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 Integration of a recent infection testing algorithm into HIV surveillance in Ireland: improving HIV knowledge to target prevention

2019 ◽  
Vol 147 ◽  
Author(s):  
E. Robinson ◽  
J. Moran ◽  
K. O'Donnell ◽  
J. Hassan ◽  
H. Tuite ◽  
...  
Keyword(s):  
Hiv Transmission ◽  
Epidemiological Data ◽  
Hiv Knowledge ◽  
Recent Infection ◽  
Transmitted Infection ◽  
Sexually Transmitted ◽  
Hiv Surveillance ◽  
Infectious Disease Reporting ◽  
Prevention Interventions ◽  
Testing Algorithm

AbstractRecent infection testing algorithms (RITA) for HIV combine serological assays with epidemiological data to determine likely recent infections, indicators of ongoing transmission. In 2016, we integrated RITA into national HIV surveillance in Ireland to better inform HIV prevention interventions. We determined the avidity index (AI) of new HIV diagnoses and linked the results with data captured in the national infectious disease reporting system. RITA classified a diagnosis as recent based on an AI < 1.5, unless epidemiological criteria (CD4 count <200 cells/mm3; viral load <400 copies/ml; the presence of AIDS-defining illness; prior antiretroviral therapy use) indicated a potential false-recent result. Of 508 diagnoses in 2016, we linked 448 (88.1%) to an avidity test result. RITA classified 12.5% of diagnoses as recent, with the highest proportion (26.3%) amongst people who inject drugs. On multivariable logistic regression recent infection was more likely with a concurrent sexually transmitted infection (aOR 2.59; 95% CI 1.04–6.45). Data were incomplete for at least one RITA criterion in 48% of cases. The study demonstrated the feasibility of integrating RITA into routine surveillance and showed some ongoing HIV transmission. To improve the interpretation of RITA, further efforts are required to improve completeness of the required epidemiological data.

scholarly journals A public health model for the molecular surveillance of HIV transmission in San Diego, California

AIDS ◽  
2009 ◽  
Vol 23 (2) ◽  
pp. 225-232 ◽  
Author(s):  
Davey M Smith ◽  
Susanne J May ◽  
Samantha Tweeten ◽  
Lydia Drumright ◽  
Mary E Pacold ◽  
...  
Keyword(s):  
Public Health ◽  
San Diego ◽  
Hiv Transmission ◽  
Molecular Surveillance ◽  
Public Health Model ◽  
Health Model

scholarly journals Using HIV Surveillance Data to Link People to HIV Medical Care, 5 US States, 2012-2015

2018 ◽  
Vol 133 (4) ◽  
pp. 385-391 ◽  
Author(s):  
John Beltrami ◽  
Odessa Dubose ◽  
Reginald Carson ◽  
Janet C. Cleveland
Keyword(s):  
Public Health ◽  
Hiv Prevention ◽  
Linkage To Care ◽  
Surveillance Data ◽  
Hiv Care ◽  
Performance Standard ◽  
Health Staff ◽  
Health Departments ◽  
Hiv Surveillance ◽  
Prevention Activities

Introduction: From 2012 through 2015, the Centers for Disease Control and Prevention (CDC) provided funding to 5 health departments for demonstration projects using HIV surveillance data to link people with newly diagnosed HIV to care. We assessed how well these health departments established linkage to care, how the demonstration projects helped them with this work, and if they sustained these activities after CDC funding ended. Materials and Methods: We obtained quantitative and qualitative data on linkage-to-care activities from health department communications and progress reports submitted to CDC. We calculated and combined linkage-to-care results for the 5 health departments, and we compared these results with the combined linkage-to-care results for 61 health departments that received CDC funding for routine HIV prevention activities (eg, HIV testing, linkage to and reengagement in HIV care, HIV partner services) and for the same 5 health departments when they used only routine HIV prevention activities for linkage to care. Results: Of 1269 people with a new HIV diagnosis at the 5 health departments, 1124 (89%) were linked to care, a result that exceeded the 2010-2015 National HIV/AIDS Strategy goal (85%), the CDC Funding Opportunity Announcement performance standard (80%), and combined results for the 61 health departments (63%) and the same 5 health departments (66%) using routine HIV prevention activities. Benefits of the projects were improved collaboration and coordination and more accurate, up-to-date surveillance data. All health departments continued linkage-to-care activities after funding ended. Practice Implications: Using HIV surveillance data to link people with HIV to care resulted in substantial clinical and public health benefits. Our observations underscore the importance of collaboration among medical providers, public health staff members, community-based organizations, and people with HIV to ensure the best possible clinical and public health outcomes.

scholarly journals What Should Health Departments Do with HIV Sequence Data?

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 1018
Author(s):  
Ethan Romero-Severson ◽  
Arshan Nasir ◽  
Thomas Leitner
Keyword(s):  
Public Health ◽  
Sequence Data ◽  
Public Health Practice ◽  
Health Benefit ◽  
Routine Care ◽  
Health Departments ◽  
Genetic Sequencing ◽  
Hiv Surveillance ◽  
Hiv Epidemic ◽  
Health Authorities

Many countries and US states have mandatory statues that require reporting of HIV clinical data including genetic sequencing results to the public health departments. Because genetic sequencing is a part of routine care for HIV infected persons, health departments have extensive sequence collections spanning years and even decades of the HIV epidemic. How should these data be used (or not) in public health practice? This is a complex, multi-faceted question that weighs personal risks against public health benefit. The answer is neither straightforward nor universal. However, to make that judgement—of how genetic sequence data should be used in describing and combating the HIV epidemic—we need a clear image of what a phylogenetically enhanced HIV surveillance system can do and what benefit it might provide. In this paper, we present a positive case for how up-to-date analysis of HIV sequence databases managed by health departments can provide unique and actionable information of how HIV is spreading in local communities. We discuss this question broadly, with examples from the US, as it is globally relevant for all health authorities that collect HIV genetic data.

Comparing those diagnosed early versus late in their HIV infection: implications for public health

2016 ◽  
Vol 28 (7) ◽  
pp. 693-701 ◽  
Author(s):  
Dara Spatz Friedman ◽  
Patrick O’Byrne ◽  
Marie Roy
Keyword(s):  
Public Health ◽  
Hiv Infection ◽  
Hiv Transmission ◽  
Hiv Positive ◽  
Newly Diagnosed ◽  
Hiv Surveillance ◽  
Hiv Epidemiology ◽  
Simple Protocol ◽  
Sex With Men ◽  
Public Health Setting

Routine HIV surveillance cannot distinguish between recent and older infections: HIV-positive individuals reported soon or long after infection are both considered new diagnoses from a surveillance perspective, notwithstanding the time since infection. This lack of specificity makes it difficult to understand the jurisdiction-specific trends in HIV epidemiology needed for prevention planning. Previous efforts have been made to discern such timing of infection, but these methodologies are not easily applied in a public health setting. We wished to develop a simple protocol, using routinely collected information, to classify newly diagnosed infections as recent or older, and to enumerate and characterize recent versus older infections. Applying our methodology to a review of HIV cases reported between January 2011 and December 2014, we classified 62% of cases; one-third of these were recent infections. Although men who have sex with men (MSM) and persons from HIV-endemic countries (HEC) disproportionally accounted for new HIV diagnoses, the dynamics of HIV transmission within these groups differed dramatically: MSM accounted for the majority of recent infections, whereas persons from HEC accounted for the majority of older infections. Among older infections, one-quarter were previously unaware of their infection. Categorizing cases in this manner yielded greater, jurisdiction-specific understanding of HIV, and guides subpopulation-specific interventions.

scholarly journals Describing the Chinese HIV Surveillance System and the Influences of Political Structures and Social Stigma

2012 ◽  
Vol 6 (1) ◽  
pp. 163-168 ◽  
Author(s):  
Lei Zhang ◽  
Eric Pui Fung Chow ◽  
Jun Zhang ◽  
Jun Jing ◽  
David P Wilson
Keyword(s):  
Public Health ◽  
Surveillance System ◽  
Hiv Transmission ◽  
Social Stigma ◽  
Large Data ◽  
Population Level ◽  
Hiv Diagnosis ◽  
Hiv Surveillance ◽  
Hiv Acquisition ◽  
Public Health Surveillance System

China’s public health surveillance system for HIV was established in late 1980s and has evolved significantly during the past three decades. With the gradually changing mode of HIV transmission from sharing of intravenous injecting equipment to sexual exposure and the rapid spread of HIV infection among Chinese homosexual men in recent years, an efficient and comprehensive population-level surveillance system for describing epidemics trends and risk behaviours associated with HIV acquisition are essential for effective public health interventions for HIV. The current review describes the overall strength of the Chinese HIV surveillance system and its structural weaknesses from a political and social perspective. The HIV surveillance system in China has undergone substantial revamping leading to a comprehensive, timely and efficient reporting system. However, large data gaps and lack of quality control and sharing of information obstruct the full performance of the system. This is largely due to fragmented authoritarianism brought about by the underlying political structure. Social stigma and discrimination in health institutes are also key barriers for further improvements of HIV diagnosis and surveillance in China.

scholarly journals Enhanced use of phylogenetic data to inform public health approaches to HIV among men who have sex with men

Sexual Health ◽  
2017 ◽  
Vol 14 (1) ◽  
pp. 89 ◽  
Author(s):  
Danielle German ◽  
Mary Kate Grabowski ◽  
Chris Beyrer
Keyword(s):  
Public Health ◽  
Hiv Transmission ◽  
Transmission Risk ◽  
Structural Factors ◽  
Ethical Considerations ◽  
Hiv Surveillance ◽  
Phylogenetic Data ◽  
Sex With Men ◽  
The Individual ◽  
Scientific Questions

The multidimensional nature and continued evolution of HIV epidemics among men who have sex with men (MSM) requires innovative intervention approaches. Strategies are needed that recognise the individual, social and structural factors driving HIV transmission; that can pinpoint networks with heightened transmission risk; and that can help target intervention in real time. HIV phylogenetics is a rapidly evolving field with strong promise for informing innovative responses to the HIV epidemic among MSM. Currently, HIV phylogenetic insights are providing new understandings of characteristics of HIV epidemics involving MSM, social networks influencing transmission, characteristics of HIV transmission clusters involving MSM, targets for antiretroviral and other prevention strategies and dynamics of emergent epidemics. Maximising the potential of HIV phylogenetics for HIV responses among MSM will require attention to key methodological challenges and ethical considerations, as well as resolving key implementation and scientific questions. Enhanced and integrated use of HIV surveillance, sociobehavioural and phylogenetic data resources are becoming increasingly critical for informing public health approaches to HIV among MSM.

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.

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