scholarly journals Integrating Phylodynamic Techniques for Next-generation HIV Surveillance in Florida

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Shannan N. Rich ◽  
Carla Mavian ◽  
Veronica Richards ◽  
Robert Cook ◽  
Mattia Prosperi ◽  
...  
Keyword(s):  
Public Health ◽  
Real Time ◽  
Hiv Transmission ◽  
The United States ◽  
Hiv Incidence ◽  
Next Generation ◽  
Viral Pathogen ◽  
Hiv Surveillance ◽  
Targeted Interventions ◽  
Precision Public Health

ObjectiveWe aim to 1) develop and implement a novel theoretical and technical framework able to dynamically model HIV transmission clusters in near-real time; 2) validate the model with real data; and 3) host focus groups with governmental stakeholders to identify optimal strategies for precision public health interventions.IntroductionReducing HIV incidence requires a ‘precision public health’ approach encompassing prevention campaigns, targeted interventions, and ‘next-generation’ surveillance through multimodal instruments, including sequencing. Molecular epidemiology methods (phylogenetics and phylodynamics) have recently gained traction for use in identifying and tracking epidemic transmission clusters, as well as reconstructing the demographic history of viral pathogen populations. However, such methods are not equipped to identify both transmission clusters and their corresponding dynamics in real time, and transmission clusters are assumed to be unrealistically static over the course of the epidemic. We will focus on the ongoing HIV epidemic in Florida, which has one of the highest HIV incidence rates in the United States. Although key HIV transmission risk groups have been identified in Florida through classical epidemiology surveillance methods, there remains a critical need for detection and tracking of expanding transmission clusters in near-real time.MethodsWe propose to develop and test a new phylodynamic method, HIV Dynamic Identification of Transmission Epicenters (HIV-DYNAMITE), that will support existing HIV surveillance efforts. In collaboration with the Florida Department of Health (FDOH), we will leverage an existing dataset, which contains over 44,300 sequences, and apply HIV-DYNAMITE to identify transmission clusters and infer growth trends of these clusters within epidemics. HIV-DYNAMITE will also be used to identify and predict infection trends and virus spread by conferring with demographic data. The system will be validated using newly obtained longitudinal data. Focus group discussions with the FDOH, the Centers for Disease Control and Prevention (CDC), and other stakeholders will be conducted to confer how to employ HIV-DYNAMITE into statewide informatics systems and to design future intervention strategies.ResultsThese methods are still under development.ConclusionsIn conclusion, this study aims to both complement and enhance existing efforts, such as the CDC’s HIV-TRACE, which is currently based on sequence data alone and lacks dynamic or geographic spread components. This approach has the potential to be incorporated into other settings within the US with comparable statewide surveillance and virus sequencing coverage through national reference centers.

scholarly journals Challenges in evaluating the use of viral sequence data to identify HIV transmission networks for public health

2020 ◽  
Vol 12 (s1) ◽  
Author(s):  
Rami Kantor ◽  
John P. Fulton ◽  
Jon Steingrimsson ◽  
Vladimir Novitsky ◽  
Mark Howison ◽  
...  
Keyword(s):  
Public Health ◽  
United States ◽  
Hiv Transmission ◽  
Sequence Data ◽  
The United States ◽  
Viral Sequence ◽  
Transmission Networks ◽  
New Methods ◽  
Hiv Epidemic ◽  
The World

AbstractGreat efforts are devoted to end the HIV epidemic as it continues to have profound public health consequences in the United States and throughout the world, and new interventions and strategies are continuously needed. The use of HIV sequence data to infer transmission networks holds much promise to direct public heath interventions where they are most needed. As these new methods are being implemented, evaluating their benefits is essential. In this paper, we recognize challenges associated with such evaluation, and make the case that overcoming these challenges is key to the use of HIV sequence data in routine public health actions to disrupt HIV transmission networks.

Are We Prepared for Precision Public Health? An Examination of Genomics Content in Graduate Public Health Programs

2021 ◽  
pp. 003335492110557
Author(s):  
Karen L. Niemchick ◽  
Ally Goerge ◽  
Amy H. Ponte
Keyword(s):  
Public Health ◽  
United States ◽  
The United States ◽  
Genome Project ◽  
Public Health Workforce ◽  
Public Health Genomics ◽  
Master Of Public Health ◽  
Precision Public Health ◽  
Populations At Risk ◽  
Genomics Education

Objective With the completion of the Human Genome Project and swift development of genomic technologies, public health practitioners can use these advancements to more precisely target disease interventions to populations at risk. To integrate these innovations into better health outcomes, public health professionals need to have at least a basic understanding of genomics within various disciplines of public health. This descriptive study focused on the current level of genomics content in accredited master of public health (MPH) programs in the United States. Methods We conducted an internet search on all 171 Council on Education for Public Health (CEPH)–accredited MPH programs in the United States for genomics content in required and elective courses using the search terms “genetics,” “genomics,” and “molecular.” Results Of the 171 CEPH-accredited MPH programs examined, 52 (30.4%) schools and programs in 34 states offered some type of genomics education. Thirty-five (20.5%) schools and programs had a course in genetic epidemiology, 29 (16.9%) had a course in genetic biostatistics or bioinformatics, and 17 (9.9%) had a course in general public health genomics. The remaining 119 offered no course with a focus on genetics or genomics. In addition, some electives or specifically focused courses related to genomics were offered. Conclusion We found inadequate training in public health genomics for MPH students. To realize the promise of precision public health and to increase the understanding of genomics among the public health workforce, MPH programs need to find ways to integrate genomics education into their curricula.

scholarly journals Grappling With Complex Food Systems to Reduce Obesity: A US Public Health Challenge

2018 ◽  
Vol 133 (1_suppl) ◽  
pp. 44S-53S ◽  
Author(s):  
Anne Barnhill ◽  
Anne Palmer ◽  
Christine M. Weston ◽  
Kelly D. Brownell ◽  
Kate Clancy ◽  
...  
Keyword(s):  
Public Health ◽  
Environmental Sustainability ◽  
Food Systems ◽  
Food System ◽  
The United States ◽  
Community Members ◽  
Targeted Interventions ◽  
Health Community ◽  
Policies And Programs ◽  
State Programs

Despite 2 decades of effort by the public health community to combat obesity, obesity rates in the United States continue to rise. This lack of progress raises fundamental questions about the adequacy of our current approaches. Although the causes of population-wide obesity are multifactorial, attention to food systems as potential drivers of obesity has been prominent. However, the relationships between broader food systems and obesity are not always well understood. Our efforts to address obesity can be advanced and improved by the use of systems approaches that consider outcomes of the interconnected global food system, including undernutrition, climate change, the environmental sustainability of agriculture, and other social and economic concerns. By implementing innovative local and state programs, taking new approaches to overcome political obstacles to effect policy, and reconceptualizing research needs, we can improve obesity prevention efforts that target the food systems, maximize positive outcomes, and minimize adverse consequences. We recommend strengthening innovative local policies and programs, particularly those that involve community members in identifying problems and potential solutions and that embrace a broad set of goals beyond making eating patterns healthier. We also recommend undertaking interdisciplinary research projects that go beyond testing targeted interventions in specific populations and aim to build an understanding of the broader social, political, and economic context.

scholarly journals A collaborative multiyear, multimodel assessment of seasonal influenza forecasting in the United States

2019 ◽  
Vol 116 (8) ◽  
pp. 3146-3154 ◽  
Author(s):  
Nicholas G. Reich ◽  
Logan C. Brooks ◽  
Spencer J. Fox ◽  
Sasikiran Kandula ◽  
Craig J. McGowan ◽  
...  
Keyword(s):  
Public Health ◽  
United States ◽  
Real Time ◽  
Forecast Accuracy ◽  
The United States ◽  
Public Health Response ◽  
Public Health Decision ◽  
Health Decision Making ◽  
Health Response ◽  
Health Decision

Influenza infects an estimated 9–35 million individuals each year in the United States and is a contributing cause for between 12,000 and 56,000 deaths annually. Seasonal outbreaks of influenza are common in temperate regions of the world, with highest incidence typically occurring in colder and drier months of the year. Real-time forecasts of influenza transmission can inform public health response to outbreaks. We present the results of a multiinstitution collaborative effort to standardize the collection and evaluation of forecasting models for influenza in the United States for the 2010/2011 through 2016/2017 influenza seasons. For these seven seasons, we assembled weekly real-time forecasts of seven targets of public health interest from 22 different models. We compared forecast accuracy of each model relative to a historical baseline seasonal average. Across all regions of the United States, over half of the models showed consistently better performance than the historical baseline when forecasting incidence of influenza-like illness 1 wk, 2 wk, and 3 wk ahead of available data and when forecasting the timing and magnitude of the seasonal peak. In some regions, delays in data reporting were strongly and negatively associated with forecast accuracy. More timely reporting and an improved overall accessibility to novel and traditional data sources are needed to improve forecasting accuracy and its integration with real-time public health decision making.

scholarly journals Students’ Perspectives: How Will COVID-19 Shape the Social Determinants of Health and Our Future as Public Health Practitioners?

2020 ◽  
Vol 47 (6) ◽  
pp. 850-854
Author(s):  
Eliyas K. Asfaw ◽  
Emily S. Guo ◽  
Sarah S. Jang ◽  
Swathi R. Komarivelli ◽  
Katherine A. Lewis ◽  
...  
Keyword(s):  
Public Health ◽  
Health Inequities ◽  
The United States ◽  
Determinants Of Health ◽  
Next Generation ◽  
Public Health Professionals ◽  
The Social ◽  
Health Practitioners ◽  
To Come ◽  
Public Health Practitioners

We are the next generation of public health practitioners. As public health students, we acknowledge that the COVID-19 (coronavirus disease 2019) pandemic will continue to fundamentally alter the field that we are preparing to enter. We will be the first wave of public health professionals whose education is being shaped by this pandemic. For decades to come, we will be working to address the impacts of this pandemic. In this commentary, we are lending our voice to discuss and highlight the importance of considering the intersections of various determinants of health and COVID-19, including education, food insecurity, housing instability, and economic hardship. We provide a discussion on what is being done across the United States in attempts to reduce the growing health inequities. As the next generation of public health leaders, we believe that only by investing in these issues can we begin to address the social and economic impact of the COVID-19 pandemic.

scholarly journals Employing Molecular Phylodynamic Methods to Identify and Forecast HIV Transmission Clusters in Public Health Settings: A Qualitative Study

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 921
Author(s):  
Shannan N. Rich ◽  
Veronica L. Richards ◽  
Carla N. Mavian ◽  
William M. Switzer ◽  
Brittany Rife Magalis ◽  
...  
Keyword(s):  
Public Health ◽  
Hiv Transmission ◽  
Epidemiological Data ◽  
Growth Trajectories ◽  
Health Departments ◽  
Implementation Barriers ◽  
Molecular Surveillance ◽  
Hiv Surveillance ◽  
Health Strategy ◽  
Potential Strategy

Molecular HIV surveillance is a promising public health strategy for curbing the HIV epidemic. Clustering technologies used by health departments to date are limited in their ability to infer/forecast cluster growth trajectories. Resolution of the spatiotemporal dynamics of clusters, through phylodynamic and phylogeographic modelling, is one potential strategy to develop a forecasting tool; however, the projected utility of this approach needs assessment. Prior to incorporating novel phylodynamic-based molecular surveillance tools, we sought to identify possible issues related to their feasibility, acceptability, interpretation, and utility. Qualitative data were collected via focus groups among field experts (n = 17, 52.9% female) using semi-structured, open-ended questions. Data were coded using an iterative process, first through the development of provisional themes and subthemes, followed by independent line-by-line coding by two coders. Most participants routinely used molecular methods for HIV surveillance. All agreed that linking molecular sequences to epidemiological data is important for improving HIV surveillance. We found that, in addition to methodological challenges, a variety of implementation barriers are expected in relation to the uptake of phylodynamic methods for HIV surveillance. The participants identified several opportunities to enhance current methods, as well as increase the usability and utility of promising works-in-progress.

scholarly journals Application of Syndromic Surveillance to Describe Gunshot-related Injuries in Houston

2015 ◽  
Vol 7 (1) ◽  
Author(s):  
Ryan M. Arnold ◽  
Wesley McNeely ◽  
Kasimu Muhetaer ◽  
Biru Yang ◽  
Raouf R. Arafat
Keyword(s):  
Public Health ◽  
United States ◽  
Health Risk ◽  
Real Time ◽  
Emergency Departments ◽  
Syndromic Surveillance ◽  
The United States ◽  
Public Health Risk ◽  
The Past ◽  
Houston Area

Firearm-related injuries pose a substantial public health risk in the United States, and traditional means of studying this issue rely primarily on retrospective analyses. Syndromic surveillance, collected in over 30 Houston area emergency departments, is well suited to characterize and analyze gunshot injuries in the area in near real-time. Over the past two years, more than 900 gunshot-related injury visits were identified using this method, and ArcGIS effectively identified incident densities in ZIP codes throughout Houston. Most patients were males (86.3%), between the ages of 18 and 34 (64.7%).

scholarly journals Resurgence of Syphilis in the United States: An Assessment of Contributing Factors

2019 ◽  
Vol 12 ◽  
pp. 117863371988328 ◽  
Author(s):  
Rebecca Schmidt ◽  
Paul James Carson ◽  
Rick J Jansen
Keyword(s):  
Public Health ◽  
United States ◽  
Hiv Transmission ◽  
Systemic Disease ◽  
Premenopausal Women ◽  
The United States ◽  
Behavioral Factors ◽  
Prevention Strategies ◽  
Contributing Factors ◽  
Effective Prevention

In the last decade, there has been a marked resurgence of syphilis in the United States despite the availability of effective treatments and previously reliable prevention strategies. The majority of cases are among the population of men who have sex with men (MSM); however, there has also been a recent increase among premenopausal women, coinciding with a concerning rise of congenital cases. The resurgence of syphilis can be largely attributed to changing social and behavioral factors, especially among young MSM. The biological association of syphilis with human immunodeficiency virus (HIV) transmission and acquisition is particularly alarming because of the increased individual and healthcare burden. In addition, some individual actions and public health efforts that are meant to reduce the risk of acquiring HIV may actually lead to risk compensation that facilitates the transmission of syphilis. Untreated syphilis is associated with detrimental health outcomes; therefore, both effective prevention strategies and treatment of this systemic disease have important short-term and long-term public health implications. This article offers a review of social and behavioral factors contributing to the current resurgence and recommendations for reducing syphilis incidence through medical and public health prevention strategies.

scholarly journals Harmonization of Bordetella pertussis Real-Time PCR Diagnostics in the United States in 2012

2014 ◽  
Vol 53 (1) ◽  
pp. 118-123 ◽  
Author(s):  
Margaret M. Williams ◽  
Thomas H. Taylor ◽  
David M. Warshauer ◽  
Monte D. Martin ◽  
Ann M. Valley ◽  
...  
Keyword(s):  
Public Health ◽  
Real Time ◽  
Bordetella Pertussis ◽  
Real Time Pcr ◽  
The United States ◽  
Extraction Methods ◽  
Clinical Samples ◽  
Acid Extraction ◽  
Rt Pcr ◽  
Content Type

Real-time PCR (rt-PCR) is an important diagnostic tool for the identification ofBordetella pertussis,Bordetella holmesii, andBordetella parapertussis. Most U.S. public health laboratories (USPHLs) target IS481, present in 218 to 238 copies in theB. pertussisgenome and 32 to 65 copies inB. holmesii. The CDC developed a multitarget PCR assay to differentiateB. pertussis,B. holmesii, andB. parapertussisand provided protocols and training to 19 USPHLs. The 2012 performance exercise (PE) assessed the capability of USPHLs to detect these threeBordetellaspecies in clinical samples. Laboratories were recruited by the Wisconsin State Proficiency Testing program through the Association of Public Health Laboratories, in partnership with the CDC. Spring and fall PE panels contained 12 samples each of viableBordetellaand non-Bordetellaspecies in saline. Fifty and 53 USPHLs participated in the spring and fall PEs, respectively, using a variety of nucleic acid extraction methods, PCR platforms, and assays. Ninety-six percent and 94% of laboratories targeted IS481in spring and fall, respectively, in either singleplex or multiplex assays. In spring and fall, respectively, 72% and 79% of USPHLs differentiatedB. pertussisandB. holmesiiand 68% and 72% identifiedB. parapertussis. IS481cycle threshold (CT) values forB. pertussissamples had coefficients of variation (CV) ranging from 10% to 28%. Of the USPHLs that differentiatedB. pertussisandB. holmesii, sensitivity was 96% and specificity was 95% for the combined panels. The 2012 PE demonstrated increased harmonization of rt-PCRBordetelladiagnostic protocols in USPHLs compared to that of the previous survey.

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