Genetic Assignment Methods for Gaining Insight into the Management of Infectious Disease by Understanding Pathogen, Vector, and Host Movement

For many pathogens with environmental stages, or those carried by vectors or intermediate hosts, disease transmission is strongly influenced by pathogen, host, and vector movements across complex landscapes, and thus quantitative measures of movement rate and direction can reveal new opportunities for disease management and intervention. Genetic assignment methods are a set of powerful statistical approaches useful for establishing population membership of individuals. Recent theoretical improvements allow these techniques to be used to cost-effectively estimate the magnitude and direction of key movements in infectious disease systems, revealing important ecological and environmental features that facilitate or limit transmission. Here, we review the theory, statistical framework, and molecular markers that underlie assignment methods, and we critically examine recent applications of assignment tests in infectious disease epidemiology. Research directions that capitalize on use of the techniques are discussed, focusing on key parameters needing study for improved understanding of patterns of disease

Early economic evaluation to identify the necessary test characteristics of a new typhoid test to be cost-effective in Ghana

Background In Ghana, there are issues with the diagnosis of typhoid fever; these include delays in diagnosis, concerns about the accuracy of current tests, and lack of availability. These issues highlight the need for the development of a rapid, accurate, and easily accessible diagnostic test. The aim of this study was to conduct an early economic analysis of a hypothetical rapid test for typhoid fever diagnosis in Ghana and identify the necessary characteristics of the test for it to be cost effective in Ghana. Methods An early cost-utility analysis was conducted using a decision tree parameterized with secondary data sources, with reasonable assumptions made for unknown parameters. The patient population considered is individuals presenting with symptoms suggestive of typhoid fever at a healthcare facility in Ghana; a time horizon of 180 days and the Ghanaian national health service perspective were adopted for the analysis. Extensive sensitivity analysis was undertaken, including headroom analysis. Results The results here show that for a hypothetical test to perform better than the existing test (Widal) in terms of QALYs gained and cost effectiveness, it is necessary for it to have a high specificity (at least 70%) and should not be priced more than US$4. The overall value of conducting research to reduce uncertainty (over 5 years) is US$3287. Conclusion The analysis shows the potential for the hypothetical test to replace the Widal test and the market potential of developing a new test in the Ghanaian setting

Mapping the spatial variability of HIV infection in Sub-Saharan Africa: Effective information for localized HIV prevention and control

Under the premise that in a resource-constrained environment such as Sub-Saharan Africa it is not possible to do everything, to everyone, everywhere, detailed geographical knowledge about the HIV epidemic becomes essential to tailor programmatic responses to specific local needs. However, the design and evaluation of national HIV programs often rely on aggregated national level data. Against this background, here we proposed a model to produce high-resolution maps of intranational estimates of HIV prevalence in Kenya, Malawi, Mozambique and Tanzania based on spatial variables. The HIV prevalence maps generated highlight the stark spatial disparities in the epidemic within a country, and localize areas where both the burden and drivers of the HIV epidemic are concentrated. Under an era focused on optimal allocation of evidence-based interventions for populations at greatest risk in areas of greatest HIV burden, as proposed by the Joint United Nations Programme on HIV/AIDS (UNAIDS) and the United States President’s Emergency Plan for AIDS Relief (PEPFAR), such maps provide essential information that strategically targets geographic areas and populations where resources can achieve the greatest impact

Analytical methods for quantifying environmental connectivity for the control and surveillance of infectious disease spread

The sustained transmission and spread of environmentally mediated infectious diseases is governed in part by the dispersal of parasites, disease vectors and intermediate hosts between sites of transmission. Functional geospatial models can be used to quantify and predict the degree to which environmental features facilitate or limit connectivity between target populations, yet typical models are limited in their geographical and analytical approach, providing simplistic, global measures of connectivity and lacking methods to assess the epidemiological implications of fine-scale heterogeneous landscapes. Here, functional spatial models are applied to problems of surveillance and control of the parasitic blood fluke Schistosoma japonicum and its intermediate snail host Oncomelania haupensis in western China. We advance functional connectivity methods by providing an analytical framework to (i) identify nodes of transmission where the degree of connectedness to other villages, and thus the potential for disease spread, is higher than is estimated using Euclidean distance alone and (ii) (re)organize transmission sites into disease surveillance units based on second-order relationships among nodes using non-Euclidean distance measures, termed effective geographical distance (EGD). Functional environmental models are parametrized using ecological information on the target organisms, and pair-wise distributions of inter-node EGD are estimated. A Monte Carlo rank product analysis is presented to identify nearby nodes under alternative distance models. Nodes are then iteratively embedded into EGD space and clustered using a k-means algorithm to group villages into ecologically meaningful surveillance groups. A consensus clustering approach is taken to derive the most stable cluster structure. The results indicate that novel relationships between nodes are revealed when non-Euclidean, ecologically determined distance measures are used to quantify connectivity in heterogeneous landscapes. These connections are not evident when analysing nodes in Euclidean space, and thus surveillance and control activities planned using Euclidean distance measures may be suboptimal. The methods developed here provide a quantitative framework for assessing the effectiveness of ecologically grounded surveillance systems and of control and prevention strategies for environmentally mediated diseases

Mobility is Associated with Higher-risk Sexual Partnerships Among Both Men and Women in Co-resident Couples in Rural Kenya and Uganda: A Longitudinal Cohort Study.

Population mobility is associated with higher-risk sexual behaviors in sub-Saharan Africa and is a key driver of the HIV epidemic. We conducted a longitudinal cohort study to estimate associations between recent mobility (overnight travel away from home in past six months) or migration (changes of residence over defined geopolitical boundaries) and higher-risk sexual behavior among co-resident couples (240 couples aged ≥ 16) from 12 rural communities in Kenya and Uganda. Data on concurrent mobility and sexual risk behaviors were collected every 6-months between 2015 and 2020. We used sex-pooled and sex-stratified multilevel models to estimate associations between couple mobility configurations (neither partner mobile, male mobile/female not mobile, female mobile/male not mobile, both mobile) and the odds of higher-risk (casual, commercial sex worker/client, one night stand, inherited partner, stranger) and concurrent sexual partnerships based on who was mobile. On average across all time points and subjects, mobile women were more likely than non-mobile women to have a higher-risk partner; similarly, mobile men were more likely than non-mobile men to report a higher-risk partnership. Men with work-related mobility versus not had higher odds of higher-risk partnerships. Women with work-related mobility versus not had higher odds of higher-risk partnerships. Couples where both members were mobile versus neither had greater odds of higher-risk partnerships. In analyses using 6-month lagged versions of key predictors, migration events of men, but not women, preceded higher-risk partnerships. Findings demonstrate HIV risks for men and women associated with mobility and the need for prevention approaches attentive to the risk-enhancing contexts of mobility

Condom, modern contraceptive, and dual method use are associated with HIV status and relationship concurrency in a context of high mobility: A cross-sectional study of women of reproductive age in rural Kenya and Uganda, 2016

ObjectivesMobility (international/internal migration, and localized mobility) is a key driver of the HIV epidemic. While mobility is associated with higher-risk sexual behavior in women, a possible association with condom, modern contraceptive, and dual method use among women living with HIV (WLHIV), is unknown. In addition, HIV status and sexual behaviors such as relationship concurrency may also affect condom, modern contraceptive, and dual method use.Study designWe surveyed sexually active women (N = 1067) aged 15 to 49 in 12 communities in Kenya and Uganda participating in a test-and-treat trial in 2015 to 2016. Generalized (unordered) multinomial logistic regression models accounting for community clustering examined associations between mobility (overnight travel away from home in past 6 months and any migration within past 2 years) and condom, modern contraceptive (i.e., oral contraceptive pills, injectables, intrauterine devices, implants, vasectomy, tubal ligation; excluding male/female condoms), and dual method use within past 6 months, adjusting for key covariates such as HIV status and relationship concurrency.ResultsWLHIV relative to HIV-negative women (ratios of relative risk [RRR] = 3.76, 95% confidence interval [CI]: 2.40-5.89), and women in concurrent relative to monogamous relationships (RRR = 4.03, 95% CI 1.9-8.50) had higher odds of condom use alone. In contraceptive use models, WLHIV relative to HIV-negative women were less likely to use modern contraceptive methods alone (RRR = 0.51, 95% CI 0.36-0.73). Relationship concurrency (RRR = 4.51, 95% CI 2.10-9.67) and HIV status (RRR = 3.97, 95% CI 2.43-6.50) were associated with higher odds of dual method use while mobility was marginally associated with higher odds of dual method use (RRR = 1.65, 95% CI 0.99-2.77, p = 0.057).ConclusionsMobility had a potential impact on dual method use in Kenya and Uganda. In addition, our findings highlight that WLHIV were using condoms and dual methods more, but modern contraceptives less, than HIV-negative women. Those in concurrent relationships were also more likely to use condoms or dual methods. These findings suggest that in a context of high mobility, women may be appropriately assessing risks and taking measures to protect themselves and their partners from unintended pregnancies and acquisition and transmission of HIV.ImplicationsOur findings point to a need to strengthen accessibility of sexual and reproductive health services for both mobile and residentially stable women in settings of high mobility and high HIV prevalence

Prioritizing Countries for Interventions to Reduce Child Mortality: Tools for Maximizing the Impact of Mass Drug Administration of Azithromycin

<div><p>Background</p><p>As new interventions to reduce childhood mortality are identified, careful consideration must be given to identifying populations that could benefit most from them. Promising reductions in childhood mortality reported in a large cluster randomized trial of mass drug administration (MDA) of azithromycin (AZM) prompted the development of visually compelling, easy-to-use tools that synthesize country-specific data on factors that would influence both potential AZM benefit and MDA implementation success.</p><p>Methodology/Principal Findings</p><p>We assessed the <i>opportunity</i> to reduce mortality and the <i>feasibility</i> of implementing such a program, creating <i>Opportunity</i> and <i>Feasibility Indices</i>, respectively. Countries with high childhood mortality were included. A <i>Country Ranking Index</i> combined key variables from the previous two Indices and applied a scoring system to identify high-priority countries. We compared four scenarios with varying weights given to each variable.</p><p>Twenty-five countries met inclusion criteria. We created easily visualized tools to display the results of the Opportunity and Feasibility Indices. The Opportunity Index revealed substantial variation in the opportunity for an MDA of AZM program to reduce mortality, even among countries with high overall childhood mortality. The Feasibility Index demonstrated that implementing such a program would be most challenging in the countries that could see greatest benefit. Based on the Country Ranking Index, Equatorial Guinea would benefit the most from the MZA of AZM in three of the four scenarios we tested.</p><p>Conclusions/Significance</p><p>These visually accessible tools can be adapted or refined to include other metrics deemed important by stakeholders, and provide a quantitative approach to prioritization for intervention implementation. The need to explicitly state metrics and their weighting encourages thoughtful and transparent decision making. The objective and data-driven approach promoted by the three Indices may foster more efficient use of resources.</p></div