Relationships between flood control and cholera in Matlab, Bangladesh

Implementation of flood control strategies has been empirically associated with rises in disease rates in the developing world. This research examines the impact of flood protection measures on cholera incidence among a rural Bangladeshi population. Using longitudinal health and demographic data collected over 21 years, analysis of clustering patterns and statistical relationships between cholera incidence and environmental factors was conducted for timeframes prior to and following the introduction of flood control in Matlab, Bangladesh. Results indicate that alteration of normal flooding patterns both temporally and spatially shifted cholera occurrence within the study area, and that these shifts demonstrate further differentiation when information on cholera strain is included in the analysis. These outcomes suggest that introducing flood protection to rural Bangladesh will have significant but complex effects on cholera incidence patterns

Space-time differentiation of drivers of and barriers to H5N1 avian influenza evolution in Vietnam

The emergence and re-emergence of human pathogens resistant to traditional medical treatment will present a challenge to the international public health community in the coming decades. Geography is uniquely positioned to examine the progressive evolution of pathogens across space and through time, and to link molecular change to interactions between population and environmental drivers. The widespread outbreak of H5N1 avian influenza across Asia in 2003, and its continued circulation within both poultry and human populations, presents an opportunity for the integration of traditional disease ecology with the emergent field of landscape genetics. Combining spatial statistical methods with genetic analytic techniques, geographic space is used to explore genetic evolution of H5N1 highly pathogenic avian influenza viruses (HPAIV) at the sub-national scale in Vietnam. This dissertation investigates the following topics: differences in genetic characteristics by species of isolation, location and timing of barriers to gene flow, and population-environment characteristics associated with increased viral evolution in Vietnam from 2003 to 2007. A variety of methods are used, including cluster analysis, multidimensional scaling, analysis of variance, and linear regression. Results indicate that genetic differentiation of these viruses varies significantly according to both their host species and the isolation time, but has a complex relationship with the geographic location of virus isolation. The effect of geographic space, and underlying landscape differentiation, does not appear to create boundaries to gene exchange across Vietnam. Taking these indicators of the influence of species, temporal characteristics and geographic space into account, the drivers of molecular evolution of H5N1 HPAIV in Vietnam are as predicted by a disease ecology framework, a combination of both population and environmental characteristics. These findings indicate that there are significant spatial and temporal effects on the evolution of H5N1 HPAIVs, and that local-level conditions can affect viral genetic evolution. Given that areas of rapid genetic evolution are more likely to produce a highly pathogenic virus capable of sustained human-to-human transmission, further exploration of spatial variation in molecular change is needed

Predicting Avian Influenza Co-Infection with H5N1 and H9N2 in Northern Egypt.

Human outbreaks with avian influenza have been, so far, constrained by poor viral adaptation to non-avian hosts. This could be overcome via co-infection, whereby two strains share genetic material, allowing new hybrid strains to emerge. Identifying areas where co-infection is most likely can help target spaces for increased surveillance. Ecological niche modeling using remotely-sensed data can be used for this purpose. H5N1 and H9N2 influenza subtypes are endemic in Egyptian poultry. From 2006 to 2015, over 20,000 poultry and wild birds were tested at farms and live bird markets. Using ecological niche modeling we identified environmental, behavioral, and population characteristics of H5N1 and H9N2 niches within Egypt. Niches differed markedly by subtype. The subtype niches were combined to model co-infection potential with known occurrences used for validation. The distance to live bird markets was a strong predictor of co-infection. Using only single-subtype influenza outbreaks and publicly available ecological data, we identified areas of co-infection potential with high accuracy (area under the receiver operating characteristic (ROC) curve (AUC) 0.991)

Genetics: A New Landscape for Medical Geography

The emergence and re-emergence of human pathogens resistant to medical treatment will present a challenge to the international public health community in the coming decades. Geography is uniquely positioned to examine the progressive evolution of pathogens across space and through time, and to link molecular change to interactions between population and environmental drivers. Landscape as an organizing principle for the integration of natural and cultural forces has a long history in geography, and, more specifically, in medical geography. Here, we explore the role of landscape in medical geography, the emergent field of landscape genetics, and the great potential that exists in the combination of these two disciplines. We argue that landscape genetics can enhance medical geographic studies of local-level disease environments with quantitative tests of how human-environment interactions influence pathogenic characteristics. In turn, such analyses can expand theories of disease diffusion to the molecular scale and distinguish the important factors in ecologies of disease that drive genetic change of pathogens

Highly Pathogenic H5N1 Avian Influenza Viruses Exhibit Few Barriers to Gene Flow in Vietnam

Locating areas where genetic change is inhibited can illuminate underlying processes that drive evolution of pathogens. The persistence of highly pathogenic H5N1 avian influenza in Vietnam since 2003, and the continuous molecular evolution of Vietnamese avian influenza viruses, indicates that local environmental factors are supportive not only of incidence but also of viral adaptation. This article explores whether gene flow is constant across Vietnam, or whether there exist boundary areas where gene flow exhibits discontinuity. Using a dataset of 125 highly pathogenic H5N1 avian influenza viruses, principal components analysis and wombling analysis are used to indicate the location, magnitude, and statistical significance of genetic boundaries. Results show that a small number of geographically minor boundaries to gene flow in highly pathogenic H5N1 avian influenza viruses exist in Vietnam, but that overall there is little division in genetic exchange. This suggests that differences in genetic characteristics of viruses from one region to another are not the result of barriers to H5N1 viral exchange in Vietnam, and that H5N1 avian influenza is able to spread relatively unimpeded across the country

Genetic Variation of Highly Pathogenic H5N1 Avian Influenza Viruses in Vietnam Shows Both Species-Specific and Spatiotemporal Associations

Domestic poultry act as a reservoir for persistent H5N1 endemicity in Vietnam, and the circulation of poultry flocks across farms and to market is thought to drive the spatial movement and evolution of avian influenza viruses. Using a dataset of complete or nearly full genomic sequences from highly pathogenic H5N1 avian influenza viruses collected in domestic poultry in Vietnam from 2003 to 2007, we explore potential differences in genetic characteristics according to species of isolation and the spatio-temporal characteristics of the viruses. Clustering algorithms and analysis of variance indicate that H5N1 viruses in Vietnam show differences in the amount of genetic change that chicken viruses experience as compared to duck viruses, with duck viruses showing higher rates of molecular evolution on all eight of influenza's gene segments. There also exist distinct patterns of genetic differentiation according to the year in which they were isolated. These findings suggest that genetic evolution of avian influenza viruses is continuous through time but could also be mediated by the species in which the viruses occur, information which has implications for prevention efforts

Spatio-temporal clustering of cholera: The impact of flood control in Matlab, Bangladesh, 1983–2003

Introducing flood control to an area of endemic waterborne diseases could have significant impacts on spatio-temporal occurrence of cholera. Using 21-years of data from Bangladesh, we conducted cluster analysis to explore changes in spatial and temporal distribution of cholera incidence since construction of flood control structures. Striking changes in temporal cluster patterns emerged, including a shift from dry season to rainy season clusters following flood protection and delayed clustering inside the protected areas. Spatial differences in pre-flood protection and post-protection cholera clusters are weaker. Changes in spatio-temporal cholera clustering, associated with implementation of flood protection strategies, could affect local cholera prevention efforts

Diarrheal disease risk in rural Bangladesh decreases as tubewell density increases: a zero-inflated and geographically weighted analysis

Abstract Background This study investigates the impact of tubewell user density on cholera and shigellosis events in Matlab, Bangladesh between 2002 and 2004. Household-level demographic, health, and water infrastructure data were incorporated into a local geographic information systems (GIS) database. Geographically-weighted regression (GWR) models were constructed to identify spatial variation of relationships across the study area. Zero-inflated negative binomial regression models were run to simultaneously measure the likelihood of increased magnitude of disease events and the likelihood of zero cholera or shigellosis events. The aim of this study was to examine the effect of tubewell density on both the occurrence of diarrheal disease and the magnitude of diarrheal disease incidence. Results In Matlab, households with greater tubewell density were more likely to report zero cholera or shigellosis events. Results for both cholera and shigellosis GWR models suggest that tubewell density effects are spatially stationary and the use of non-spatial statistical methods is appropriate. Conclusions Increasing the amount of drinking water available to households through increased density of tubewells contributed to lower reports of cholera and shigellosis events in rural Bangladesh. Our findings demonstrate the importance of tubewell installation and access to groundwater in reducing diarrheal disease events in the developing world

Spatial Epidemiology of Recently Acquired HIV Infections across Rural and Urban Areas of North Carolina

Transmission of HIV continues in the United States (US), despite prevention efforts aimed at education and treatment. Concurrently, drug resistance in HIV, particularly in patients being infected with HIV for the first time, poses a threat to the continued success of treatment for HIV positive individuals. In North Carolina, nearly one in five individuals with acute HIV infection (AHI) is infected with a drug-resistant strain, a phenomenon known as transmitted drug resistance (TDR). Few studies of AHI or TDR take into account both the spatial aspects of residence at time of infection and the genetic characteristics of the viruses, and questions remain about how viruses are transmitted across space and the rural-urban divide. Using AHI strains from North Carolina, we examined whether differences exist in the spatial patterns of AHI versus AHI with TDR, as well as whether the genetic characteristics of these HIV infections vary by rural-urban status and across Health Service Areas. The highest amounts of TDR were detected in persons under age 30, African Americans, and men who have sex with men (MSM) - similar to the populations where the highest numbers of AHI without TDR are observed. Nearly a quarter of patients reside in rural areas, and there are no significant differences between rural and urban residence among individuals infected with drug resistant or drug susceptible viruses. We observe similar levels of genetic distance between HIV found in rural and urban areas, indicating that viruses are shared across the rural-urban divide. Genetic differences are observed, however, across Health Service Areas, suggesting that local areas are sites of genetic differentiation in viruses being transmitted to newly infected individuals. These results indicate that future efforts to prevent HIV transmission need to be spatially targeted, focusing on local-level transmission in risky populations, in addition to statewide anti- HIV efforts

Changing spatial patterns and increasing rurality of HIV prevalence in the Democratic Republic of the Congo between 2007 and 2013

The Democratic Republic of the Congo (DRC) has one of the lowest HIV prevalence in sub-Saharan Africa, estimated at 1.1% [0.9-1.3] of adults aged 15-49 in 2013 (UNAIDS). Within the 2 million km2 country, however, there exists spatial variation in HIV prevalence, with the highest HIV prevalence observed in the large cities of Kinshasa and Lubumbashi. Globally, HIV is an increasingly rural disease, diffusing outwards from urban centers of high HIV prevalence to places where HIV was previously absent or present at very low levels. Utilizing data collected during Demographic and Health Surveillance (DHS) in 2007 and 2013 in the DRC, we sought to update the map of HIV prevalence in the DRC as well as to explore whether HIV in the DRC is an increasingly rural disease or remains confined to urban areas. Bayesian kriging and regression indicate that HIV prevalence in rural areas of the DRC is higher in 2013 than in 2007 and that increased distance to an urban area is no longer protective against HIV as it was in 2007. These findings suggest that HIV education, testing and prevention efforts need to diffuse from urban to rural areas just as HIV is doing