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

Health policy counterpublics: Enacting collective resistances to US molecular HIV surveillance and cluster detection and response programs

Health policies and the problems they constitute are deeply shaped by multiple publics. In this article we conceptualize health policy counterpublics: temporally bounded socio-political forms that aim to cultivate particular modes of conduct, generally to resist trajectories set by arms of the state. These counterpublics often emerge from existing social movements and involve varied forms of activism and advocacy. We examine a health policy counterpublic that has arisen in response to new forms of HIV public health surveillance by drawing on public documents and interview data from 2021 with 26 stakeholders who were critical of key policy developments. Since 2018, the national rollout of molecular HIV surveillance (MHS) and cluster detection and response (CDR) programs in the United States has produced sustained controversies among HIV stakeholders, including among organized networks of people living with HIV. This article focuses on how a health policy counterpublic formed around MHS/CDR and how constituents problematized the policy agenda set in motion by federal health agencies, including in relation to data ethics, the meaningful involvement of affected communities, informed consent, the digitization of health systems, and HIV criminalization. Although familiar problems in HIV policymaking, concerns about these issues have been reconfigured in response to the new sociotechnical milieu proffered by MHS/CDR, generating new critical positions aiming to remake public health. Critical attention to the scenes within which health policy controversies play out ought to consider how (counter)publics are made, how problems are constituted, and the broader social movement dynamics and activist resources drawn upon to contest and reimagine policymaking in public life.

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.

Advancing Dialogue About Consent and Molecular HIV Surveillance in the United States: Four Proposals Following a Federal Advisory Panel's Call for Major Reforms

Policy Points Molecular HIV surveillance and cluster detection and response (MHS/CDR) programs have been a core public health activity in the United States since 2018 and are the "fourth pillar" of the Ending the HIV Epidemic initiative launched in 2019. MHS/CDR has caused controversy, including calls for a moratorium from networks of people living with HIV. In October 2022, the Presidential Advisory Council on HIV/AIDS (PACHA) adopted a resolution calling for major reforms. We analyze the policy landscape and present four proposals to federal stakeholders pertaining to PACHA's recommendations about incorporating opt-outs and plain-language notifications into MHS/CDR programs.

Botswana tuberculosis (TB) stakeholders broadly support scaling up next-generation whole genome sequencing: Ethical and practical considerations for Botswana and global health

Global health agencies are increasingly promoting the scale-up of next-generation whole genome sequencing (NG-WGS) of pathogens into infectious disease control programs, including for tuberculosis (TB). However, little is known about how stakeholders in low-to-middle income countries (LMICs) understand the ethics, benefits, and risks of these proposals. We conducted a qualitative study in Greater Gaborone, Botswana to learn how TB stakeholders there viewed a potential scale-up of NG-WGS into Botswana's TB program. We conducted 30 interviews and four deliberative dialogues with TB stakeholders based in Greater Gaborone, the country's largest city and capital. We created and showed participants an animated video series about a fictional family that experienced TB diagnosis, treatment, contact tracing, and data uses that were informed by NG-WGS. We analyzed transcripts using reflexive thematic analysis. We found broad support for the scale-up of TB NG-WGS in Botswana, owing to perceived benefits. Support was qualified with statements about ensuring adequate planning, resource-allocation, community and stakeholder engagement, capacity-building, and assessing ethical norms around publishing data. Our results suggest that scaling up NG-WGS for TB in Botswana would be supported by stakeholders there, contingent upon the government and other entities adequately investing in the initiative. These findings are relevant to other LMICs considering scale-ups of NG-WGS and related technologies for infectious diseases and suggest the need for sustained research into the acceptability of pathogen sequencing in other contexts.

Modeling homophily in dynamic networks with application to HIV molecular surveillance

BACKGROUND

Efforts to control the HIV epidemic can benefit from knowledge of the relationships between the characteristics of people who have transmitted HIV and those who became infected by them. Investigation of this relationship is facilitated by the use of HIV genetic linkage analyses, which allows inference about possible transmission events among people with HIV infection. Two persons with HIV (PWH) are considered linked if the genetic distance between their HIV sequences is less than a given threshold, which implies proximity in a transmission network. The tendency of pairs of nodes (in our case PWH) that share (or differ in) certain attributes to be linked is denoted homophily. Below, we describe a novel approach to modeling homophily with application to analyses of HIV viral genetic sequences from clinical series of participants followed in San Diego. Over the 22-year period of follow-up, increases in cluster size results from HIV transmissions to new people from those already in the cluster-either directly or through intermediaries.

METHODS

Our analytical approach makes use of a logistic model to describe homophily with regard to demographic, clinical, and behavioral characteristics-that is we investigate whether similarities (or differences) between PWH in these characteristics are associated with their sequences being linked. To investigate the performance of our methods, we conducted on a simulation study for which data sets were generated in a way that reproduced the structure of the observed database.

RESULTS

Our results demonstrated strong positive homophily associated with hispanic ethnicity, and strong negative homophily, with birth year difference. The second result implies that the larger the difference between the age of a newly-infected PWH and the average age for an available cluster, the lower the odds of a newly infected person joining that cluster. We did not observe homophily associated with prior diagnosis of sexually transmitted diseases. Our simulation studies demonstrated the validity of our approach for modeling homophily, by showing that the estimates it produced matched the specified values of the statistical network generating model.

CONCLUSIONS

Our novel methods provide a simple and flexible statistical network-based approach for modeling the growth of viral (or other microbial) genetic clusters from linkage to new infections based on genetic distance.

Public health use of HIV phylogenetic data in sub-Saharan Africa: ethical issues

Phylogenetic analyses of HIV are an increasingly accurate method of clarifying population-level patterns of transmission and linking individuals or groups with transmission events. Viral genetic data may be used by public health agencies to guide policy interventions focused on clusters of transmission or segments of the population in which transmission is concentrated. Analyses of HIV phylogenetics in high-income countries have often found that clusters of transmission play a significant role in HIV epidemics. In sub-Saharan Africa, HIV phylogenetic analyses to date suggest that clusters of transmission play a relatively minor role in local epidemics. Such analyses could nevertheless be used to guide priority setting and HIV public health programme design in Africa for sub-populations in which transmission events are more concentrated. Phylogenetic analysis raises ethical issues, in part due to the range of potential benefits and potential harms (ie, risks). Potential benefits include (1) improving knowledge of transmission patterns, (2) informing the design of focused public health interventions for subpopulations in which transmission is concentrated, (3) identifying and responding to clusters of transmission, (4) reducing stigma (in some cases) and (5) informing estimates of the (cost-)effectiveness of HIV treatment programmes. Potential harms include (1) privacy infringements, (2) increasing stigma (in some cases), (3) reducing trust in public health programmes, and (4) increased prosecution of legal cases where HIV transmission, homosexuality or sex work is criminalised. This paper provides analysis of relevant issues with a focus on sub-Saharan Africa in order to inform consultations regarding ethical best practice for HIV phylogenetics.

Community Insights in Phylogenetic HIV Research: The CIPHR Project Protocol

Inferring HIV transmission networks from HIV sequences is gaining popularity in the field of HIV molecular epidemiology. However, HIV sequences are often analyzed at distance from those affected by HIV epidemics, namely without the involvement of communities most affected by HIV. These remote analyses often mean that knowledge is generated in absence of lived experiences and socio-economic realities that could inform the ethical application of network-derived information in 'real world' programmes. Procedures to engage communities are noticeably absent from the HIV molecular epidemiology literature. Here we present our team's protocol for engaging community activists living in Nairobi, Kenya in a knowledge exchange process - The CIPHR Project (Community Insights in Phylogenetic HIV Research). Drawing upon a community-based participatory approach, our team will (1) explore the possibilities and limitations of HIV molecular epidemiology for key population programmes, (2) pilot a community-based HIV molecular study, and (3) co-develop policy guidelines on conducting ethically safe HIV molecular epidemiology. Critical dialogue with activist communities will offer insight into the potential uses and abuses of using such information to sharpen HIV prevention programmes. The outcome of this process holds importance to the development of policy frameworks that will guide the next generation of the global response.

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."

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.

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.