travel and infection. Population attributable fractions quantified travel's contribution to malaria. Results: Over the study, 283 infections (244 symptomatic episodes and 39 asymptomatic infections) were recorded. Associations between travel and malaria varied spatially and temporally, with positive associations in lower transmission villages (OR = 4.38, 95% CI 1.80–10.64) and during periods of low transmission. Associations were strongest for short-distance trips to nearby areas of higher incidence. Population attributable fraction analyses suggested travel accounted directly for 14% of malaria cases in low-transmission villages overall, rising to 30% during periods of low transmission. Conclusions: Overnight travel contributed to malaria burden, particularly in low-transmission villages and during low seasons, highlighting the need for strategies that address both local transmission and importation.

Background: Parasite importation remains a critical challenge to malaria elimination efforts. The extent to which human travel contributes to sustained transmission in low-to-moderate burden areas of highly endemic African countries is poorly understood. Methods: We conducted a 14-month longitudinal cohort study in Kamwezi subcounty in Southwest Uganda, an area targeted for malaria elimination where sustained transmission poses challenges. A total of 1,918 individuals from 400 households were enrolled and followed bi-monthly. Travel histories, malaria episodes, and household characteristics were collected through structured surveys. Incident malaria was captured via passive case detection at the local health facility and self-report. Multilevel logistic regression models estimated the association between overnight travel and incident malaria, adjusting for demographic and household factors. Population attributable fractions (PAF) quantified the contribution of travel to malaria burden, stratified by transmission intensity, season, and village of residence. Results: Over the study period, 244 malaria episodes were recorded, with incidence highest in villages with greater baseline transmission. Nearly one-third of participants reported at least one overnight trip. We found that associations between travel and malaria varied spatially and temporally, with positive associations in villages of lower transmission (odds ratio=5.65, 95% CI: 2.06-15.45) and during periods of low overall malaria transmission. We found these associations to be strongest for short-distance trips to nearby areas of higher incidence. PAF analyses suggested that travel accounted directly for 17% of malaria cases in low-transmission villages overall, rising to 44.6% during periods of low transmission. Conclusion: Overnight travel contributed meaningfully to malaria burden, especially in villages with low local burden and during periods of seasonally low transmission. These effects were evident even at small geographic and temporal scales. These findings underscore the importance of malaria surveillance and control strategies that account for both local transmission and travel-related importation, even outside of elimination contexts.

The invasion of Africa by the Asian urban malaria vector, Anopheles stephensi, endangers 126 million people across a rapidly urbanising continent where malaria is primarily a rural disease. Control of An. stephensi requires greater understanding of its origin, invasion dynamics, and mechanisms of widespread resistance to vector control insecticides. We present a genomic surveillance study of 551 An. stephensi sampled across the invasive and native ranges in Africa and Asia. Our findings support a hypothesis that an initial invasion from Asia to Djibouti seeded separate incursions to Sudan, Ethiopia, and Yemen before spreading inland, aided by favourable temperature, vegetation cover, and human transit conditions. Insecticide resistance in invasive An. stephensi is conferred by detoxification genes introduced from Asia. These findings, and a companion genomic data catalogue, will form the foundation of an evidence base for surveillance and management strategies for An. stephensi .

Introduction: Malaria remains a significant public health challenge globally, particularly in sub-Saharan Africa, where progress has stalled in recent years. Long-lasting insecticidal nets (LLINs) are a critical preventive tool against malaria. This study investigated the effectiveness of newer-generation LLINs following a universal coverage campaign in Uganda. Methods: Health facility data collected 36 months prior to LLIN distribution and 24 months after LLIN distribution were used from 64 sites that took part in a cluster-randomised trial comparing two newer-generation LLINs (pyrethroid-piperonyl butoxide and pyrethroid-pyriproxyfen). Using an interrupted time-series approach, we compared observed malaria incidence with counterfactual scenarios if no LLINs were distributed, adjusting for precipitation, vegetation, seasonality and care-seeking behaviour. Analyses were also stratified by LLIN type and study-site level estimates of transmission intensity. Results: Overall, malaria incidence decreased from 827 cases per 1000 person-years in the predistribution period to 538 per 1000 person-years in the postdistribution period. Interrupted time-series analyses estimated a 23% reduction in malaria incidence (incidence rate ratio [IRR]=0.77, 95% CI 0.65 to 0.91) in the first 12 months following distribution relative to what would be expected had no distribution occurred, which was not sustained in the 13–24 month post-distribution period (IRR=0.97, 95% CI 0.75 to 1.28). Findings were similar when stratified by LLIN type. In the first 12 months following distribution, LLIN effectiveness was greater in the high-transmission sites (IRR=0.67, 95% CI 0.54 to 0.86) compared with the medium- (IRR=0.74, 95% CI 0.59 to 0.92) and low-transmission sites (IRR=0.87, 95% CI 0.56 to 1.32). Conclusion: This study demonstrated a modest reduction in malaria incidence following the distribution of newer-generation LLINs that was sustained for only 12 months, highlighting the need for improved strategies to maintain net effectiveness. Adjusting the frequency of universal coverage campaigns based on local malaria transmission intensity may enhance control efforts.

Introduction: Malaria remains a significant public health challenge globally, particularly in sub-Saharan Africa, where progress has stalled in recent years. Long-lasting insecticidal nets (LLINs) are a critical preventive tool against malaria. This study investigated the effectiveness of newer-generation LLINs following a universal coverage campaign in Uganda. Methods: Health facility data collected 36 months prior to LLIN distribution and 24 months after LLIN distribution were utilized from 64 sites that took part in a cluster randomized trial comparing two newer-generation LLINs (pyrethroid-PBO and pyrethroid-pyriproxyfen). Using an interrupted time series approach, we compared observed malaria incidence with counterfactual scenarios if no LLINs were distributed adjusting for precipitation, vegetation, seasonality, and care-seeking behavior. Analyses were also stratified by LLIN type and study-site level estimates of transmission intensity. Results: Overall, malaria incidence decreased from 827 cases per 1,000 person-years in the pre-distribution period to 538 per 1,000 person-years in the post-distribution period. Interrupted time series analyses estimated a 23% reduction in malaria incidence (IRR = 0.77, 95% CI 0.65-0.91) in the first 12 months following distribution relative to what would be expected had no distribution occurred, which was not sustained in the 13-24 month post-distribution period (IRR = 0.97, 95% CI 0.75-1.28). Findings were similar when stratified by LLIN type. In the first 12 months following distribution, LLIN effectiveness was greater in the high transmission sites (IRR = 0.67, 95% CI 0.54-0.86) compared to the medium (IRR = 0.74, 95% CI 0.59-0.92) and low transmission sites (IRR = 0.87, 95% CI 0.56-1.32). Conclusion: This study demonstrated a modest reduction in malaria incidence following the distribution of newer-generation LLINs that was sustained for only 12 months, highlighting the need for improved strategies to maintain net effectiveness. Adjusting the frequency of universal coverage campaigns based on local malaria transmission intensity may enhance control efforts.