Social network-based recruitment successfully reveals HIV-1 transmission networks among high-risk individuals in El Salvador

Dynamics of clustering rates in the Rhode Island HIV-1 epidemic

BACKGROUND

Characterizing HIV clustering rates and their trends over time can improve understanding a local epidemic and enhance its control.

METHODS

Leveraging an academic-public health partnership in Rhode Island, we explored longitudinal dynamics of statewide clustering rates among key populations from 1991 to 2023. Partial HIV-1 pol sequences were grouped by year of HIV-1 diagnosis. Molecular clusters were identified in cumulative annual phylogenies. Overall clustering rates, and clustering rates of newly diagnosed and prevalent infections, and of specific sociodemographic characteristics of key populations over time were determined. Mann-Kendall statistics were used to estimate clustering rate trends and relationships among groups.

RESULTS

By the end of 2023, 2630 individuals with sequences represented the statewide epidemic in Rhode Island. Overall clustering rates increased from 7% in 1991 to 46% in 2023, correlating with cumulative sequence increase. Clustering rates of newly diagnosed and prevalent infections significantly increased over time, higher in newly diagnosed individuals since the early 2000s. Increases were also observed among groups defined by gender, age, transmission risks, race, mental illness, HIV-1 subtypes, and country of birth, with some crossovers and divergence patterns over time.

CONCLUSION

Exploring dynamics of HIV clustering rates over three decades in a statewide HIV-1 epidemic expanded its characterization and provided insight into its evolving changes. These dynamics may indicate a gradual shift towards a more concentrated and localized HIV-1 epidemic, highlighting important opportunities for targeted interventions to effectively prevent new HIV transmissions.

Using HIV and Hepatitis C Molecular Epidemiology to Investigate Assisted Partner Services Recruitment Among People Who Inject Drugs in Kenya

Sexual and/or injecting partners of people who inject drugs (PWID) may have an elevated risk of HIV infection either from sharing a transmission network or an epidemiological environment. We estimated the degree of similarity between HIV and hepatitis C (HCV) sequences from PWID and their partners to assess whether partner-based recruitment identifies sexual or injecting partners within transmission networks. We used assisted partner services (APS) to recruit sexual and injecting partners of PWID living with HIV in Kenya and evaluated trends in the TN93 distances (an adjusted measure of sequence similarity) of the HIV-1 and HCV sequences from partner pairs. Of 135 unique pairs identified, 2 sexual, 2 injecting, and 3 unique sexual and injecting partner pairs had HIV sequences within a TN93 distance of 0.045, and 4 unique partner pairs had HCV sequences with distances <0.015. Sexual but not injecting partner pairs had HIV sequences with significantly smaller distances than non-partners, on average, but injecting partner pairs did have significantly smaller HCV-4a patristic distances than non-partners. APS recruitment partly reflects the HIV transmission network among sexual, but not injecting, partners of PWID. The relationship between the injecting partner recruitment and molecular networks is stronger for HCV than HIV and may reflect some recent parenteral HCV transmission. Our results show the importance of continued focus on reducing sexual HIV transmission among PWID and on education and services to address HCV transmission through needle- and/or equipment-sharing.

Respondent-driven sampling is more efficient than facility-based strategies at identifying undiagnosed people who inject drugs living with HIV in India

INTRODUCTION

Injection drug use drives HIV epidemics in many low-resource settings, yet many people who inject drugs (PWID) living with HIV are not diagnosed. We assessed the ability of respondent-driven sampling (RDS) - which uses peer network connections - to identify undiagnosed PWID living with HIV compared to a facility-based strategy in India.

METHODS

In six Indian cities from 2014 to 2017, integrated care centers (ICCs) provided HIV testing. From 2016 to 2017, RDS samples of PWID in these same cities were conducted. Using biometric matching, characteristics associated with identification by RDS only and both RDS and ICC, compared to ICC only were explored. Undiagnosed individuals tested positive and did not report a prior diagnosis. The number needed to recruit (NNR) (average number recruited to find one undiagnosed PWID living with HIV) and the identification rate (average number undiagnosed PWID identified per week) assessed the efficiency of RDS vs. ICCs.

RESULTS

There were 10,759 ICC clients and 6012 RDS participants; 40% of RDS participants were also ICC clients resulting in 14,397 unduplicated PWID. PWID identified by RDS vs. ICC only were more likely to be male (adjusted odds ratios [aOR] RDS only: 6.8, both: 2.7) and living with HIV but undiagnosed (aOR RDS only: 2.5, both: 1.5). Overall, the RDS NNR was 11 and the ICC NNR was 26. The RDS identification rate (18.6/week) was faster than the ICC identification rate (2.7/week) overall and in all cities.

CONCLUSIONS

RDS required screening fewer PWID and more rapidly identified undiagnosed PWID living with HIV as compared to ICCs.

HIV Response Interventions that Integrate HIV Molecular Cluster and Social Network Analysis: A Systematic Review

Due to improved efficiency and reduced cost of viral sequencing, molecular cluster analysis can be feasibly utilized alongside existing human immunodeficiency virus (HIV) prevention strategies. The goal of this paper is to elucidate how HIV molecular cluster and social network analyses are being integrated to implement HIV response interventions. We searched PubMed, Scopus, PsycINFO, and Cochrane Library databases for studies incorporating both HIV molecular cluster and social network data. We identified 32 articles that combined analyses of HIV molecular sequences and social or sexual networks. All studies were descriptive. Six studies described network interventions informed by molecular and social data but did not fully evaluate their efficacy. There is no current standard for incorporating molecular and social network analyses to inform interventions or data demonstrating its utility. More research must be conducted to delineate benefits and best practices for leveraging molecular data for network-based interventions.

Use of HIV Recency Assays for HIV Incidence Estimation and Other Surveillance Use Cases: Systematic Review

BACKGROUND

HIV assays designed to detect recent infection, also known as "recency assays," are often used to estimate HIV incidence in a specific country, region, or subpopulation, alone or as part of recent infection testing algorithms (RITAs). Recently, many countries and organizations have become interested in using recency assays within case surveillance systems and routine HIV testing services to measure other indicators beyond incidence, generally referred to as "non-incidence surveillance use cases."

OBJECTIVE

This review aims to identify published evidence that can be used to validate methodological approaches to recency-based incidence estimation and non-incidence use cases. The evidence identified through this review will be used in the forthcoming technical guidance by the World Health Organization (WHO) and United Nations Programme on HIV/AIDS (UNAIDS) on the use of HIV recency assays for identification of epidemic trends, whether for HIV incidence estimation or non-incidence indicators of recency.

METHODS

To identify the best methodological and field implementation practices for the use of recency assays to estimate HIV incidence and trends in recent infections for specific populations or geographic areas, we conducted a systematic review of the literature to (1) understand the use of recency testing for surveillance in programmatic and laboratory settings, (2) review methodologies for implementing recency testing for both incidence estimation and non-incidence use cases, and (3) assess the field performance characteristics of commercially available recency assays.

RESULTS

Among the 167 documents included in the final review, 91 (54.5%) focused on assay or algorithm performance or methodological descriptions, with high-quality evidence of accurate age- and sex-disaggregated HIV incidence estimation at national or regional levels in general population settings, but not at finer geographic levels for prevention prioritization. The remaining 76 (45.5%) described the field use of incidence assays including field-derived incidence (n=45), non-incidence (n=25), and both incidence and non-incidence use cases (n=6). The field use of incidence assays included integrating RITAs into routine surveillance and assisting with molecular genetic analyses, but evidence was generally weaker or only reported on what was done, without validation data or findings related to effectiveness of using non-incidence indicators calculated through the use of recency assays as a proxy for HIV incidence.

CONCLUSIONS

HIV recency assays have been widely validated for estimating HIV incidence in age- and sex-specific populations at national and subnational regional levels; however, there is a lack of evidence validating the accuracy and effectiveness of using recency assays to identify epidemic trends in non-incidence surveillance use cases. More research is needed to validate the use of recency assays within HIV testing services, to ensure findings can be accurately interpreted to guide prioritization of public health programming.

Integrated molecular and affiliation network analysis: Core-periphery social clustering is associated with HIV transmission patterns

This study investigates the two-mode core-periphery structures of venue affiliation networks of younger Black men who have sex with men (YBMSM). We examined the association between these structures and HIV phylogenetic clusters, defined as members who share highly similar HIV strains that are regarded as a proxy for sexual affiliation networks. Using data from 114 YBMSM who are living with HIV in two large U.S. cities, we found that HIV phylogenetic clustering patterns were associated with social clustering patterns whose members share affiliation with core venues that overlap with those of YBMSM. Distinct HIV transmission patterns were found in each city, a finding that can help to inform tailored venue-based and network intervention strategies.

Sexual health norms and communication patterns within the close social networks of men who have sex with men and transgender women in Lima, Peru: a 2017 cross-sectional study

BACKGROUND

Social networks, norms, and discussions about sexual health may inform sexual practices, influencing risk of human immunodeficiency virus (HIV) or sexually transmitted infection (STI) acquisition. To better understand social networks of Peruvian men who have sex with men (MSM) and transgender women (trans women), we examined key social network members (SNMs), participant perceptions of these network members' opinions toward sexual health behaviors, and associations between network member characteristics and condomless anal intercourse (CAI).

METHODS

In a 2017 cross-sectional study, a convenience sample of 565 MSM and trans women with HIV-negative or unknown serostatus was asked to identify three close SNMs; describe discussions about HIV and STI prevention with each; and report perceived opinions of condom use, HIV/STI testing, and partner notification of STIs. Generalized estimating equations evaluated relationships between SNM characteristics, opinions, and discussions and participant-reported CAI.

RESULTS

Among participants who identified as MSM, 42.3% of key SNMs were perceived to identify as gay. MSM "never" discussed HIV and STI prevention concerns with 42.4% of heterosexual SNMs, but discussed them "at least once weekly" with 16.9 and 16.6% of gay- and bisexual- identifying SNMs, respectively. Among participants who identified as trans women, 28.2% of key SNMs were perceived as heterosexual; 25.9%, as bisexual; 24.7%, as transgender; and 21.2%, as gay. Trans women discussed HIV/STI prevention least with cis-gender heterosexual network members (40.2% "never") and most with transgender network members (27.1% "at least once weekly"). Participants perceived most of their close social network to be completely in favor of condom use (71.2% MSM SNMs, 61.5% trans women SNMs) and HIV/STI testing (73.1% MSM SNMs, 75.6% trans women SNMs), but described less support for partner STI notification (33.4% MSM SNMs, 37.4% trans women SNMs). Most participants reported CAI with at least one of their past three sexual partners (77.5% MSM, 62.8% trans women). SNM characteristics were not significantly associated with participant-reported frequency of CAI.

CONCLUSIONS

Findings compare social support, perceived social norms, and discussion patterns of Peruvian MSM and trans women, offering insight into social contexts and sexual behaviors.

TRIAL REGISTRATION

The parent study from which this analysis was derived was registered at ClinicalTrials.gov (Identifier: NCT03010020 ) on January 4, 2017.

Surveillance of HIV-1 primary infections in France from 2014 to 2016: toward stable resistance, but higher diversity, clustering and virulence?

OBJECTIVES

Patients with primary HIV-1 infection (PHI) are a particular population, giving important insight about ongoing evolution of transmitted drug resistance-associated mutation (TDRAM) prevalence, HIV diversity and clustering patterns. We describe these evolutions of PHI patients diagnosed in France from 2014 to 2016.

METHODS

A total of 1121 PHI patients were included. TDRAMs were characterized using the 2009 Stanford list and the French ANRS algorithm. Viral subtypes and recent transmission clusters (RTCs) were also determined.

RESULTS

Patients were mainly MSM (70%) living in the Paris area (42%). TDRAMs were identified among 10.8% of patients and rose to 18.6% when including etravirine and rilpivirine TDRAMs. Prevalences of PI-, NRTI-, first-generation NNRTI-, second-generation NNRTI- and integrase inhibitor-associated TDRAMs were 2.9%, 5.0%, 4.0%, 9.4% and 5.4%, respectively. In a multivariable analysis, age >40 years and non-R5 tropic viruses were associated with a >2-fold increased risk of TDRAMs. Regarding HIV diversity, subtype B and CRF02_AG (where CRF stands for circulating recombinant form) were the two main lineages (56% and 20%, respectively). CRF02_AG was associated with higher viral load than subtype B (5.83 versus 5.40 log10 copies/mL, P=0.004). We identified 138 RTCs ranging from 2 to 14 patients and including overall 41% from the global population. Patients in RTCs were younger, more frequently born in France and more frequently MSM.

CONCLUSIONS

Since 2007, the proportion of TDRAMs has been stable among French PHI patients. Non-B lineages are increasing and may be associated with more virulent CRF02_AG strains. The presence of large RTCs highlights the need for real-time cluster identification to trigger specific prevention action to achieve better control of the epidemic.

Genetic clustering analysis for HIV infection among MSM in Nigeria: implications for intervention

BACKGROUND

The HIV epidemic continues to grow among MSM in countries across sub-Saharan Africa including Nigeria. To inform prevention efforts, we used a phylogenetic cluster method to characterize HIV genetic clusters and factors associated with cluster formation among MSM living with HIV in Nigeria.

METHODS

We analyzed HIV-1 pol sequences from 417 MSM living with HIV enrolled in the TRUST/RV368 cohort between 2013 and 2017 in Abuja and Lagos, Nigeria. A genetically linked cluster was defined among participants whose sequences had pairwise genetic distance of 1.5% or less. Binary and multinomial logistic regressions were used to estimate adjusted odds ratios (AORs) and 95% confidence intervals (CIs) for factors associated with HIV genetic cluster membership and size.

RESULTS

Among 417 MSM living with HIV, 153 (36.7%) were genetically linked. Participants with higher viral load (AOR = 1.72 95% CI: 1.04-2.86), no female partners (AOR = 3.66; 95% CI: 1.97-6.08), and self-identified as male sex (compared with self-identified as bigender) (AOR = 3.42; 95% CI: 1.08-10.78) had higher odds of being in a genetic cluster. Compared with unlinked participants, MSM who had high school education (AOR = 23.84; 95% CI: 2.66-213.49), were employed (AOR = 3.41; 95% CI: 1.89-10.70), had bacterial sexually transmitted infections (AOR = 3.98; 95% CI: 0.89-17.22) and were not taking antiretroviral therapy (AOR = 6.61; 95% CI: 2.25-19.37) had higher odds of being in a large cluster (size > 4).

CONCLUSION

Comprehensive HIV prevention packages should include behavioral and biological components, including early diagnosis and treatment of both HIV and bacterial sexually transmitted infections to optimally reduce the risk of HIV transmission and acquisition.

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

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.

Phylogenetic analysis highlights the role of older people in the transmission of HIV-1 in Fuyang, Anhui Province, China

Background

The proportion of older HIV-1 infected people in China has increased rapidly in recent years. Elucidation of the transmission characteristics of this high-risk population subgroup is helpful for the development of tailored interventions.

Methods

A phylogenetic analysis was performed that uses available HIV-1 pol sequences amplified with nested RT-PCR from plasma samples of all newly diagnosed participants spanning from October 2017 to September 2018 in Fuyang, Anhui Province. Transmission clusters were identified as two or more sequences that shared a corresponding node with an aLRT-SH value ≥90 in the maximum-likelihood phylogenetic tree and had an overall mean genetic distance of ≤1.5%. A local transmission cluster was defined as a cluster that had more than 80% of its sequences from Fuyang. The role of older people in local HIV-1 transmission was determined using an integration of molecular and demographic data.

Results

Of 362 available sequences, 14 subtypes, and 28 local transmission clusters were identified. It was found that the proportion of older people in the local transmission cluster (69/77, 89.61%) was much higher than that of younger people (46/114, 40.35%) (χ² test, P < 0.001). In the pretreatment drug resistance analysis, the proportion of sequences with PDRMs in the local transmission cluster was not significantly different between the older people group (57.14%, 4/7) and non-old-aged group (11.11%, 1/9) (Fisher’s exact test, P > 0.05).

Conclusion

By combining phylogenetic analyses with demographic data, more detailed information was provided about the local transmission structure in Fuyang. These findings suggested that older people play an important role in local transmission, and more tailored interventions for this population subgroup are urgently needed.

In-depth Sampling of High-risk Populations to Characterize HIV Transmission Epidemics Among Young MSM Using PrEP in France and Quebec

Background

A better understanding of HIV transmission dynamics among populations at high risk is important for development of prevention strategies. We determined HIV transmission networks from infected individuals enrolled in the pre-exposure prophylaxis (PrEP) IPERGAY trial in combination with the ANRS PRIMO and Montreal PHI cohorts to identify and characterize active clusters of transmission in this high-risk population.

Methods

Genotypic resistance tests were performed on plasma samples from 31 IPERGAY participants. Reverse transcriptase sequences were analyzed in combination with unique HIV pol sequences from 1351 individuals enrolled in the PRIMO ANRS cohort (1999–2014) and 511 individuals enrolled in the Montreal PHI cohort (1996–2016). Network analyses were performed to infer putative relationships between all participants.

Results

Overall, 1893 participants were included. Transmission network analyses revealed that 14 individuals (45.2%) from the IPERGAY trial were involved in 13 clusters sampled over a median period (interquartile range) of 2 (0.3–7.8) years, including 7 dyads and 6 larger clusters ranging from 4 to 28 individuals. When comparing characteristics between clustering individuals enrolled in the PRIMO cohort (n = 377) and in IPERGAY (n = 14), we found that IPERGAY participants had a higher viral load (5.93 vs 5.20 log₁₀ copies/mL, P = .032) and reported a higher number of partners in the last 2 months (P < .01).

Conclusions

These results demonstrate high rates of HIV transmission clustering among young high-risk MSM enrolled in the IPERGAY trial. In-depth sampling of high-risk populations may help to uncover unobserved transmission intermediaries and improve prevention efforts that could be targeted to the most active clusters.

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.

Molecular Analysis of Human Immunodeficiency Virus Type 1 (HIV-1)-Infected Individuals in a Network-Based Intervention (Transmission Reduction Intervention Project): Phylogenetics Identify HIV-1-Infected Individuals With Social Links

Background

The Transmission Reduction Intervention Project (TRIP) is a network-based intervention that aims at decreasing human immunodeficiency virus type 1 (HIV-1) spread. We herein explore associations between transmission links as estimated by phylogenetic analyses, and social network-based ties among persons who inject drugs (PWID) recruited in TRIP.

Methods

Phylogenetic trees were inferred from HIV-1 sequences of TRIP participants. Highly supported phylogenetic clusters (transmission clusters) were those fulfilling 3 different phylogenetic confidence criteria. Social network-based ties (injecting or sexual partners, same venue engagement) were determined based on personal interviews, recruitment links, and field observation.

Results

TRIP recruited 356 individuals (90.2% PWID) including HIV-negative controls; recently HIV-infected seeds; long-term HIV-infected seeds; and their social network members. Of the 150 HIV-infected participants, 118 (78.7%) were phylogenetically analyzed. Phylogenetic analyses suggested the existence of 13 transmission clusters with 32 sequences. Seven of these clusters included 14 individuals (14/32 [43.8%]) who also had social ties with at least 1 member of their cluster. This proportion was significantly higher than what was expected by chance.

Conclusions

Molecular methods can identify HIV-infected people socially linked with another person in about half of the phylogenetic clusters. This could help public health efforts to locate individuals in networks with high transmission rates.

Comparison of Self-report to Biomarkers of Recent HIV Infection: Findings from the START Trial

Identifying individuals with recent HIV infection is critical to research related to viral reservoirs, outbreak investigations and intervention applications. A multi-assay algorithm (MAA) for recency of infection was used in conjunction with self-reported date of infection and documented date of diagnosis to estimate the number of participants recently infected in the Strategic Timing of AntiRetroviral Treatment (START) trial. We tested samples for three groups of participants from START using a MAA: (1) 167 individuals who reported being infected ≤ 6 months before randomization; (2) 771 individuals who did not know their date of infection but were diagnosed within 6 months before randomization; and (3) as controls for the MAA, 199 individuals diagnosed with HIV ≥ 2 years before randomization. Participants with low titer and avidity and a baseline viral load > 400 copies/mL were classified as recently infected. A significantly higher percentage of participants who self-reported being infected ≤ 6 months were classified as recently infected compared to participants diagnosed ≥ 2 years (65% [109/167] vs. 2.5% [5/199], p < 0.001). Among the 771 individuals who did not know their duration of infection at randomization, 206 (26.7%) were classified as recently infected. Among those diagnosed with HIV in the 6 months prior to enrollment, the 373 participants who reported recent infection (n = 167) or who had confirmed recent infection by the MAA (n = 206) differed significantly on a number of baseline characteristics from those who had an unknown date of infection and were not confirmed by the MAA (n = 565). Participants recently infected by self-report and/or MAA were younger, more likely to be Asian, less likely to be black, less likely to be heterosexual, more likely to be enrolled at sites in the U.S., Europe or Australia, and have higher HIV RNA levels. There was good agreement between self-report of recency of infection and the MAA. We estimate that 373 participants enrolled in START were infected within 6 months of randomization. Compared to those not recently infected, these participants were younger, had higher HIV RNA levels and were more likely to come from high income countries and from populations such as MSM with more regular HIV testing.

Network Viral Load: A Critical Metric for HIV Elimination

BACKGROUND

Associations have been observed between an aggregate viral load measure, the community viral load, and new HIV diagnoses. The community viral load aggregates viral loads within chosen geographic areas, restricting inferences about HIV acquisition risk to these areas. We develop a more precise metric, the network viral load (NVL), to measure the composite viral load within a risk network of a HIV-negative individual.

METHODS

We examined the relationship between NVL and HIV infection among young men who have sex with men in Chicago, United States. Networks were generated using respondent-driven sampling. NVL was defined as the prevalence of viremic individuals in one's risk network, characterized as those with a viral load ≥20 k copies per milliliter. Permutation tests were conducted to account for dependency.

RESULTS

After controlling for total connections, age, substance use during sex, syphilis diagnosis (previous 12 months), and frequency of condomless anal sex (previous 6 months), we found a positive association between NVL and HIV infection. Compared with a network with all HIV-seronegative members, the odds of HIV infection with an NVL of <10% viremia were 1.85 (95% confidence interval: 1.18 to 2.92) times higher and those with an NVL of ≥10% viremia were 2.73 (95% confidence interval: 1.54 to 4.85) times higher.

CONCLUSIONS

We found a positive association between NVL and HIV seroprevalence. Although limited in its ability to infer causality, NVL could have substantial public health implications for persons most at risk for HIV infection, given that this novel metric avoids overreliance on individual level behavior or broad community indices.

Short Communication: Lack of Support for Socially Connected HIV-1 Transmission Among Young Adult Black Men Who Have Sex with Men

We explore the phylogenetic relationships among HIV sequences sampled from young adult black men who have sex with men (YAB-MSM), who are connected through peer referral/social ties and who attend common venues. Using 196 viral sequences sampled from the peripheral blood mononuclear cells of 10 individuals, our preliminary phylogenetic results indicate that these socially connected YAB-MSM are infected with distantly related viruses and provide no evidence for viral transmission between network members. Our results suggest that HIV-prevention strategies that target young adult MSM should extend beyond their network members and local community.

Defining HIV-1 transmission clusters based on sequence data

Understanding HIV-1 transmission dynamics is relevant to both screening and intervention strategies of HIV-1 infection. Commonly, HIV-1 transmission chains are determined based on sequence similarity assessed either directly from a sequence alignment or by inferring a phylogenetic tree. This review is aimed at both nonexperts interested in understanding and interpreting studies of HIV-1 transmission, and experts interested in finding the most appropriate cluster definition for a specific dataset and research question. We start by introducing the concepts and methodologies of how HIV-1 transmission clusters usually have been defined. We then present the results of a systematic review of 105 HIV-1 molecular epidemiology studies summarizing the most common methods and definitions in the literature. Finally, we offer our perspectives on how HIV-1 transmission clusters can be defined and provide some guidance based on examples from real life datasets.

Social and Genetic Networks of HIV-1 Transmission in New York City

Background

Sexually transmitted infections spread across contact networks. Partner elicitation and notification are commonly used public health tools to identify, notify, and offer testing to persons linked in these contact networks. For HIV-1, a rapidly evolving pathogen with low per-contact transmission rates, viral genetic sequences are an additional source of data that can be used to infer or refine transmission networks.

Methods and Findings

The New York City Department of Health and Mental Hygiene interviews individuals newly diagnosed with HIV and elicits names of sexual and injection drug using partners. By law, the Department of Health also receives HIV sequences when these individuals enter healthcare and their physicians order resistance testing. Our study used both HIV sequence and partner naming data from 1342 HIV-infected persons in New York City between 2006 and 2012 to infer and compare sexual/drug-use named partner and genetic transmission networks. Using these networks, we determined a range of genetic distance thresholds suitable for identifying potential transmission partners. In 48% of cases, named partners were infected with genetically closely related viruses, compatible with but not necessarily representing or implying, direct transmission. Partner pairs linked through the genetic similarity of their HIV sequences were also linked by naming in 53% of cases. Persons who reported high-risk heterosexual contact were more likely to name at least one partner with a genetically similar virus than those reporting their risk as injection drug use or men who have sex with men.

Conclusions

We analyzed an unprecedentedly large and detailed partner tracing and HIV sequence dataset and determined an empirically justified range of genetic distance thresholds for identifying potential transmission partners. We conclude that genetic linkage provides more reliable evidence for identifying potential transmission partners than partner naming, highlighting the importance and complementarity of both epidemiological and molecular genetic surveillance for characterizing regional HIV-1 epidemics.

Understanding the path over which viruses such as HIV have been transmitted may be crucial for directing public health resources and guiding policy decisions. Contact tracing of named sexual and injection drug-use partners of people recently diagnosed with HIV is an indispensible tool for reconstructing this transmission network. Viral genetic sequence data—routinely collected by public health agencies—can also be used to infer the dynamics of HIV transmission. We analyzed partner naming and viral genetic sequence data in 1342 people living with HIV in New York City reported to the New York City Department of Health and Mental Hygiene between 2006 and 2012. Genetically linked partners were more likely to be named partners than named partners were to be genetically linked. This finding indicates that genetic sequence data are better than partner naming data for reconstructing this viral transmission network. Importantly, the success rate in naming a genetically linked partner varied by transmission risk category (e.g., men who have sex with men, heterosexuals, and injection drug users). This study validates the use viral genetic sequences in reconstructing these viral transmission networks in a public health surveillance setting.

A Systematic Review of Published Respondent-Driven Sampling Surveys Collecting Behavioral and Biologic Data

Reporting key details of respondent-driven sampling (RDS) survey implementation and analysis is essential for assessing the quality of RDS surveys. RDS is both a recruitment and analytic method and, as such, it is important to adequately describe both aspects in publications. We extracted data from peer-reviewed literature published through September, 2013 that reported collected biological specimens using RDS. We identified 151 eligible peer-reviewed articles describing 222 surveys conducted in seven regions throughout the world. Most published surveys reported basic implementation information such as survey city, country, year, population sampled, interview method, and final sample size. However, many surveys did not report essential methodological and analytical information for assessing RDS survey quality, including number of recruitment sites, seeds at start and end, maximum number of waves, and whether data were adjusted for network size. Understanding the quality of data collection and analysis in RDS is useful for effectively planning public health service delivery and funding priorities.

A comparative analysis of behaviors and sexual affiliation networks among men who have sex with men in Hong Kong

In Hong Kong, men who have sex with men (MSM) account for a significant proportion of HIV infections. While perceived as a hidden population, they constitute a distinct social network shaped by their differential use of unique channels for sex partnership. To characterize their pattern of connectivity and association with high-risk sexual behaviors, 311 MSM were recruited via saunas and the internet to participate in a questionnaire survey. Internet recruits were younger, and many (31/43) were solely reliant on the internet to seek sex partners, while visiting a similar number of venues as the sauna recruits (p = 0.98). Internet users generally had a high frequency of unprotected anal intercourse (UAI). MSM who had visited only a single venue reported more UAI with their regular partners (adjusted OR 6.86, 1.88-24.96) and sought fewer casual partners than those frequenting multiple venues (adjusted OR 0.33, 0.19-0.60). This study provides evidence for the heterogeneity of the sexual affiliation networks of MSM in Hong Kong. High HIV risk of UAI could be offset by fewer casual partners in certain venues, the implications of which would need to be explored in longitudinal studies. Methodologically, internet sampling was very efficient in identifying sex networking venues, while internet recruits gave a high retention rate for updating profiles. However, sampling at high centrality saunas did not necessarily identify the MSM-affiliating venues in the networks efficiently. The sampling strategy of MSM survey should therefore be objective-driven, which may differ for health message dissemination and social marketing, versus HIV surveillance or risk assessment.

HIV Drug Resistance Surveillance Among Jamaican Men Who Have Sex with Men Should Be Prioritized for Reducing HIV Transmission

The prevalence of human immunodeficiency virus type 1 (HIV-1) is highest among men who have sex with men (MSM) in Jamaica but no genotypic data are available on the virus strains that are responsible for the epidemic among this key population. HIV-1 polymerase (pol) genes from 65 MSM were sequenced and used to predict drug resistance mutations. An HIV drug resistance prevalence of 28% (minimum 13%) was observed among this cohort, with the most frequent mutations conferring resistance to efavirenz, nevirapine, and lamivudine. Phylogenetic analysis of the sequences revealed 10 times the number of linked HIV infections among this cohort than respondent reporting. HIV treatment and prevention efforts in Jamaica could benefit significantly from Pol genotyping of the HIV strains infecting socially vulnerable MSM prior to initiating antiretroviral therapy (ART), as this would guide suppressive ART and unearth HIV transmission clusters to enable more effective delivery of treatment and prevention programs.

Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering

To improve the methodology of HIV cluster analysis, we addressed how analysis of HIV clustering is associated with parameters that can affect the outcome of viral clustering. The extent of HIV clustering and tree certainty was compared between 401 HIV-1C near full-length genome sequences and subgenomic regions retrieved from the LANL HIV Database. Sliding window analysis was based on 99 windows of 1,000 bp and 45 windows of 2,000 bp. Potential associations between the extent of HIV clustering and sequence length and the number of variable and informative sites were evaluated. The near full-length genome HIV sequences showed the highest extent of HIV clustering and the highest tree certainty. At the bootstrap threshold of 0.80 in maximum likelihood (ML) analysis, 58.9% of near full-length HIV-1C sequences but only 15.5% of partial pol sequences (ViroSeq) were found in clusters. Among HIV-1 structural genes, pol showed the highest extent of clustering (38.9% at a bootstrap threshold of 0.80), although it was significantly lower than in the near full-length genome sequences. The extent of HIV clustering was significantly higher for sliding windows of 2,000 bp than 1,000 bp. We found a strong association between the sequence length and proportion of HIV sequences in clusters, and a moderate association between the number of variable and informative sites and the proportion of HIV sequences in clusters. In HIV cluster analysis, the extent of detectable HIV clustering is directly associated with the length of viral sequences used, as well as the number of variable and informative sites. Near full-length genome sequences could provide the most informative HIV cluster analysis. Selected subgenomic regions with a high extent of HIV clustering and high tree certainty could also be considered as a second choice.

Methods for Collection of Participant-aided Sociograms for the Study of Social, Sexual and Substance-using Networks Among Young Men Who Have Sex with Men

In this study, we adapted and tested a participant-aided sociogram approach for the study of the social, sexual, and substance use networks of young men who have sex with men (YMSM); a population of increasing and disproportionate risk of HIV infection. We used a combination of two interviewer-administered procedures: completion of a pre-numbered list form to enumerate alters and to capture alter attributes; and a participant-aided sociogram to capture respondent report of interactions between alters on an erasable whiteboard. We followed the collection of alter interactions via the sociogram with a traditional matrix-based tie elicitation approach for a sub-sample of respondents for comparison purposes. Digital photographs of each network drawn on the whiteboard serve as the raw data for entry into a database in which group interactions are stored. Visual feedback of the network was created at the point of data entry, using NetDraw network visualization software for comparison to the network structure elicited via the sociogram. In a sample of 175 YMSM, we found this approach to be feasible and reliable, with high rates of participation among those eligible for the study and substantial agreement between the participant-aided sociogram in comparison to a traditional matrix-based approach. We believe that key strengths of this approach are the engagement and maintenance of participant attention and reduction of participant burden for alter tie elicitation. A key weakness is the challenge of entry of interview-based list form and sociogram data into the database. Our experience suggests that this approach to data collection is feasible and particularly appropriate for an adolescent and young adult population. This builds on and advances visualization-based approaches to social network data collection.

Nonprobability and probability-based sampling strategies in sexual science

With few exceptions, much of sexual science builds upon data from opportunistic nonprobability samples of limited generalizability. Although probability-based studies are considered the gold standard in terms of generalizability, they are costly to apply to many of the hard-to-reach populations of interest to sexologists. The present article discusses recent conclusions by sampling experts that have relevance to sexual science that advocates for nonprobability methods. In this regard, we provide an overview of Internet sampling as a useful, cost-efficient, nonprobability sampling method of value to sex researchers conducting modeling work or clinical trials. We also argue that probability-based sampling methods may be more readily applied in sex research with hard-to-reach populations than is typically thought. In this context, we provide three case studies that utilize qualitative and quantitative techniques directed at reducing limitations in applying probability-based sampling to hard-to-reach populations: indigenous Peruvians, African American youth, and urban men who have sex with men (MSM). Recommendations are made with regard to presampling studies, adaptive and disproportionate sampling methods, and strategies that may be utilized in evaluating nonprobability and probability-based sampling methods.

Social networks, sexual networks and HIV risk in men who have sex with men

Worldwide, men who have sex with men (MSM) remain one of the most HIV-vulnerable community populations. A global public health priority is developing new methods of reaching MSM, understanding HIV transmission patterns, and intervening to reduce their risk. Increased attention is being given to the role that MSM networks play in HIV epidemiology. This review of MSM network research studies demonstrates that: (1) Members of the same social network often share similar norms, attitudes, and HIV risk behavior levels; (2) Network interventions are feasible and powerful for reducing unprotected sex and potentially for increasing HIV testing uptake; (3) HIV vulnerability among African American MSM increases when an individual enters a high-risk sexual network characterized by high density and racial homogeneity; and (4) Networks are primary sources of social support for MSM, particularly for those living with HIV, with greater support predicting higher care uptake and adherence.

Antiretroviral therapy uptake, attrition, adherence and outcomes among HIV-infected female sex workers: a systematic review and meta-analysis

Purpose

We aimed to characterize the antiretroviral therapy (ART) cascade among female sex workers (FSWs) globally.

Methods

We systematically searched PubMed, Embase and MEDLINE in March 2014 to identify studies reporting on ART uptake, attrition, adherence, and outcomes (viral suppression or CD4 count improvements) among HIV-infected FSWs globally. When possible, available estimates were pooled using random effects meta-analyses (with heterogeneity assessed using Cochran's Q test and I² statistic).

Results

39 studies, reporting on 21 different FSW study populations in Asia, Africa, North America, South America, and Central America and the Caribbean, were included. Current ART use among HIV-infected FSWs was 38% (95% CI: 29%–48%, I² = 96%, 15 studies), and estimates were similar between high-, and low- and middle-income countries. Ever ART use among HIV-infected FSWs was greater in high-income countries (80%; 95% CI: 48%–94%, I² = 70%, 2 studies) compared to low- and middle-income countries (36%; 95% CI: 7%–81%, I² = 99%, 3 studies). Loss to follow-up after ART initiation was 6% (95% CI: 3%–11%, I² = 0%, 3 studies) and death after ART initiation was 6% (95% CI: 3%–11%, I² = 0%, 3 studies). The fraction adherent to ≥95% of prescribed pills was 76% (95% CI: 68%–83%, I² = 36%, 4 studies), and 57% (95% CI: 46%–68%, I² = 82%, 4 studies) of FSWs on ART were virally suppressed. Median gains in CD4 count after 6 to 36 months on ART, ranged between 103 and 241 cells/mm³ (4 studies).

Conclusions

Despite global increases in ART coverage, there is a concerning lack of published data on HIV treatment for FSWs. Available data suggest that FSWs can achieve levels of ART uptake, retention, adherence, and treatment response comparable to that seen among women in the general population, but these data are from only a few research settings. More routine programme data on HIV treatment among FSWs across settings should be collected and disseminated.

Molecular tools for studying HIV transmission in sexual networks

PURPOSE OF REVIEW

Phylogenetics is frequently used for studies of population-based HIV transmission. The purpose of this review is to highlight the current utilities and limitations of phylogenetics in HIV epidemiological research from sample collection through to data analysis.

RECENT FINDINGS

Studies of HIV phylogenies can provide critical information about HIV epidemics that are otherwise difficult to obtain through traditional study design such as transmission of drug-resistant virus, mixing between demographic groups, and rapidity of viral spread within populations. However, recent results from empirical and theoretical studies of HIV phylogenies challenge some of the key assumptions and interpretations from phylogenetic studies. Recent findings include lack of transmission bottlenecks in MSM and injection drug use epidemics, evidence for preferential transmission of HIV virus in heterosexual epidemics, and limited evidence that tree topologies correlate directly with underlying network structures. Other challenges include a lack of a standardized definition for a phylogenetic transmission cluster and biased or sparse sampling of HIV transmission networks.

SUMMARY

Phylogenetics is an important tool for HIV research, and offers opportunities to understand critical aspects of the HIV epidemic. Like all epidemiological research, the methods used and interpretation of results from phylogenetic studies should be made cautiously with careful consideration.

Epidemiology of HIV in Latin America and the Caribbean

PURPOSE OF REVIEW

The aim of the present review is to update HIV/AIDS Epidemiology in Latin America and the Caribbean highlighting the concentrated aspect of epidemic in the region.

RECENT FINDINGS

Among general population, HIV prevalence in Latin America is at stable levels (0.2-0.7%). The Caribbean still has one of the highest HIV prevalence rates in the world (<0.1-3%), but incidences have declined around 49%. This is not the current situation for high-risk key populations; most incident cases occur among MSM. Available data on transgender women suggest that they are the most-at-risk group. Female sex workers still have a 12-fold the chance of being HIV positive compared with other women. IDU prevalence was revised to 0.45%, but non-IDU has been suggested as a mediator between sexual risk and HIV.

SUMMARY

The increase in treatment coverage (mean is at 63%) resulted in modifications of HIV/AIDS epidemiology. New strategies to seek, test and link key populations to care are urgently needed and targeted interventions to prevent HIV expansion among them must be adopted. These strategies should consider the particular situation regarding social inequalities, discrimination and violence that pervade the HIV epidemic among key populations.

The HIV care cascade and antiretroviral therapy in female sex workers: implications for HIV prevention

To achieve viral suppression and fully benefit from antiretroviral therapy (ART), it is important that individuals with HIV know that they are HIV infected, link to and remain in HIV care, start and remain on ART and adhere to treatment. In HIV epidemics where female sex workers (FSWs) are key drivers of HIV transmission, the extent to which FSWs use ART and engage in the HIV care cascade could have a considerable impact on HIV transmission from FSWs to the wider population. In this article we review the spectrum of FSW engagement in the HIV care cascade, look at the impact of the HIV care cascade and ART use among FSWs on population-level HIV transmission and discuss HIV prevention for FSWs in the context of ART and the HIV care cascade.

STI patients are effective recruiters of undiagnosed cases of HIV: results of a social contact recruitment study in Malawi

BACKGROUND

Patients with newly diagnosed HIV may be part of social networks with elevated prevalence of undiagnosed HIV infection. Social network recruitment by persons with newly diagnosed HIV may efficiently identify undiagnosed cases of HIV infection. We assessed social network recruitment as a strategy for identifying undiagnosed cases of HIV infection.

METHODS

In a sexually transmitted infection (STI) clinic in Lilongwe, Malawi, 3 groups of 45 "seeds" were enrolled: STI patients with newly diagnosed HIV, STI patients who were HIV-uninfected, and community controls. Seeds were asked to recruit up to 5 social "contacts" (sexual or nonsexual). Mean number of contacts recruited per group was calculated. HIV prevalence ratios (PRs) and number of contacts needed to test to identify 1 new case of HIV were compared between groups using generalized estimating equations with exchangeable correlation matrices.

RESULTS

Mean number of contacts recruited was 1.3 for HIV-infected clinic seeds, 1.8 for HIV-uninfected clinic seeds, and 2.3 for community seeds. Contacts of HIV-infected clinic seeds had a higher HIV prevalence (PR: 3.2, 95% confidence interval: 1.3 to 7.8) than contacts of community seeds, but contacts of HIV-uninfected clinic seeds did not (PR: 1.1, 95% confidence interval: 0.4 to 3.3). Results were similar when restricted to nonsexual contacts. To identify 1 new case of HIV, it was necessary to test 8 contacts of HIV-infected clinic seeds, 10 contacts of HIV-uninfected clinic seeds, and 18 contacts of community seeds.

CONCLUSIONS

Social contact recruitment by newly diagnosed STI patients efficiently led to new HIV diagnoses. Research to replicate findings and guide implementation is needed.

'Getting to zero' in Asia and the Pacific through more strategic use of antiretrovirals for HIV prevention

Encouraged by experimental trials demonstrating the efficacy of antiretrovirals (ARVs) in preventing HIV infection, countries across the Asia-Pacific region have committed to the achievement of ambitious targets tantamount to ending AIDS. The available data suggest that some countries still can make progress through targeted condom promotion and the expansion of harm-reduction interventions, but that none may realise its vision of ‘zero new HIV infections’ without more strategic use of ARVs as part of a combination of HIV prevention efforts targeting key populations. Low rates of HIV testing among men who have sex with men, people who inject drugs, sex workers and other key populations evidence low treatment coverage where treatment could have the greatest impact on curbing local epidemics. Studies have demonstrated the promise of adding ARV treatment and pre-exposure prophylaxis to the existing HIV prevention toolkit, but achieving population-level impact will require service-delivery approaches that overcome traditional prevention, care and treatment program distinctions. Priorities include: (1) innovative strategies to reach, test, treat and retain in services the individuals most likely to acquire or transmit HIV; (2) task shifting and enhanced partnerships between the public sector and civil society; (3) improved ‘cascade’ data systems to assess and promote service uptake and retention; and (4) policy and financing reform to enhance HIV testing and treatment access among key populations.

Phylogenetic relatedness of circulating HIV-1C variants in Mochudi, Botswana

BACKGROUND

Determining patterns of HIV transmission is increasingly important for the most efficient use of modern prevention interventions. HIV phylogeny can provide a better understanding of the mechanisms underlying HIV transmission networks in communities.

METHODS

To reconstruct the structure and dynamics of a local HIV/AIDS epidemic, the phylogenetic relatedness of HIV-1 subtype C env sequences obtained from 785 HIV-infected community residents in the northeastern sector of Mochudi, Botswana, during 2010-2013 was estimated. The genotyping coverage was estimated at 44%. Clusters were defined based on relatedness of HIV-1C env sequences and bootstrap support of splits.

RESULTS

The overall proportion of clustered HIV-1C env sequences was 19.1% (95% CI 17.5% to 20.8%). The proportion of clustered sequences from Mochudi was significantly higher than the proportion of non-Mochudi sequences that clustered, 27.0% vs. 14.7% (p = 5.8E-12; Fisher exact test). The majority of clustered Mochudi sequences (90.1%; 95% CI 85.1% to 93.6%) were found in the Mochudi-unique clusters. None of the sequences from Mochudi clustered with any of the 1,244 non-Botswana HIV-1C sequences. At least 83 distinct HIV-1C variants, or chains of HIV transmission, in Mochudi were enumerated, and their sequence signatures were reconstructed. Seven of 20 genotyped seroconverters were found in 7 distinct clusters.

CONCLUSIONS

The study provides essential characteristics of the HIV transmission network in a community in Botswana, suggests the importance of high sampling coverage, and highlights the need for broad HIV genotyping to determine the spread of community-unique and community-mixed viral variants circulating in local epidemics. The proposed methodology of cluster analysis enumerates circulating HIV variants and can work well for surveillance of HIV transmission networks. HIV genotyping at the community level can help to optimize and balance HIV prevention strategies in trials and combined intervention packages.