Perceptions of molecular epidemiology studies of HIV among stakeholders

User experience with HIV molecular epidemiology in research, surveillance, and cluster detection and response: a needs assessment

OBJECTIVE

HIV molecular epidemiology (HIV ME) is a tool that aims to improve HIV research, surveillance, and cluster detection and response. HIV ME is a core pillar of the U.S. initiative to End the HIV Epidemic but faces some challenges and criticisms from stakeholders. We sought to assess user experience to identify the current needs for HIV ME.

METHODS

Users of HIV ME, including researchers and public health practitioners, were engaged via a structured survey. Needs were assessed via open-ended questions about HIV ME. Data were analyzed using reflexive thematic analysis; the concordance of results was assessed semi-quantitatively.

RESULTS

Of 90 possible HIV-ME end-users, 57 completed the survey (response rate = 63%), which included users engaged in research (n = 29) and public health (n = 28). Respondents identified current imperatives, challenges, and strategies to improve HIV ME. Imperatives included characterization of the virus, identification of HIV hotspots, and tailoring of HIV interventions. Challenges encompassed technological issues, ethical concerns, and implementation difficulties. Strategies to improve HIV ME involved improving data access and analysis, enhancing implementation guidance and resources, and fostering community engagement and support. Researchers and public health practitioners prioritized different imperatives, but similarly emphasized the ethical concerns with HIV ME.

CONCLUSION

The imperatives identified by users underscore the necessity of HIV ME, while the challenges highlight the hurdles to be overcome, including ethical concerns which emerged as a shared emphasis across user groups. The strategies outlined offer a roadmap for overcoming these challenges. These insights, drawn from user experience, present a valuable opportunity to inform the development of guidelines for the ethical application of HIV ME in research, surveillance, and cluster detection and response.

Prioritization of ethical concerns regarding HIV molecular epidemiology by public health practitioners and researchers

BACKGROUND

HIV molecular epidemiology (HIV ME) can support the early detection of emerging clusters of new HIV infections by combining HIV sequence data routinely obtained during the clinical treatment of people living with HIV with behavioral, geographic, and sociodemographic information. While information about emerging clusters promises to facilitate HIV prevention and treatment efforts, the use of this data also raises several ethical concerns. We sought to assess how those working on the frontlines of HIV ME, specifically public health practitioners (PHPs) and researchers, prioritized these issues.

METHODS

Ethical issues were identified through literature review, qualitative in-depth interviews, and stakeholder engagement. PHPs and researchers using HIV ME prioritized the issues using best-worst scaling (BWS). A balanced incomplete block design was used to generate 11 choice tasks each consisting of a sub-set of 5 ethical concerns. In each task, respondents were asked to assess the most and least concerning issue. Data were analyzed using conditional logit, with a Swait-Louviere test of poolability. Latent class analysis was then used to explore preference heterogeneity.

RESULTS

In total, 57 respondents completed the BWS experiment May-June 2023 with the Swait-Louviere test indicating that researchers and PHPs could be pooled (p = 0.512). Latent class analysis identified two classes, those highlighting "Harms" (n = 29) (prioritizing concerns about potential risk of legal prosecution, individual harm, and group stigma) and those highlighting "Utility" (n = 28) (prioritizing concerns about limited evidence, resource allocation, non-disclosure of data use for HIV ME, and the potential to infer the directionality of HIV transmission). There were no differences in the characteristics of members across classes.

CONCLUSIONS

The ethical issues of HIV ME vary in importance among stakeholders, reflecting different perspectives on the potential impact and usefulness of the data. Knowing these differences exist can directly inform the focus of future deliberations about the policies and practices of HIV ME in the United States.

Assessing transmission attribution risk from simulated sequencing data in HIV molecular epidemiology

BACKGROUND

HIV molecular epidemiology (ME) is the analysis of sequence data together with individual-level clinical, demographic, and behavioral data to understand HIV epidemiology. The use of ME has raised concerns regarding identification of the putative source in direct transmission events. This could result in harm ranging from stigma to criminal prosecution in some jurisdictions. Here we assessed the risks of ME using simulated HIV genetic sequencing data.

METHODS

We simulated social networks of men-who-have-sex-with-men, calibrating the simulations to data from San Diego. We used these networks to simulate consensus and next-generation sequence (NGS) data to evaluate the risks of identifying direct transmissions using different HIV sequence lengths, and population sampling depths. To identify the source of transmissions, we calculated infector probability and used phyloscanner software for the analysis of consensus and NGS data, respectively.

RESULTS

Consensus sequence analyses showed that the risk of correctly inferring the source (direct transmission) within identified transmission pairs was very small and independent of sampling depth. Alternatively, NGS analyses showed that identification of the source of a transmission was very accurate, but only for 6.5% of inferred pairs. False positive transmissions were also observed, where one or more unobserved intermediaries were present when compared to the true network.

CONCLUSION

Source attribution using consensus sequences rarely infers direct transmission pairs with high confidence but is still useful for population studies. In contrast, source attribution using NGS data was much more accurate in identifying direct transmission pairs, but for only a small percentage of transmission pairs analyzed.

Toward Consent in Molecular HIV Surveillance?: Perspectives of Critical Stakeholders

BACKGROUND

The emergence of molecular HIV surveillance (MHS) and cluster detection and response (CDR) programs as key features of the United States (US) HIV strategy since 2018 has caused major controversies. HIV surveillance programs that re-use individuals' routinely collected clinical HIV data do not require consent on the basis that the public benefit of these programs outweighs individuals' rights to opt out. However, criticisms of MHS/CDR have questioned whether expanded uses of HIV genetic sequence data for prevention reach beyond traditional public health ethics frameworks. This study aimed to explore views on consent within MHS/CDR among critical stakeholders.

METHODS

In 2021 we interviewed 26 US HIV stakeholders who identified as being critical or concerned about the rollout of MHS/CDR. Stakeholders included participants belonging to networks of people living with HIV, other advocates, academics, and public health professionals. This analysis focused on identifying the range of positions among critical and concerned stakeholders on consent affordances, opt-outs, how to best inform people living with HIV about how data about them are used in public health programs, and related ethical issues.

RESULTS

Participants were broadly supportive of introducing some forms of consent into MHS/CDR. However, they differed on the specifics of implementing consent. While some participants did not support introducing consent affordances, all supported the idea that people living with HIV should be informed about how HIV surveillance and prevention is conducted and how individuals' data are used.

CONCLUSIONS

MHS/CDR has caused sustained controversy. Among critical stakeholders, consent is generally desirable but contested, although the right for people living with HIV to be informed was centrally supported. In an era of big data-driven public health interventions and routine uses of HIV genetic sequence data in surveillance and prevention, CDC and other agencies should revisit public health ethics frameworks and consider the possibility of consent processes.

Brief Report: Challenges in Obtaining the Informed Perspectives of Stakeholders Regarding HIV Molecular Epidemiology

BACKGROUND

HIV molecular epidemiology (HIV-ME) is now being used in a variety of ways, including molecular HIV surveillance to help identify and respond to emerging HIV transmission clusters as specified in the Ending the HIV Epidemic in the U.S. initiative. However, HIV-ME in general, and its use for cluster detection and response, in particular, raises significant ethical and social concerns, which have spurred vigorous debates. Nevertheless, there is a paucity of information regarding how these potential benefits and concerns are perceived among people living with HIV and people without HIV at an increased risk.

SETTING

Virtual engagement with US participants.

METHODS

We rigorously developed a brief informational video about HIV-ME and conducted a series of in-depth interviews with people living with HIV and people without HIV at an increased risk.

RESULTS

Through extensive stakeholder engagement during the video development process and subsequent in-depth interviews (N = 24), several preliminary findings surfaced. In contrast to the high level of concern raised by some critics of HIV-ME, our data appear to show broad support for it. In addition, we observed conflation of perspectives about HIV-ME with concerns about HIV public health surveillance more generally.

CONCLUSION

Our experiences reveal substantial communication challenges related to the nature of HIV-ME that need to be overcome to ensure that it is properly understood, which is necessary for meaningfully engaging stakeholders in discussions about its use. Moreover, ongoing, responsive, engagement efforts are critical. Additional systematic data are needed to help inform policy making and practice regarding HIV-ME.

Integrating Phylogenetic Biomarker Data and Qualitative Approaches: An example of HIV Transmission Clusters as a Sampling Frame for Semistructured Interviews and Implications for the COVID-19 Era

Mixed methods studies of human disease that combine surveillance, biomarker, and qualitative data can help elucidate what drives epidemiological trends. Viral genetic data are rarely coupled with other types of data due to legal and ethical concerns about patient privacy. We developed a novel approach to integrate phylogenetic and qualitative methods in order to better target HIV prevention efforts. The overall aim of our mixed methods study was to characterize HIV transmission clusters. We combined surveillance data with HIV genomic data to identify cases whose viruses share enough similarities to suggest a recent common source of infection or participation in linked transmission chains. Cases were recruited through a multi-phase process to obtain consent for recruitment to semi-structured interviews. Through linkage of viral genetic sequences with epidemiological data, we identified individuals in large transmission clusters, which then served as a sampling frame for the interviews. In this article, we describe the multi-phase process and the limitations and challenges encountered. Our approach contributes to the mixed methods research field by demonstrating that phylogenetic analysis and surveillance data can be harnessed to generate a sampling frame for subsequent qualitative data collection, using an explanatory sequential design. The process we developed also respected protections of patient confidentiality. The novel method we devised may offer an opportunity to implement a sampling frame that allows for the recruitment and interview of individuals in high-transmission clusters to better understand what contributes to spread of other infectious diseases, including COVID-19.

Molecular epidemiology in the HIV and SARS-CoV-2 pandemics

PURPOSE OF REVIEW

The aim of this review was to compare and contrast the application of molecular epidemiology approaches for the improved management and understanding of the HIV versus SARS-CoV-2 epidemics.

RECENT FINDINGS

Molecular biology approaches, including PCR and whole genome sequencing (WGS), have become powerful tools for epidemiological investigation. PCR approaches form the basis for many high-sensitivity diagnostic tests and can supplement traditional contact tracing and surveillance strategies to define risk networks and transmission patterns. WGS approaches can further define the causative agents of disease, trace the origins of the pathogen, and clarify routes of transmission. When coupled with clinical datasets, such as electronic medical record data, these approaches can investigate co-correlates of disease and pathogenesis. In the ongoing HIV epidemic, these approaches have been effectively deployed to identify treatment gaps, transmission clusters and risk factors, though significant barriers to rapid or real-time implementation remain critical to overcome. Likewise, these approaches have been successful in addressing some questions of SARS-CoV-2 transmission and pathogenesis, but the nature and rapid spread of the virus have posed additional challenges.

SUMMARY

Overall, molecular epidemiology approaches offer unique advantages and challenges that complement traditional epidemiological tools for the improved understanding and management of epidemics.

Addressing Ethical Challenges in US-Based HIV Phylogenetic Research

In recent years, phylogenetic analysis of HIV sequence data has been used in research studies to investigate transmission patterns between individuals and groups, including analysis of data from HIV prevention clinical trials, in molecular epidemiology, and in public health surveillance programs. Phylogenetic analysis can provide valuable information to inform HIV prevention efforts, but it also has risks, including stigma and marginalization of groups, or potential identification of HIV transmission between individuals. In response to these concerns, an interdisciplinary working group was assembled to address ethical challenges in US-based HIV phylogenetic research. The working group developed recommendations regarding (1) study design; (2) data security, access, and sharing; (3) legal issues; (4) community engagement; and (5) communication and dissemination. The working group also identified areas for future research and scholarship to promote ethical conduct of HIV phylogenetic research.

Reassessing the Ethics of Molecular HIV Surveillance in the Era of Cluster Detection and Response: Toward HIV Data Justice

In the United States, clinical HIV data reported to surveillance systems operated by jurisdictional departments of public health are re-used for epidemiology and prevention. In 2018, all jurisdictions began using HIV genetic sequence data from clinical drug resistance tests to identify people living with HIV in "clusters" of others with genetically similar strains. This is called "molecular HIV surveillance" (MHS). In 2019, "cluster detection and response" (CDR) programs that re-use MHS data became the "fourth pillar" of the national HIV strategy. Public health re-uses of HIV data are done without consent and are a source of concern among stakeholders. This article presents three cases that illuminate bioethical challenges associated with re-uses of clinical HIV data for public health. We focus on evidence-base, risk-benefit ratio, determining directionality of HIV transmission, consent, and ethical re-use. The conclusion offers strategies for "HIV data justice." The essay contributes to a "bioethics of the oppressed."

I wanted it as soon as possible: a qualitative exploration of reactions to access to same-day ART start among participants in San Diego's ART-NET project

Rapid start of antiretroviral therapy (ART) is quickly becoming best practice around the world. In the US, programs exist to facilitate rapid ART start, but little is known about the experiences of newly diagnosed individuals receiving these recommendations and services. Twenty participants (19 men who have sex with men and 1 transgender woman) from an early ART start program were interviewed to better understand these experiences. Interviews were analyzed for main themes in three general areas: reasons to start, reasons to delay, and factors influencing early ART adherence. Participants reported starting anywhere from right away (same visit as diagnosis) to within a few weeks (median 10.5 days). Reasons to start right away included fear of what could happen if not treated, personal health, influence of people/resources at the clinic, and study participation. Most had small delays in ART start because of structural (insurance, costs) and intentional delays (getting additional medical consultations). Adherence facilitators included desires to improve CD4/viral load and positive beliefs in benefits of suppression. Participants were largely supportive of rapid ART start and appeared to rely on CD4/viral load as "proof" of need for ART, which may be particularly helpful for asymptomatic, newly diagnosed individuals starting ART.

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

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.

Ethical challenges in pathogen sequencing: a systematic scoping review

Background: Going forward, the routine implementation of genomic surveillance activities and outbreak investigation is to be expected. We sought to systematically identify the emerging ethical challenges; and to systematically assess the gaps in ethical frameworks or thinking and identify where further work is needed to solve practical challenges.

Methods: We systematically searched indexed academic literature from PubMed, Google Scholar, and Web of Science from 2000 to April 2019 for peer-reviewed articles that substantively engaged in discussion of ethical issues in the use of pathogen genome sequencing technologies for diagnostic, surveillance and outbreak investigation.

Results: 28 articles were identified; nine United States, five United Kingdom, five The Netherlands, three Canada, two Switzerland, one Australia, two South Africa, and one Italy. Eight articles were specifically about the use of sequencing in HIV. Eleven were not specific to a particular disease. Results were organized into four themes: tensions between public and private interests; difficulties with translation from research to clinical and public health practice; the importance of community trust and support; equity and global partnerships; and the importance of context.

Conclusion: While pathogen sequencing has the potential to be transformative for public health, there are a number of key ethical issues that must be addressed, particularly around the conditions of use for pathogen sequence data. Ethical standards should be informed by public values, and further empirical work investigating stakeholders’ views are required. Development in the field should also be under-pinned by a strong commitment to values of justice, in particular global health equity.

Ethical issues associated with HIV molecular epidemiology: a qualitative exploratory study using inductive analytic approaches

Background

HIV molecular epidemiology is increasingly recognized as a vital source of information for understanding HIV transmission dynamics. Despite extensive use of these data-intensive techniques in both research and public health settings, the ethical issues associated with this science have received minimal attention. As the discipline evolves, there is reasonable concern that existing ethical and legal frameworks and standards might lag behind the rapid methodological developments in this field. This is a follow-up on our earlier work that applied a predetermined analytical framework to examine the perspectives of a sample of scientists from the fields of epidemiology, public health, virology and bioethics on key ethical issues associated with HIV molecular epidemiology in HIV network research.

Methods

Fourteen in-depth interviews were conducted with scientists from the fields of molecular epidemiology, public health, virology and bioethics. Inductive analytical approaches were applied to identify key themes that emerged from the data.

Results

Our interviewees acknowledged the potential positive impact of molecular epidemiology in the fight against HIV. However, they were concerned that HIV phylogenetics research messages may be incorrectly interpreted if not presented at the appropriate level. There was consensus that HIV phylogenetics research presents a potential risk to privacy, but the probability and magnitude of this risk was less obvious. Although participants acknowledged the social value that could be realized from the analysis of HIV genetic sequences, there was a perceived fear that the boundaries for use of HIV sequence data were not clearly defined.

Conclusions

Our findings highlight distinct ethical issues arising from HIV molecular epidemiology. As the discipline evolves and HIV sequence data become increasingly available, it is critical to ensure that ethical standards keep pace with biomedical advancements. We argue that the ethical issues raised in this study, whether real or perceived, require further conceptual and empirical examination.

Trust and Expectations of Researchers and Public Health Departments for the Use of HIV Molecular Epidemiology

Background: Molecular epidemiology (ME) is a technique used to study the dynamics of pathogen transmission through a population. When used to study HIV infections, ME generates powerful information about how HIV is transmitted, including epidemiologic patterns of linkage and, potentially, transmission direction. Thus, ME raises challenging questions about the most responsible way to protect individual privacy while acquiring and using these data to advance public health and inform HIV intervention strategies. Here, we report on stakeholders' expectations for how researchers and public health agencies might use HIV ME. Methods: We conducted in-depth semistructured interviews with 40 key stakeholders to find out how these individuals respond to the proposed risks and benefits of HIV ME. Transcripts were coded and analyzed using Atlas.ti. Expectations were assessed through analysis of responses to hypothetical scenarios designed to help interviewees think through the implications of this emerging technique in the contexts of research and public health. Results: Our analysis reveals a wide range of imagined responsibilities, capabilities, and trustworthiness of researchers and public health agencies. Specifically, many respondents expect researchers and public health agencies to use HIV ME carefully and maintain transparency about how data will be used. Informed consent was discussed as an important opportunity for notification of privacy risks. Furthermore, some respondents wished that public health agencies were held to the same form of oversight and accountability represented by informed consent in research. Conclusions: To prevent HIV ME from becoming a barrier to testing or a source of public mistrust, the sense of vulnerability expressed by some respondents must be addressed. In research, informed consent is an obvious opportunity for this. Without giving specimen donors a similar opportunity to opt out, public health agencies may find it difficult to adopt HIV ME without deterring testing and treatment.

Ethical issues in HIV phylogenetics and molecular epidemiology

PURPOSE OF REVIEW

HIV phylogenetic and molecular epidemiology analyses are increasingly being performed with a goal of improving HIV prevention efforts. However, ethical, legal and social issues are associated with these analyses, and should be considered when performed.

RECENT FINDINGS

Several working groups have recently outlined the major issues surrounding the use of molecular epidemiology for HIV prevention. First, the benefits of HIV molecular epidemiology remain unclear, and further work is needed to quantitatively demonstrate the benefits that can be expected. Second, privacy loss is an important risk, with implications of disclosure varying by the regional legal and social climate. Inferential privacy risks will increase with technological improvements in sequencing and analysis. Third, data sharing, which enhances the utility of the data, may also increase the risk of inferential privacy loss. Mitigation strategies are available to address each of these issues.

SUMMARY

HIV molecular epidemiology for research and public health pose significant ethical issues that continue to evolve with improving technology, increased sampling and a changing legal and social climate. Guidance surrounding these issues needs to be developed for researchers and public health officials in an iterative and region specific manner that accounts for the potential benefits and risks of this technology.

Comparative analysis of HIV sequences in real time for public health

PURPOSE OF REVIEW

The purpose of this study is to summarize recent advances in public health applications of comparative methods for HIV-1 sequence analysis in real time, including genetic clustering methods.

RECENT FINDINGS

Over the past 2 years, several groups have reported the deployment of established genetic clustering methods to guide public health decisions for HIV prevention in 'near real time'. However, it remains unresolved how well the readouts of comparative methods like clusters translate to events that are actionable for public health. A small number of recent studies have begun to elucidate the linkage between clusters and HIV-1 incidence, whereas others continue to refine and develop new comparative methods for such applications.

SUMMARY

Although the use of established methods to cluster HIV-1 sequence databases has become a widespread activity, there remains a critical gap between clusters and public health value.

Social Networks of Substance-Using Populations: Key Issues and Promising New Approaches for HIV

PURPOSE OF REVIEW

This paper presents recent literature on substance using networks and HIV, highlighting renewed and emerging themes in the field. The goal is to draw attention to research that holds considerable promise for advancing our understanding of the role of networks in shaping behaviors, while also providing critical information for the development of interventions, programs, and policies to reduce HIV and other drug-related harms.

RECENT FINDINGS

Recent research advances our understanding of networks and HIV, including among understudied populations, and provides new insight into how risk environments shape the networks and health of substance-using populations. In particular, the integration of network approaches with molecular epidemiology, research on space and place, and intervention methods provides exciting new avenues of investigation. Continued advances in network research are critical to supporting the health and rights of substance-using populations and ensuring the development of high-impact HIV programs and policies.

Experts' Perspectives on Key Ethical Issues Associated With HIV Phylogenetics as Applied in HIV Transmission Dynamics Research

The use of phylogenetics in HIV molecular epidemiology has considerably increased our ability to understand the origin, spread, and characteristics of HIV epidemics. Despite its potential to advance knowledge on HIV transmission dynamics, the ethical issues associated with HIV molecular epidemiology have received minimal attention. In-depth interviews were conducted with scientists from diverse backgrounds to explore their perspectives on ethical issues associated with phylogenetic analysis of HIV genetic data as applied to HIV transmission dynamics studies. The Emanuel framework was used as the analytical framework. Favorable risk-benefit ratio and informed consent were the most invoked ethical principles and fair participant selection the least. Fear of loss of privacy and disclosure of HIV transmission were invariably cited as key ethical concerns. As HIV sequence data become increasingly available, comprehensive guidelines should be developed to guide its access, sharing and use, cognizant of the potential harms that may result.