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Abstract Cholera is a bacterial water-borne diarrheal disease transmitted via the fecal-oral route that causes high morbidity in sub-Saharan Africa and Asia. It is preventable with vaccination, and Water, Sanitation, and Hygiene (WASH) improvements. However, the impact of vaccination in endemic settings remains unclear. Cholera is endemic in the city of Kalemie, on the shore of Lake Tanganyika, in the Democratic Republic of Congo, where both seasonal mobility and the lake, a potential environmental reservoir, may promote transmission. Kalemie received a vaccination campaign and WASH improvements in 2013-2016. We assessed the impact of this intervention to inform future control strategies in endemic settings. We fit compartmental models considering seasonal mobility and environmentally-based transmission. We estimated the number of cases the intervention avoided, and the relative contributions of the elements promoting local cholera transmission. We estimated the intervention avoided 5,259 cases (95% credible interval: 1,576.6-11,337.8) over 118 weeks. Transmission did not rely on seasonal mobility and was primarily environmentally-driven. Removing environmental exposure or contamination could control local transmission. Repeated environmental exposure could maintain high population immunity and decrease the impact of vaccination in similar endemic areas. Addressing environmental exposure and contamination should be the primary target of interventions in such settings. Author summaryCholera is a major global health concern that causes high morbidity. It is a bacterial water-borne disease that can be transmitted via the fecal-oral route or the ingestion of contaminated water. Hence, both population mobility and environmental exposure can promote cholera persistence. The primary tools to prevent cholera include vaccination and Water, Sanitation, and Hygiene (WASH) improvements. The effectiveness of these interventions is well understood in epidemic settings, but their impact in endemic settings is unclear. Achieving cholera elimination requires disentangling the contributors to transmission, specifically population mobility and aquatic reservoirs, and assessing the impact of interventions performed in endemic settings.This study focuses on Kalemie, a cholera endemic city in the Democratic Republic of Congo, on shore of a lake that serves as a potential environmental reservoir. It quantifies the short-term impact of an intervention that used targeted vaccination and WASH. The study shows that the impact of vaccination was dampened by very high background immunity due to constant environmental exposure. This suggests that WASH improvements should be the primary intervention in such settings despite the time- and resource-intensive nature of implementation. 

Human movement and population connectivity inform infectious disease management. Remote data, particularly mobile phone usage data, are frequently used to track mobility in outbreak response efforts without measuring representation in target populations. Using a detailed interview instrument, we measure population representation in phone ownership, mobility, and access to healthcare in a highly mobile population with low access to health care in Namibia, a middle-income country. We find that 1) phone ownership is both low and biased by gender, 2) phone ownership is correlated with differences in mobility and access to healthcare, and 3) reception is spatially unequal and scarce in non-urban areas. We demonstrate that mobile phone data do not represent the populations and locations that most need public health improvements. Finally, we show that relying on these data to inform public health decisions can be harmful with the potential to magnify health inequities rather than reducing them. To reduce health inequities, it is critical to integrate multiple data streams with measured, non-overlapping biases to ensure data representativeness for vulnerable populations. 

Abstract Analyses of transient dynamics are critical to understanding infectious disease transmission and persistence. Identifying and predicting transients across scales, from within-host to community-level patterns, plays an important role in combating ongoing epidemics and mitigating the risk of future outbreaks. Moreover, greater emphases on non-asymptotic processes will enable timely evaluations of wildlife and human diseases and lead to improved surveillance efforts, preventive responses, and intervention strategies. Here, we explore the contributions of transient analyses in recent models spanning the fields of epidemiology, movement ecology, and parasitology. In addition to their roles in predicting epidemic patterns and endemic outbreaks, we explore transients in the contexts of pathogen transmission, resistance, and avoidance at various scales of the ecological hierarchy. Examples illustrate how (i) transient movement dynamics at the individual host level can modify opportunities for transmission events over time; (ii) within-host energetic processes often lead to transient dynamics in immunity, pathogen load, and transmission potential; (iii) transient connectivity between discrete populations in response to environmental factors and outbreak dynamics can affect disease spread across spatial networks; and (iv) increasing species richness in a community can provide transient protection to individuals against infection. Ultimately, we suggest that transient analyses offer deeper insights and raise new, interdisciplinary questions for disease research, consequently broadening the applications of dynamical models for outbreak preparedness and management. 

The scale and accessibility of passive global surveillance have rapidly increased over time. This provides an opportunity to calibrate the performance of models, algorithms, and reflectance ratios between remote-sensing devices. Here, we test the sensitivity and specificity of the Eucalypt chlorophyll-a reflectance ratio (ECARR) and Eucalypt chlorophyll-b reflectance ratio (ECBRR) to remotely identify eucalypt vegetation in Queensland, Australia. We compare the reflectance ratio values from Sentinel-2 and Planet imagery across four sites of known vegetation composition. All imagery was transformed to reflectance values, and Planet imagery was additionally scaled to harmonize across Planet scenes. ECARR can identify eucalypt vegetation remotely with high sensitivity but shows low specificity and is impacted by the density of the vegetation. ECBRR reflectance ratios show similar sensitivity and specificity when identifying eucalypt vegetation but with values an order of magnitude smaller than ECARR. We find that ECARR was better at identifying eucalypt vegetation in the Sentinel-2 imagery than Planet imagery. ECARR can serve as a general chlorophyll indicator but is not a specific index to identify Eucalyptus vegetation with certainty. 

Abstract Pathogens can spill over and infect new host species by overcoming a series of ecological and biological barriers. Hendra virus (HeV) circulates in Australian flying foxes and provides a data‐rich study system for identifying environmental drivers underlying spillover events. The frequency of spillover events to horses has varied interannually since the virus was first discovered in 1994. These observations suggest that HeV spillover events are driven, in part, by environmental factors, including loss of flying fox habitat and climate variability.We explicitly examine the impact of environmental variation on the risk of HeV spillover at three spatial scales relevant to this system. We use a dataset of 60 spillover events and boosted regression tree methods to identify environmental features (including concurrent and lagged temperature, rainfall, vegetation indices, land cover, and climate indices) at three spatial scales (1‐km, 20‐km, 100‐km radii) associated with horse contacts and reservoir species ecology.We find that temperature, local (1‐km radius) human population density, and landscape (100‐km radius) forest cover and pasture are the most influential environmental features associated with HeV spillover risk. By including multiple spatial scales and temporal lags in environmental features, we can more accurately quantify risk across space and time than with models that use a single scale. For example, high quality vegetation at the local scale and within a foraging radius (20‐km) in the concurrent month and previous years, combined with poorer quality vegetation at the landscape scale in the concurrent month increase risk of HeV spillover. These and other environmental associations likely influence the dynamic foraging behaviour of reservoir flying foxes and drive contacts that facilitate spillover into horse populations.Synthesis and application: Current management of HeV spillover focuses on local‐scale interventions – primarily through vaccination and detection of infected horses. Our study finds that HeV spillover risk is also driven by environmental changes over much larger scales and demonstrates management practices would benefit from incorporating landscape interventions alongside local interventions. 

Abstract Vector‐borne diseases (VBDs) are embedded within complex socio‐ecological systems. While research has traditionally focused on the direct effects of VBDs on human morbidity and mortality, it is increasingly clear that their impacts are much more pervasive. VBDs are dynamically linked to feedbacks between environmental conditions, vector ecology, disease burden, and societal responses that drive transmission. As a result, VBDs have had profound influence on human history. Mechanisms include: (1) killing or debilitating large numbers of people, with demographic and population‐level impacts; (2) differentially affecting populations based on prior history of disease exposure, immunity, and resistance; (3) being weaponised to promote or justify hierarchies of power, colonialism, racism, classism and sexism; (4) catalysing changes in ideas, institutions, infrastructure, technologies and social practices in efforts to control disease outbreaks; and (5) changing human relationships with the land and environment. We use historical and archaeological evidence interpreted through an ecological lens to illustrate how VBDs have shaped society and culture, focusing on case studies from four pertinent VBDs: plague, malaria, yellow fever and trypanosomiasis. By comparing across diseases, time periods and geographies, we highlight the enormous scope and variety of mechanisms by which VBDs have influenced human history.