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.

The RSVP Project: Factors Related to Disengagement From Human Immunodeficiency Virus Care Among Persons in San Francisco.

BACKGROUND: In the United States, an estimated two-thirds of persons with human immunodeficiency virus (HIV) infection do not achieve viral suppression, including those who have never engaged in HIV care and others who do not stay engaged in care. Persons with an unsuppressed HIV viral load might experience poor clinical outcomes and transmit HIV. OBJECTIVE: The goal of the Re-engaging Surveillance-identified Viremic Persons (RSVP) project in San Francisco, CA, was to use routine HIV surveillance databases to identify, contact, interview, and reengage in HIV care persons who appeared to be out of care because their last HIV viral load was unsuppressed. We aimed to interview participants about their HIV care and barriers to reengagement. METHODS: Using routinely collected HIV surveillance data, we identified persons with HIV who were out of care (no HIV viral load and CD4 laboratory reports during the previous 9-15 months) and with their last plasma HIV RNA viral load >200 copies/mL. We interviewed the located persons, at baseline and 3 months later, about whether and why they disengaged from HIV care and the barriers they faced to care reengagement. We offered them assistance with reengaging in HIV care from the San Francisco Department of Public Health linkage and navigation program (LINCS). RESULTS: Of 282 persons selected, we interviewed 75 (26.6%). Of these, 67 (89%) reported current health insurance coverage, 59 (79%) had ever been prescribed and 45 (60%) were currently taking HIV medications, 59 (79%) had seen an HIV provider in the past year, and 34 (45%) had missed an HIV appointment in the past year. Reasons for not seeing a provider included feeling healthy, using alcohol or drugs, not having enough money or health insurance, and not wanting to take HIV medicines. Services needed to get to an HIV medical care appointment included transportation assistance, stable living situation or housing, sound mental health, and organizational help and reminders about appointments. A total of 52 (69%) accepted a referral to LINCS. Additionally, 64 (85%) of the persons interviewed completed a follow-up interview 3 months later and, of these, 62 (97%) had health insurance coverage and 47 (73%) reported having had an HIV-related care appointment since the baseline interview. CONCLUSIONS: Rather than being truly out of care, most participants reported intermittent HIV care, including recent HIV provider visits and health insurance coverage. Participants also frequently reported barriers to care and unmet needs. Health department assistance with HIV care reengagement was generally acceptable. Understanding why people previously in HIV care disengage from care and what might help them reengage is essential for optimizing HIV clinical and public health outcomes.

Using HIV surveillance registry data to re-link persons to care: the RSVP Project in San Francisco.

BACKGROUND: Persons with unsuppressed HIV viral load (VL) who disengage from care may experience poor clinical outcomes and potentially transmit HIV. We assessed the feasibility and yield of using the San Francisco Department of Public Health (SFDPH) enhanced HIV surveillance system (eHARS) to identify and re-engage such persons in care. METHODS: Using SFDPH eHARS data as of 4/20/2012 (index date), we selected HIV-infected adults who were alive, had no reported VL or CD4 cell count results in the past nine months (proxy for "out-of-care") and a VL >200 copies/mL drawn nine to 15 months earlier. We prioritized cases residing locally for investigation, and used information from eHARS and medical and public health databases to contact them for interview and referral to the SFDPH linkage services (LINCS). Twelve months later, we matched-back to eHARS data to assess how HIV laboratory reporting delays affected original eligibility, and if persons had any HIV laboratory results performed and reported within 12 months after index date ('new labs'). RESULTS: Among 434 eligible persons, 282 were prioritized for investigation, of whom 75 (27%) were interviewed, 79 (28%) could not be located, and 48 (17%) were located out of the area. Among the interviewed, 54 (72%) persons accepted referral to LINCS. Upon match-back to eHARS data, 324 (75%) in total were confirmed as eligible, including 221 (78%) of the investigated; most had new labs. CONCLUSIONS: Among the investigated persons presumed out-of-care, we interviewed and offered LINCS referral to about one-quarter, demonstrating the feasibility but limited yield of our project. Matching to updated surveillance data revealed that a substantial minority did not disengage from care and that most re-engaged in HIV care. Verifying persons' HIV care status with medical providers and improving timeliness of transfer and cross-jurisdictional sharing of HIV laboratory data may aid future efforts.

Frequent international travel by men who have sex with men recently diagnosed with HIV-1: potential for transmission of primary HIV-1 drug resistance.

We assessed the potential for international transmission of primary drug resistance among men who have sex with men newly diagnosed with human immunodeficiency virus (HIV) (n = 64) during the period in which they were unaware of their infection. During their exposure period, 55% of participants lived or traveled outside of the United States, and 59% had foreign-born sexual partners. Eighteen participants (28%) were classified as recently infected with HIV. Primary HIV-1 drug resistance was detected in eight participants (13%), four of whom were recently infected. Given the high frequency of international travel and prevalence of primary HIV-1 drug resistance among study participants, prevention strategies should incorporate specific counseling on risk of cross-border transmission.

Does name-based HIV reporting deter high-risk persons from HIV testing? Results from San Francisco.

OBJECTIVE: Name-based HIV reporting has been recommended as a method to track the HIV epidemic but may deter or delay at-risk persons from HIV testing. Previous studies of a deterrent effect of HIV reporting were not conducted in areas with high HIV infection rates and politically active populations. METHODS: In a cross-sectional survey, men who have sex with men (MSM) recruited from gay bars, heterosexuals recruited from the sexually transmitted disease clinic, and injection drug users (IDUs) recruited from street venues were administered a face-to-face anonymous questionnaire. RESULTS: Ninety-four percent of the 118 MSM, 76% of the 99 heterosexuals, and 97% of 105 IDUs surveyed were tested. Six percent of MSM, 9% of heterosexuals, and none of the IDUs correctly identified California's HIV reporting regulations. Of the 75 (25%) participants who thought California had a name-based HIV reporting system, 2 were never tested and 23 had not been tested in the past 12 months. None of those who had never been tested and 2 of those who had not been tested in the past 12 months cited fear of being reported as a reason for not testing recently. CONCLUSION: Fear of reporting is an infrequently cited reason for deterring or delaying testing.

Self-reported sexual identity, sexual behaviors and health risks.

SUMMARY Data from a population-based survey of low-income young women (n = 2,438) was used to examine substance use patterns and exposure to coerced sexual activity among women who self-identify as lesbian (n = 34) or bisexual (n = 91), or who report sexual behavior exclusively with other women (n = 17) or with both women and men (n = 189). Findings for women classified by self-identity and by sexual behavior are compared. Women who identified as bisexual or lesbian reported higher rates of lifetime and recent substance use and were more likely to report experiences of coerced sex than women who identified as heterosexual. Women with both male and female sex partners reported higher rates of substance use and coerced sexual experiences than did women with male partners only. Heterosexual women with both male and female partners were more similar to self-identified bisexuals, compared to heterosexual women with male partners only. The implications of assessing multiple dimensions of sexual orientation in research focusing on lesbians' mental health are discussed.