HIV Transmission Networks in the San Diego-Tijuana Border Region

HIV-1 transmission dynamics among people who inject drugs on the US/Mexico border during the COVID-19 pandemic: a prosepective cohort study

Background

We examined HIV prevalence and transmission dynamics among people who inject drugs in the U.S./Mexico border region during the COVID-19 pandemic.

Methods

People who inject drugs aged ≥18 years from 3 groups were recruited: people who inject drugs who live in San Diego (SD) and engaged in cross-border drug use in Tijuana, Mexico (SD CBDUs), and people who inject drugs in SD and Tijuana (TJ) who did not engage in cross-border drug use (NCBDUs). We computed HIV prevalence at baseline and bivariate incidence-density rates (IR) at 18-month follow-up. Bayesian phylogenetic analysis was used to identify local transmission clusters, estimate their age, and effective reproductive number (Re) over time within the clusters.

Findings

At baseline (n = 612), 26% of participants were female, 9% engaged in sex work, and HIV prevalence was 8% (4% SD CBDU, 4% SD NCBDU, 16% TJ NCBDU). Nine HIV seroconversions occurred over 18 months, IR: 1.357 per 100 person-years (95% CI: 0.470, 2.243); 7 in TJ NCBDU and 2 in SD CBDU. Out of 16 identified phylogenetic clusters, 9 (56%) had sequences from both the U.S. and Mexico (mixed-country). The age of three youngest mixed-country dyads (2018-2021) overlapped with the COVID-related US-Mexico border closure in 2020. One large mixed-country cluster (N = 15) continued to grow during the border closure (Re = 4.8, 95% Highest Posterior Density (HPD) 1.5-9.1) with 47% engaging in sex work.

Interpretation

Amidst the COVID-19 pandemic and the border closure, cross-border HIV clusters grew. Efforts to end the HIV epidemic in the U.S. should take into account cross-border HIV-1 transmission from Tijuana. Mobile harm reduction services and coordination with municipal HIV programs to initiate anti-retroviral therapy and pre-exposure prophylaxisis are needed to reduce transmission.

Funding

This research was supported by the James B. Pendleton Charitable Trust and the San Diego Center for AIDS Research.

Long-acting Injectable PrEP Interest and General PrEP Awareness among People who Inject Drugs in the San Diego-Tijuana Border Metroplex

Long-acting injectable HIV pre-exposure prophylaxis (LAI-PrEP) could help overcome multilevel challenges to HIV prevention for people who inject drugs (PWID), including those in the binational San Diego-Tijuana metroplex. Yet, general PrEP awareness and interest in LAI-PrEP remain underexplored among PWID. From 2020 to 2021, 562 HIV-negative PWID in San Diego and Tijuana completed surveys assessing general PrEP awareness and interest in oral and LAI-PrEP. Modified Poisson regression examined factors associated with general PrEP awareness. Multinomial logistic regression assessed factors associated with interest in both oral and LAI-PrEP, oral PrEP only, LAI-PrEP only, or neither. General PrEP awareness was low (18%) and associated with experiencing unsheltered homelessness (adjusted prevalence ratio [APR] = 1.50, 95% confidence interval [CI]: 0.96-2.33), past 6-month fentanyl injection (APR = 1.53, 95% CI: 1.04-2.25), and transactional sex (APR = 1.71, 95% CI: 1.06-2.76). Interest in oral PrEP only was most common (44%), followed by LAI-PrEP only (25%) and neither (16%). Compared to the odds of being interested in LAI-PrEP only, the odds of being interested in oral PrEP only were lower among those who were stopped by police (AOR = 0.38, 95% CI: 0.22-0.65), reported past 6-month fentanyl injection (AOR = 0.33, 95% CI: 0.20-0.56), polydrug use (AOR = 0.48, 95% CI: 0.27-0.86), injecting multiple times daily (AOR = 0.26, 95% CI: 0.14-0.46), receptive syringe use (AOR = 0.30, 95% CI: 0.19-0.49), and higher perceived HIV risk (AOR = 0.24, 95% CI: 0.15-0.39). Interest in LAI-PrEP was more common among PWID reporting social and structural factors that could interfere with oral PrEP adherence, suggesting LAI-PrEP implementation could increase PrEP coverage among those most vulnerable to HIV.

Interpersonal and Community-Level Influences Across the PrEP Cascade Among Young Adult Latinx Men who Have Sex with Men Living in a US-Mexico Border Region: A Qualitative Study

Latinx men who have sex with men (MSM) are an at-risk population for new HIV diagnoses. Pre-exposure prophylaxis (PrEP) is a suite of biomedical approaches to prevent HIV infection. Latinx MSM are less likely to take PrEP compared to non-Latinx White MSM. This qualitative study identified interpersonal- and community-level barriers and facilitators of PrEP among young adult Latinx MSM. Using stratified purposeful sampling, 27 Latinx men, ages 19-29 years and living in a US-Mexico border region, completed self-report demographic surveys and participated in semi-structured in-depth interviews assessing barriers and facilitators to PrEP. Directed content analysis was used to identify both a priori and emerging themes. Most participants reported that other people, including peers, friends, partners, and health care providers were both supportive and discouraging of PrEP use. Participants' intersectional identities as members of both Latinx and LGBTQ+ (Lesbian, Gay, Bisexual, Transgender, Queer) communities both hindered and facilitated PrEP use.

Distinct Rates and Transmission Patterns of Major HIV-1 Subtypes among Men who Have Sex with Men in Guangxi, China

The diversity and transmission patterns of major HIV-1 subtypes among MSM population in Guangxi remains unknown. Understanding the characteristics is crucial for effective intervention strategies. Between 2016 and 2021, we recruited individuals newly diagnosed with HIV-1 from MSM population in Guangxi. HIV-1 pol region was amplified and sequenced, and constructed molecular network, assessed clustering rate, cluster growth rate, spatial clustering, and calculating the basic reproductive number (R0) based on sequences data. We identified 16 prevalent HIV-1 subtypes among Guangxi MSM, with CRF07_BC (53.1%), CRF01_AE (26.23%), and CRF55_01B (12.96%) predominating. In the network, 618 individuals (66.17%) formed 59 clusters. Factors contributing to clustering included age < 30 years (AOR = 1.35), unmarried status (AOR = 1.67), CRF07_BC subtype (AOR = 3.21), and high viral load (AOR = 1.43). CRF07_BC had a higher likelihood of forming larger clusters and having higher degree than CRF01_AE and CRF55_01B. Notably, CRF07_BC has higher cluster growth rate and higher basic reproductive number than CRF01_AE and CRF55_01B. Our findings underscore CRF07_BC as a prominent driver of HIV-1 spread among Guangxi's MSM population, highlighting the viability of targeted interventions directed at specific subtypes and super clusters to control HIV-1 transmission within this population.

Willingness to use and distribute HIV self-testing kits among people who inject drugs in the San Diego-Tijuana border region

BACKGROUND

HIV self-testing (HIVST) could increase HIV testing access among people who inject drugs (PWID), and secondary distribution (i.e., peer-delivery) of HIVST kits in PWID social networks could further expand coverage. We assessed willingness to use and distribute HIVST kits among PWID in the San Diego-Tijuana border region.

METHODS

From 2020 to 2021, HIV-negative PWID in San Diego, USA, and Tijuana, Mexico, completed surveys and provided data on individual (N = 539) and social network (N = 366) characteristics. We used modified Poisson regression to examine the effects of individual and social network characteristics on willingness to use and distribute HIVST kits.

RESULTS

Most participants were willing to use (81%) and distribute (81%) HIVST kits. At the individual level, prior HIV testing was positively associated with willingness to use (adjusted prevalence ratio [aPR] = 1.24, 95% confidence interval [CI] 1.10-1.40) and distribute (aPR = 1.27, 95% CI 1.12-1.43) HIVST kits, while perceiving oneself to be at higher HIV risk than others was negatively associated with willingness to use HIVST kits (aPR = 0.83, 95% CI 0.74-0.93). At the network level, willingness to distribute HIVST kits was positively associated with network size (aPR = 1.04 per member, 95% CI 1.01-1.08) and greater proportions of one's network encouraging them to use drugs (aPR = 1.29, 95% CI 1.16-1.44) and having a history of homelessness (aPR = 1.51, 95% CI 1.31-1.74) or detention/arrest (aPR = 1.57, 95% CI 1.36-1.82), and negatively associated with a greater proportion of one's network including "very close" persons (aPR = 0.80, 95% CI 0.69-0.94).

CONCLUSIONS

We found high potential for HIVST kits and their secondary distribution to increase HIV testing among PWID who face the greatest barriers to facility-based testing.

WaSH insecurity and anxiety among people who inject drugs in the Tijuana-San Diego border region

BACKGROUND

Water, sanitation, and hygiene (WaSH) insecurity increases the risk of water-related diseases. However, limited research has been conducted on psychosocial distress as it relates to WaSH insecurity, especially among people who inject drugs (PWID). We examined the relationship between WaSH insecurity and related anxiety among PWID living in different housing conditions along the US-Mexico border region.

METHODS

From 2020-2021, a cross-sectional study was conducted among 585 people who injected drugs within the last month in Tijuana (N = 202), San Diego (N = 182), and in both Tijuana and San Diego (N = 201). Participants underwent interviewer-administered surveys related to WaSH access, substance use, and generalized anxiety disorder (GAD-7). Quasi-Poisson regressions were used to assess associations between WaSH insecurity and anxiety in the prior 6-months.

RESULTS

Participants were 75% male, 42% were unhoused and 91% experienced WaSH insecurity in the prior 6-months. After adjusting for housing status, gender, and age, lack of access to basic drinking water (Adj RR: 1.28; 95% CI: 1.02-1.58), sanitation (Adj RR:1.28; 95% CI: 1.07-1.55), and a daily bath/shower (Adj RR: 1.38; 95% CI: 1.15-1.66) were associated with mild-severe anxiety. The number of WaSH insecurities was independently associated with a 20% increased risk of experiencing anxiety per every additional insecurity experienced (Adj RR: 1.20; CI: 1.12-1.27). We also found a significant interaction between gender and housing status (p = 0.003), indicating that among people experiencing sheltered/unsheltered homelessness, women had a higher risk of mild-severe anxiety compared to men (Adj RR: 1.55; 95% CI: 1.27-1.89). At the same time, among women, those who are unhoused have 37% increased risk of anxiety than those who live in stable housing conditions (Adj RR: 1.37; 95% CI: 1.01-1.89).

CONCLUSION

The lack of specific WaSH services, particularly lack of drinking water, toilets, and daily showers were associated with higher levels of anxiety among PWID in the Tijuana-San Diego border region. Women experiencing homelessness were especially vulnerable. WaSH interventions that provide safe, 24-h access may help to reduce anxiety and health risks associated with WaSH insecurity.

Network-level HIV risk norms are associated with individual-level HIV risk and harm reduction behaviors among people who inject drugs: a latent profile analysis

The COVID-19 related U.S.-Mexico border-crossing restrictions disrupted social networks and HIV harm reduction services among people who inject drugs (PWID) in San Diego and Tijuana. We assessed associations of descriptive network norms on PWID's HIV vulnerability during this period. Between 10/2020 and 10/2021, 399 PWID completed a behavioral and egocentric questionnaire. We used Latent Profile Analysis to categorize PWID into network norm risk profiles based on proportions of their network (n = 924 drug use alters) who injected drugs and engaged in cross-border drug use (CBDU), among other vulnerabilities. We used logistic and linear regressions to assess network profile associations with individual-level index of HIV vulnerability and harm reduction behaviors. Fit indices specified a 4-latent profile solution of descriptive network risk norms: lower (n = 178), moderate with (n = 34) and without (n = 94) CBDU and obtainment, and higher (n = 93). Participants in higher risk profiles reported more HIV vulnerability behaviors and fewer harm reduction behaviors. PWID's gradient of HIV risk was associated with network norms, warranting intervention on high-vulnerability networks when services are limited.

Phylodynamics of HIV in the Mexico City Metropolitan Region

Evolutionary analyses of viral sequences can provide insights into transmission dynamics, which in turn can optimize prevention interventions. Here, we characterized the dynamics of HIV transmission within the Mexico City metropolitan area. HIV pol sequences from persons recently diagnosed at the largest HIV clinic in Mexico City (between 2016 and 2021) were annotated with demographic/geographic metadata. A multistep phylogenetic approach was applied to identify putative transmission clades. A data set of publicly available sequences was used to assess international introductions. Clades were analyzed with a discrete phylogeographic model to evaluate the timing and intensity of HIV introductions and transmission dynamics among municipalities in the region. A total of 6,802 sequences across 96 municipalities (5,192 from Mexico City and 1,610 from the neighboring State of Mexico) were included (93.6% cisgender men, 5.0% cisgender women, and 1.3% transgender women); 3,971 of these sequences formed 1,206 clusters, involving 78 municipalities, including 89 clusters of ≥10 sequences. Discrete phylogeographic analysis revealed (i) 1,032 viral introductions into the region, over one-half of which were from the United States, and (ii) 354 migration events between municipalities with high support (adjusted Bayes factor of ≥3). The most frequent viral migrations occurred between northern municipalities within Mexico City, i.e., Cuauhtémoc to Iztapalapa (5.2% of events), Iztapalapa to Gustavo A. Madero (5.4%), and Gustavo A. Madero to Cuauhtémoc (6.5%). Our analysis illustrates the complexity of HIV transmission within the Mexico City metropolitan area but also identifies a spatially active transmission area involving a few municipalities in the north of the city, where targeted interventions could have a more pronounced effect on the entire regional epidemic. IMPORTANCE Phylogeographic investigation of the Mexico City HIV epidemic illustrates the complexity of HIV transmission in the region. An active transmission area involving a few municipalities in the north of the city, with transmission links throughout the region, is identified and could be a location where targeted interventions could have a more pronounced effect on the entire regional epidemic, compared with those dispersed in other manners.

Long-Acting Injectable Human Immunodeficiency Virus Pre-Exposure Prophylaxis Preferred Over Other Modalities Among People Who Inject Drugs: Findings from a Qualitative Study in California

People who inject drugs (PWID) have extraordinarily low uptake of human immunodeficiency virus (HIV) pre-exposure prophylaxis (PrEP) despite high levels of need. Long-acting PrEP modalities hold promise for HIV prevention among PWID, but product preferences remain poorly understood. From September to November 2021, we conducted qualitative interviews with 28 HIV-negative, adult (≥18 years) PWID in San Diego County, CA, to explore their perspectives on daily oral PrEP pills and long-acting PrEP modalities (i.e., injections, implants, intravaginal rings, and broadly neutralizing antibodies), which we explained using standard scripts. Thematic analysis identified variations in PrEP modality interest and acceptability. We identified three key factors across the 28 interviews that appeared to influence PrEP modality preferences: perceived convenience of use, invasiveness, and familiarity (based on past experience). Overall, most participants preferred injectable PrEP over other modalities because they viewed injectable medications as convenient, noninvasive, and familiar. While injectable PrEP was recently approved for use in the United States and was most the acceptable PrEP modality in this sample, our findings suggest that intervention and implementation research is urgently needed to improve our understanding of strategies that could support access, uptake, and sustained adherence to longer-acting PrEP for PWID.

Community and Provider Perspectives on Molecular HIV Surveillance and Cluster Detection and Response for HIV Prevention: Qualitative Findings From King County, Washington

ABSTRACT

Responding quickly to HIV outbreaks is one of four pillars of the U.S. Ending the HIV Epidemic (EHE) initiative. Inclusion of cluster detection and response in the fourth pillar of EHE has led to public discussion concerning bioethical implications of cluster detection and response and molecular HIV surveillance (MHS) among public health authorities, researchers, and community members. This study reports on findings from a qualitative analysis of interviews with community members and providers regarding their knowledge and perspectives of MHS. We identified five key themes: (a) context matters, (b) making sense of MHS, (c) messaging, equity, and resource prioritization, (d) operationalizing confidentiality, and (e) stigma, vulnerability, and power. Inclusion of community perspectives in generating innovative approaches that address bioethical concerns related to the use of MHS data is integral to ensure that widely accessible information about the use of these data is available to a diversity of community members and providers.

Using molecular transmission networks to understand the epidemic characteristics of HIV-1 CRF08_BC across China

HIV-1 CRF08_BC has become a major epidemic in heterosexuals and intravenous drug users (IDUs) in southern China. In order to evaluate the trends of its epidemic and facilitate targeted HIV prevention, we constructed the genetic transmission networks based on its pol sequences, derived from the National HIV Molecular Epidemiology Survey. Through retrospective network analysis, to study the epidemiological and demographic correlations with the transmission network. Of the 1,829 study subjects, 639 (34.9%) were clustered in 151 transmission networks. Factors associated with increased clustering include IDUs, heterosexual men, young adults and people with lower education (P < 0.05 for all). The IDUs, MSM, young adult and person with low education had more potential transmission links as well (P < 0.05 for all). The most crossover links were found between heterosexual women and IDUs, with 30.9% heterosexual women linked to IDUs. The crossover links heterosexual women were mainly those with middle age and single (P < 0.001). This study indicated that the HIV-1 CRF08_BC epidemic was still on going in China with more than one third of the infected people clustered in the transmission networks. Meanwhile, the study could help identify the active CRF08_BC spreader in the local community and greatly facilitate précising AIDS prevention with targeted intervention.

Overlapping Key Populations and HIV Transmission in Tijuana, Mexico: A Modelling Analysis of Epidemic Drivers

Tijuana, Mexico, has a concentrated HIV epidemic among overlapping key populations (KPs) including people who inject drugs (PWID), female sex workers (FSW), their male clients, and men who have sex with men (MSM). We developed a dynamic HIV transmission model among these KPs to determine the extent to which their unmet prevention and treatment needs is driving HIV transmission. Over 2020-2029 we estimated the proportion of new infections acquired in each KP, and the proportion due to their unprotected risk behaviours. We estimate that 43.7% and 55.3% of new infections are among MSM and PWID, respectively, with FSW and their clients making-up < 10% of new infections. Projections suggest 93.8% of new infections over 2020-2029 will be due to unprotected sex between MSM or unsafe injecting drug use. Prioritizing interventions addressing sexual and injecting risks among MSM and PWID are critical to controlling HIV in Tijuana.

Distribution characteristics of drug resistance mutations of HIV CRF01_AE, CRF07_BC and CRF08_BC from patients under ART in Ganzhou, China

BACKGROUND

Drug resistance mutation (DRM)-associated virological failure has become a critical issue for ART and the elimination of HIV.

OBJECTIVES

To investigate the distribution characteristics of DRMs of HIV CRF01_AE, CRF07_BC and CRF08_BC, the predominant subtypes in China.

METHODS

Patients receiving ART up to 31 August 2020 in Ganzhou in China were recruited. Full-length sequences of the HIV pol gene were amplified from patients with virological failure. DRMs and antiretroviral susceptibility were explored using the Stanford University HIV Drug Resistance Database HIVdb Program.

RESULTS

Overall, 279 of 2204 patients under ART were found to have virological failure. Nine HIV subtypes were identified among 211 sequences that were amplified successfully and CRF08_BC (37.0%), CRF01_AE (26.1%) and CRF07_BC (25.6%) were the most prevalent, with mutation frequencies of 44.9% (35/78), 52.7% (29/55) and 35.2% (19/54), respectively. The most common DRMs of these three subtypes were K103N and M184V, while the mutation frequencies of M41L, D67N, K70R, K101E, V106M, Y181C, K219E, H221Y and N348I were obviously different among subtypes. The resistance levels and frequencies for antiretroviral drugs for these three subtypes were similar and resistances to nevirapine, efavirenz, lamivudine and emtricitabine were the most frequently observed. Compared with CRF01_AE and CRF07_BC, CRF08_BC had higher proportions of DRMs for NRTIs and lower frequencies of resistance to NRTIs and NNRTIs.

CONCLUSIONS

The distribution characteristics of DRMs of HIV CRF01_AE, CRF07_BC and CRF08_BC were inconsistent and should be considered when selecting antiretroviral strategies, developing new drugs and controlling HIV strains containing DRMs.

Using molecular transmission networks to understand the epidemic characteristics of HIV-1 CRF08_BC across China

HIV-1 CRF08_BC has become a major epidemic in heterosexuals and intravenous drug users (IDUs) in southern China. In order to evaluate the trends of its epidemic and facilitate targeted HIV prevention, we constructed the genetic transmission networks based on its pol sequences, derived from the National HIV Molecular Epidemiology Survey. Through retrospective network analysis, to study the epidemiological and demographic correlations with the transmission network. Of the 1,829 study subjects, 639 (34.9%) were clustered in 151 transmission networks. Factors associated with increased clustering include IDUs, heterosexual men, young adults and people with lower education (P < 0.05 for all). The IDUs, MSM, young adult and person with low education had more potential transmission links as well (P < 0.05 for all). The most crossover links were found between heterosexual women and IDUs, with 30.9% heterosexual women linked to IDUs. The crossover links heterosexual women were mainly those with middle age and single (P < 0.001). This study indicated that the HIV-1 CRF08_BC epidemic was still on going in China with more than one third of the infected people clustered in the transmission networks. Meanwhile, the study could help identify the active CRF08_BC spreader in the local community and greatly facilitate précising AIDS prevention with targeted intervention.

High Prevalence of HIV-1 Drug Resistance and Dynamics of Transmission Among High-Risk Populations in Port-au-Prince, Haiti

BACKGROUND

In low HIV prevalence settings, understanding the transmission dynamics and the impact of drug resistance is critical to curb down the epidemic. This study aims to explore the prevalence and dynamics of transmission of HIV drug-resistance mutations (DRMs) among key populations in Haiti.

SETTINGS

Eligible participants (naive, treated) were selected from 7 key population friendly health care centers in Port-au-Prince, Haiti, from September 2018 to July 2019.

METHODS

A total of 119 HIV-1 pol sequences were analyzed from men having sex with men (MSM), female sex workers (FSWs), and their sexual partners. Screening for HIV DRMs was performed using the Stanford University Drug Resistance Database. Phylogenetic and network analyses using HIV-TRACE software were performed to infer putative relationships and shared DRMs.

RESULTS

Of the 119 participants, 62.2% were men (74/119), and 75.7% of them (56/74) reported MSM as a main risk factor. The overall DRM prevalence was 58.8% (70/119). A DRM was observed in 37.5% of MSM (21/56), 82.2% of FSWs (37/45), and 66.7% (12/18) among FSWs' clients. In a multivariate model, age and FSWs were significant predictors for DRMs (P = 0.001). Transmission network analysis found 24 of the 119 (20.2%) genetically linked individuals forming 8 clusters. Clustering participants were mostly MSM (15/24; 62.5%). Five clusters (62.5%) had shared DRMs, and K103N and M184V were the main shared mutations.

CONCLUSIONS

High prevalence of HIV DRMs was observed among MSM, FSWs, and their clients in Port-au-Prince, Haiti. Network analysis revealed frequent DRM transmission among genetically linked individuals, highlighting the need for appropriate interventions to limit HIV transmission in these high-risk populations.

Dynamics and Dispersal of Local HIV Epidemics Within San Diego and Across The San Diego-Tijuana Border

BACKGROUND

Evolutionary analyses of well-annotated HIV sequence data can provide insights into viral transmission patterns and associated factors. Here, we explored the transmission dynamics of the HIV-1 subtype B epidemic across the San Diego (US) - Tijuana (Mexico) border region to identify factors that could help guide public health policy.

METHODS

HIV pol sequences were collected from people with HIV in San Diego County and from Tijuana between 1996-2018. A multistep phylogenetic approach was used to characterize the dynamics of spread. The contribution of geospatial factors and HIV risk group to the local dynamics were evaluated.

RESULTS

Phylogeographic analyses of the 2,034 sequences revealed an important contribution of local transmission in sustaining the epidemic, as well as a complex viral migration network across the region. Geospatial viral dispersal between San Diego communities occurred predominantly among men-who-have-sex with-men with central San Diego being the main source (34.9%) and recipient (39.5%) of migration events. HIV migration was more frequent from San Diego county towards Tijuana than vice versa. Migrations were best explained by driving time between locations.

CONCLUSION

The US-Mexico border may not be a major barrier to the spread of HIV, which may stimulate coordinated transnational intervention approaches. Whereas a focus on central San Diego has the potential to avert most spread, the substantial viral migration independent of central San Diego shows that county-wide efforts will be more effective. Combined, this work shows that epidemiological information gleaned from pathogen genomes can uncover mechanisms that underlie sustained spread and, in turn, can be a building block of public health decision making.

Informed consent for HIV phylogenetic research: A case study of urban individuals living with HIV approached for enrollment in an HIV study

INTRODUCTION

Phylogenetic analyses can provide insights on HIV tansmission dynamics. Country and state-level differences in HIV criminalization and disclosure laws and advances in next generation sequencing could impact perceived study risks.

METHODS

We present study opt-out rates and the reasons provided during enrollment for a study conducted in Boston (6/2017-8/2018).

RESULTS

Of 90 patients approached to participate, 45 did not consent to participate. Reasons for not participating included unwillingness to discuss their HIV status, privacy and confidentiality concerns, disinterest, and lack of time.

CONLUSIONS

Given low participation rates and concerns related to HIV disclosure, privacy, and confidentiality, these questions remain (1) should informed consent be required for all phylogenetic analyses, including deidentified and surveillance data? (2) what additional steps can researchers take to protect the privacy of individuals, particularly in contexts where HIV is criminalized or there have been civil/criminal cases investigating HIV transmission? And (3) what role can community members play to minimize the potential risks, particularly for those most marginalized? These questions require input from both researchers and community members living with HIV/AIDS.

Molecular network-based intervention brings us closer to ending the HIV pandemic

Precise identification of HIV transmission among populations is a key step in public health responses. However, the HIV transmission network is usually difficult to determine. HIV molecular networks can be determined by phylogenetic approach, genetic distance-based approach, and a combination of both approaches. These approaches are increasingly used to identify transmission networks among populations, reconstruct the history of HIV spread, monitor the dynamics of HIV transmission, guide targeted intervention on key subpopulations, and assess the effects of interventions. Simulation and retrospective studies have demonstrated that these molecular network-based interventions are more cost-effective than random or traditional interventions. However, we still need to address several challenges to improve the practice of molecular network-guided targeting interventions to finally end the HIV epidemic. The data remain limited or difficult to obtain, and more automatic real-time tools are required. In addition, molecular and social networks must be combined, and technical parameters and ethnic issues warrant further studies.

Pretreatment HIV drug resistance spread within transmission clusters in Mexico City

BACKGROUND

Pretreatment HIV drug resistance (HIVDR) to NNRTIs has consistently increased in Mexico City during the last decade.

OBJECTIVES

To infer the HIV genetic transmission network in Mexico City to describe the dynamics of the local HIV epidemic and spread of HIVDR.

PATIENTS AND METHODS

HIV pol sequences were obtained by next-generation sequencing from 2447 individuals before initiation of ART at the largest HIV clinic in Mexico City (April 2016 to June 2018). Pretreatment HIVDR was estimated using the Stanford algorithm at a Sanger-like threshold (≥20%). Genetic networks were inferred with HIV-TRACE, establishing putative transmission links with genetic distances <1.5%. We examined demographic associations among linked individuals with shared drug resistance mutations (DRMs) using a ≥ 2% threshold to include low-frequency variants.

RESULTS

Pretreatment HIVDR reached 14.8% (95% CI 13.4%-16.2%) in the cohort overall and 9.6% (8.5%-10.8%) to NNRTIs. Putative links with at least one other sequence were found for 963/2447 (39%) sequences, forming 326 clusters (2-20 individuals). The inferred network was assortative by age and municipality (P < 0.001). Clustering individuals were younger [adjusted OR (aOR) per year = 0.96, 95% CI 0.95-0.97, P < 0.001] and less likely to include women (aOR = 0.46, 95% CI 0.28-0.75, P = 0.002). Among clustering individuals, 175/963 (18%) shared DRMs (involving 66 clusters), of which 66/175 (38%) shared K103N/S (24 clusters). Eight municipalities (out of 75) harboured 65% of persons sharing DRMs. Among all persons sharing DRMs, those sharing K103N were younger (aOR = 0.93, 95% CI 0.88-0.98, P = 0.003).

CONCLUSIONS

Our analyses suggest age- and geographically associated transmission of DRMs within the HIV genetic network in Mexico City, warranting continuous monitoring and focused interventions.

The Impact of Human Mobility on Regional and Global Efforts to Control HIV Transmission

HIV prevention and control methods are implemented on different scales to reduce the spread of the virus amongst populations. However, despite such efforts, HIV continues to persist in populations with a global incidence rate of 1.8 million in 2017 alone. The introduction of new infections into susceptible regional populations promotes the spread of HIV, indicating a crucial need to study the impact of migration and mobility on regional and global efforts to prevent HIV transmission. Here we reviewed studies that assess the impact of human mobility on HIV transmission and spread. We found an important role for both travel and migration in driving the spread of HIV across regional and national borders. Combined, our results indicate that even in the presence of control and preventive efforts, if migration and travel are occurring, public health efforts will need to remain persistent to ensure that new infections do not grow into outbreaks.

Pervasive and non-random recombination in near full-length HIV genomes from Uganda

Recombination is an important feature of HIV evolution, occurring both within and between the major branches of diversity (subtypes). The Ugandan epidemic is primarily composed of two subtypes, A1 and D, that have been co-circulating for 50 years, frequently recombining in dually infected patients. Here, we investigate the frequency of recombinants in this population and the location of breakpoints along the genome. As part of the PANGEA-HIV consortium, 1,472 consensus genome sequences over 5 kb have been obtained from 1,857 samples collected by the MRC/UVRI & LSHTM Research unit in Uganda, 465 (31.6 per cent) of which were near full-length sequences (>8 kb). Using the subtyping tool SCUEAL, we find that of the near full-length dataset, 233 (50.1 per cent) genomes contained only one subtype, 30.8 per cent A1 (n = 143), 17.6 per cent D (n = 82), and 1.7 per cent C (n = 8), while 49.9 per cent (n = 232) contained more than one subtype (including A1/D (n = 164), A1/C (n = 13), C/D (n = 9); A1/C/D (n = 13), and 33 complex types). K-means clustering of the recombinant A1/D genomes revealed a section of envelope (C2gp120-TMgp41) is often inherited intact, whilst a generalized linear model was used to demonstrate significantly fewer breakpoints in the gag-pol and envelope C2-TM regions compared with accessory gene regions. Despite similar recombination patterns in many recombinants, no clearly supported circulating recombinant form (CRF) was found, there was limited evidence of the transmission of breakpoints, and the vast majority (153/164; 93 per cent) of the A1/D recombinants appear to be unique recombinant forms. Thus, recombination is pervasive with clear biases in breakpoint location, but CRFs are not a significant feature, characteristic of a complex, and diverse epidemic.

Identification of a Syndemic of Blood-Borne Disease Transmission and Injection Drug Use Initiation at the US-Mexico Border

BACKGROUND

Efforts to prevent injection drug use (IDU) are increasingly focused on the role that people who inject drugs (PWID) play in the assistance with injection initiation. We studied the association between recent (ie, past 6 months) injection-related HIV risk behaviors and injection initiation assistance into IDU among PWID in the US-Mexico border region.

SETTING

Preventing Injecting by Modifying Existing Responses (PRIMER) is a multicohort study assessing social and structural factors related to injection initiation assistance. This analysis included data collected since 2014 from 2 participating cohorts in San Diego and Tijuana.

METHODS

Participants were 18 years and older and reported IDU within the month before study enrollment. Logistic regression analyses were conducted to assess the association between recent injection-related HIV risk behaviors (eg, distributive/receptive syringe sharing, dividing drugs in a syringe, and paraphernalia sharing) and recent injection initiation assistance.

RESULTS

Among 892 participants, 41 (4.6%) reported recently providing injection initiation assistance. In multivariable analysis adjusting for potential confounders, reporting a higher number of injection-related risk behaviors was associated with an increased odds of recently assisting others with injection initiation (adjusted odds ratio per risk behavior: 1.3; 95% confidence interval: 1.0 to 1.6, P = 0.04).

CONCLUSIONS

PWID who recently engaged in one or more injection-related HIV risk behavior were more likely to assist others in injection initiation. These results stress the syndemic of injection initiation and risk behaviors, which indicates that prevention of injection-related HIV risk behaviors might also reduce the incidence of injection initiation.

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.

Proliferative memory SAMHD1low CD4+ T cells harbour high levels of HIV-1 with compartmentalized viral populations

We previously reported the presence of memory CD4⁺ T cells that express low levels of SAMHD1 (SAMHD1^low) in peripheral blood and lymph nodes from both HIV-1 infected and uninfected individuals. These cells are enriched in Th17 and Tfh subsets, two populations known to be preferentially targeted by HIV-1. Here we investigated whether SAMHD1^low CD4⁺ T-cells harbour replication-competent virus and compartimentalized HIV-1 genomes. We sorted memory CD4⁺CD45RO⁺SAMHD1^low, CD4⁺CD45RO⁺SAMHD1⁺ and naive CD4⁺CD45RO^-SAMHD1⁺ cells from HIV-1-infected patients on anti-retroviral therapy (c-ART) and performed HIV-1 DNA quantification, ultra-deep-sequencing of partial env (C2/V3) sequences and phenotypic characterization of the cells. We show that SAMHD1^low cells include novel Th17 CCR6⁺ subsets that lack CXCR3 and CCR4 (CCR6⁺DN). There is a decrease of the % of Th17 in SAMHD1^low compartment in infected compared to uninfected individuals (41% vs 55%, p<0.05), whereas the % of CCR6⁺DN increases (7.95% vs 3.8%, p<0.05). Moreover, in HIV-1 infected patients, memory SAMHD1^low cells harbour high levels of HIV-1 DNA compared to memory SAMHD1⁺ cells (4.5 vs 3.8 log/10⁶cells, respectively, p<0.001), while naïve SAMHD1⁺ showed significantly lower levels (3.1 log/10⁶cells, p<0.0001). Importantly, we show that SAMHD1^low cells contain p24-producing cells. Moreover, phylogenetic analyses revealed well-segregated HIV-1 DNA populations with compartmentalization between SAMHD1^low and SAMHD1⁺ memory cells, and limited viral exchange. As expected, the % of Ki67⁺ cells was significantly higher in SAMHD1^low compared to SAMHD1⁺ cells. There was positive association between levels of HIV-1 DNA and Ki67⁺ in memory SAMHD1^low cells, but not in memory and naïve SAMHD1⁺ CD4⁺ T-cells. Altogether, these data suggest that proliferative memory SAMHD1^low cells contribute to viral persistence.

In our previous results we reported that memory CD4⁺ T cells expressing low levels of SAMHD1 (SAMHD1^low) are present in peripheral blood and lymph nodes from HIV-1 infected and uninfected individuals. These cells were enriched in Th17 and Tfh, two populations targeted by HIV-1. Here we used purified memory CD4⁺CD45RO⁺SAMHD1^low, CD4⁺CD45RO⁺SAMHD1⁺ and naive CD4⁺CD45RO^-SAMHD1⁺ cells from HIV-1-infected and treated patients to perform cell-associated HIV-1 DNA quantification, p24-producing cells detection, ultra-deep-sequencing of partial env (C2/V3) HIV-1 DNA and further phenotypic characterization. Our results demonstrate that (i) Th17 and CCR6⁺DN-expressing transcriptional signature of early Th17, two major populations that are susceptible to HIV-1 infection, are present in SAMHD1^low cells, and while the former decreased significantly in c-ART HIV-1 infected compared to uninfected individuals, the latter significantly increased; (ii) memory SAMHD1^low cells from c-ART patients carry high levels of HIV-1 DNA compared to SAMHD1⁺ cells, and these levels positively and significantly correlated with Ki67 expression; (iii) memory SAMHD1^low cells from patients harbour p24-producing cells; (iv) phylogenetic analyses revealed well-segregated HIV-1 DNA populations with significant compartmentalization between SAMHD1^low and SAMHD1⁺ cells and limited viral exchange. Our data demonstrate that memory SAMHD1^low cells contribute to HIV-1 persistence.

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.

HIV-1 drug resistance before initiation or re-initiation of first-line ART in eight regions of Mexico: a sub-nationally representative survey

BACKGROUND

HIV pretreatment drug resistance (PDR) to NNRTIs in persons initiating ART is increasing in Mexico.

OBJECTIVES

To compare HIV PDR in eight sub-regions of Mexico.

PATIENTS AND METHODS

A large PDR survey was implemented in Mexico (September 2017-March 2018) across eight sub-regions. All larger clinics (which provide ART to 90% of all initiators) were included, allocating sample size using the probability-proportional-to-size method. Both antiretroviral-naive and prior antiretroviral-exposed persons were included. HIV PDR levels were estimated from pol Sanger sequences obtained at a WHO-designated laboratory.

RESULTS

A total of 2006 participants were enrolled from 74 clinics. PDR to NNRTIs was higher than to other drug classes (P < 0.0001), crossing the 10% threshold in the North-East, East, South-West and South-East. NNRTI PDR was higher in the South-West (P = 0.02), coinciding with the highest proportion of restarters in this sub-region (14%). We observed higher PDR prevalence to any drug in women compared with men (16.5% versus 12.2%, P = 0.04). After multivariable adjustment, higher NNRTI PDR remained significantly associated with previous antiretroviral exposure in the Centre-North, North-West, South-West and South-East [adjusted OR (aOR): 21, 5, 8 and 25, respectively; P < 0.05]. Genetic network analyses showed high assortativity by sub-region (P < 0.0001), with evidence of drug resistance mutation transmission within local clusters.

CONCLUSIONS

Diversification of the public health response to HIV drug resistance based on sub-regional characteristics could be considered in Mexico. Higher NNRTI PDR levels were associated with poorer regions, suggesting opportunities to strengthen local HIV programmes. Price and licensing negotiations of drug regimens containing integrase inhibitors are warranted.

Superimposing incident sexually transmitted infections on HIV phylogram to investigate possible misclassification of men who have sex with men as heterosexuals in a cohort in Antwerp, Belgium

In this study, we assessed if the superimposition of incident sexually transmitted infections (STIs) on HIV phylogenetic analyses could reveal possible sexual behaviour misclassifications in our HIV-infected population. HIV-1 sequences collected between 1997 and 2014 from 1169 individuals attending a HIV clinic in Antwerp, Belgium were analysed to infer a partial HIV transmission network. Individual demographic, clinical and laboratory data collected during routine HIV follow-up were used to compare clustered and non-clustered individuals using logistic regression analyses. In total, 438 (37.5%) individuals were identified in 136 clusters, including 76 transmission pairs and 60 clusters consisting of three or more individuals. Individuals in a cluster were more likely to have a history of syphilis, Chlamydia and/or gonorrhoea (P < 0.05); however, when analyses were stratified by HIV transmission risk groups (heterosexual and men who have sex with men [MSM]), this association only remained significant for heterosexuals with syphilis (P = 0.001). Under closer scrutiny, this association was driven by six heterosexual men who were located in six almost exclusively MSM clusters. A parsimonious conclusion is that these six individuals were potentially misclassified as heterosexual. Improving the accuracy of sexual behaviour reporting could improve care.

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.

Evaluating the impact of global fund withdrawal on needle and syringe provision, cost and use among people who inject drugs in Tijuana, Mexico: a costing analysis

OBJECTIVE

From 2011 to 2013, the Global Fund (GF) supported needle and syringe programmes in Mexico to prevent transmission of HIV among people who inject drugs. It remains unclear how GF withdrawal affected the costs, quality and coverage of needle and syringe programme provision.

DESIGN

Costing study and longitudinal cohort study.

SETTING

Tijuana, Mexico.

PARTICIPANTS

Personnel from a local needle and syringe programme (n=6) and people who inject drugs (n=734) participating in a longitudinal study.

PRIMARY OUTCOME MEASURES

Provision of needle and syringe programme services and cost (per contact and per syringe distributed, in 2017 $USD) during GF support (2012) and after withdrawal (2015/16). An additional outcome included needle and syringe programme utilisation from a concurrent cohort of people who inject drugs during and after GF withdrawal.

RESULTS

During the GF period, the needle and syringe programme distributed 55 920 syringes to 932 contacts (60 syringes/contact) across 14 geographical locations. After GF withdrew, the needle and syringe programme distributed 10 700 syringes to 2140 contacts (five syringes/contact) across three geographical locations. During the GF period, the cost per harm reduction contact was approximately 10-fold higher compared with after GF ($44.72 vs $3.81); however, the cost per syringe distributed was nearly equal ($0.75 vs $0.76) due to differences in syringes per contact and reductions in ancillary kit components. The mean log odds of accessing a needle and syringe programme in the post-GF period was significantly lower than during the GF period (p=0.02).

CONCLUSIONS

Withdrawal of GF support for needle and syringe programme provision in Mexico was associated with a substantial drop in provision of sterile syringes, geographical coverage and recent clean syringe utilisation among people who inject drugs. Better planning is required to ensure harm reduction programme sustainability is at scale after donor withdrawal.

Persistence of Human Immunodeficiency Virus-1 Drug Resistance Mutations in Proviral Deoxyribonucleic Acid After Virologic Failure of Efavirenz-Containing Antiretroviral Regimens

Background

Efavirenz (EFV)-based regimens select broad drug resistance to nonnucleoside reverse-transcriptase inhibitors (NNRTIs), limiting the effectiveness of EFV and other NNRTIs. The duration, persistence, and decay of drug resistance mutations (DRMs) in the proviral reservoir is not well defined.

Methods

Participants with virologic failure of EFV-based regimens and drug-resistant viremia with the K103N mutation in plasma ribonucleic acid (RNA) were identified from AIDS Clinical Trials Group (ACTG) studies A364 and A5095. These individuals received a second-line, boosted protease inhibitor-based regimen with suppression of viremia for up to10 years during long-term follow-up (median = 3.6 years; interquartile range, 2.1-6.9 years). Proviral deoxyribonucleic acid (DNA) from cryopreserved peripheral blood mononuclear cells was sequenced to identify the persistence of DRM.

Results

Twenty-eight participants from ACTG 364 and ACTG 5095 were evaluated. Sanger sequencing of proviral DNA detected K103N as well as additional reverse-transcriptase inhibitor (RTI) mutations. Ultradeep sequencing confirmed persistence of K103N in 71% of participants with minimal decay over time. In an adjusted model including years since suppression, persistent proviral K103N was 2.6 times more likely (95% confidence interval, 1.0-6.4) per log₁₀ higher human immunodeficiency virus RNA at EFV failure.

Conclusions

Persistence of RTI mutations in proviral DNA after virologic failure has implications for the effectiveness of future drug regimens and the recycling of RTI drugs.

Combining Phylogenetic and Network Approaches to Identify HIV-1 Transmission Links in San Mateo County, California

The HIV epidemic in San Mateo County is sustained by multiple overlapping risk groups and is an important hub for HIV transmission in northern California. Limited access to care has led historically to delayed clinical presentation, higher rates of opportunistic infections, and an increased prevalence of antiretroviral drug resistance. The virologic and clinical consequences of treatment within these multiple ethnic and behavioral groups are poorly understood, highlighting the need for efficient surveillance strategies that are able to elucidate transmission networks and drug resistance patterns. We obtained sequence data from a group of 316 HIV-positive individuals in the San Mateo AIDS Program over a 14-year period and integrated epidemiologic, phylogenetic, and network approaches to characterize transmission clusters, risk factors and drug resistance. Drug resistance mutations were identified using the Stanford HIV Drug Resistance Database. A maximum likelihood tree was inferred in RAxML and subjected to clustering analysis in Cluster Picker. Network analysis using pairwise genetic distances was performed in HIV-TRACE. Participants were primarily male (60%), white Hispanics and non-Hispanics (32%) and African American (20.6%). The most frequent behavior risk factor was male-male sex (33.5%), followed by heterosexual (23.4%) and injection drug use (9.5%). Nearly all sequences were subtype B (96%) with subtypes A, C, and CRF01_AE also observed. Sequences from 65% of participants had at least one drug resistance mutation. Clustered transmissions included a higher number of women when compared to non-clustered individuals and were more likely to include heterosexual or people who inject drugs (PWID). Detailed analysis of the largest network (N = 47) suggested that PWID played a central role in overall transmission of HIV-1 as well as bridging men who have sex with men (MSM) transmission with heterosexual/PWID among primarily African American men. Combined phylogenetic and network analysis of HIV sequence data identified several overlapping risk factors in the epidemic, including MSM, heterosexual and PWID transmission with a disproportionate impact on African Americans and a high prevalence of drug resistance.

Growth of HIV-1 Molecular Transmission Clusters in New York City

Background

HIV-1 genetic sequences can be used to infer viral transmission history and dynamics. Throughout the United States, HIV-1 sequences from drug resistance testing are reported to local public health departments.

Methods

We investigated whether inferred HIV transmission network dynamics can identify individuals and clusters of individuals most likely to give rise to future HIV cases in a surveillance setting. We used HIV-TRACE, a genetic distance-based clustering tool, to infer molecular transmission clusters from HIV-1 pro/RT sequences from 65736 people in the New York City surveillance registry. Logistic and LASSO regression analyses were used to identify correlates of clustering and cluster growth, respectively. We performed retrospective transmission network analyses to evaluate individual- and cluster-level prioritization schemes for identifying parts of the network most likely to give rise to new cases in the subsequent year.

Results

Individual-level prioritization schemes predicted network growth better than random targeting. Across the 3600 inferred molecular transmission clusters, previous growth dynamics were superior predictors of future transmission cluster growth compared to individual-level prediction schemes. Cluster-level prioritization schemes considering previous cluster growth relative to cluster size further improved network growth predictions.

Conclusions

Prevention efforts based on HIV molecular epidemiology may improve public health outcomes in a US surveillance setting.

Burmese injecting drug users in Yunnan play a pivotal role in the cross-border transmission of HIV-1 in the China-Myanmar border region

Injecting drug users (IDUs) are the major risk group for HIV-1 infection in the China-Myanmar border area. There are a large number of Burmese IDUs living in Yunnan (Yunnan-mIDUs) who might be associated with the cross-border transmission of HIV-1. From 2010 to 2013, 617 Yunnan-mIDUs were recruited from three counties of Yunnan, 19.0% of whom were detected to be HIV-1 positive by serological testing. Partial HIV-1 p17, pol, vif-env, and env genes were amplified from the positive samples and were sequenced. Phylogenetic and HIV-1 subtyping analyses revealed that HIV-1 recombinant forms (RFs), including RF_BC (36.4%), RF_01BC (26.1%), RF_01C (9.1%) and RF_01B (1.1%), were predominant among this cohort. Of the identified HIV-1 strains, 14.8%, 9.1% and 3.4% belonged to subtype C, CRF01_AE and subtype B, respectively. Transmission cluster analysis showed that sequences from the Yunnan-mIDUs formed transmission clusters not only with those from Burmese IDUs but also with those from Chinese IDUs, indicating that Yunnan-mIDUs might acquire HIV-1 infection from or spread HIV-1 to both Burmese and Chinese IDUs. Phylogeographic analyses revealed three cross-border transmission patterns associated with Yunnan-mIDUs, in which Yunnan-mIDUs served as the crucial nodes linking the Burmese and Chinese IDUs. These results suggest that Yunnan-mIDUs are a potential viral reservoir for the diffusion of HIV-1 in Yunnan and play a pivotal role in the bidirectional cross-border transmission of HIV-1 in the China-Myanmar border region. More intervention efforts that focus on Yunnan-mIDUs are recommended in Yunnan’s campaign against HIV/AIDS.

Enhanced immigration enforcement in the USA and the transnational continuity of HIV care for Latin American immigrants in deportation proceedings

In our work as clinicians, researchers, and immigrant rights advocates, we have noted increased anxiety about the possibility of deportation and disruptions in care among immigrants with HIV. Before the 2016 US elections, patients rarely asked about HIV treatment in their home countries. However, since the increase in anti-immigrant rhetoric and arrests by US Immigration and Customs Enforcement, patients have voiced concerns about the availability of HIV treatment in their home countries much more frequently. Although antiretroviral therapy is available throughout Latin America, access depends on economic, social, and political circumstances. Maintaining uninterrupted continuity of care among immigrants held in detention or deported to their home countries is challenging. In this Viewpoint, we identify periods of particular vulnerability for immigrants during deportation proceedings, from initial detention to deposition in their country of origin. We discuss the effect of enhanced immigration enforcement on the health and wellbeing of HIV-infected immigrants, and on public health. Finally, we also discuss recommendations for clinicians, immigration authorities, and public health institutions in the USA and in receiving countries.

HIV pretreatment drug resistance trends in three geographic areas of Mexico

Background

Pretreatment drug resistance (PDR) levels to NNRTI approaching 10% have recently been reported in Mexico. However, subnational differences may exist in PDR prevalence and transmission dynamics.

Objectives

We longitudinally assessed HIV PDR in three geographic areas of Mexico.

Patients and methods

HIV-infected, antiretroviral-naive individuals were recruited from 2008 to 2016, from the Central Metropolitan Zone (CMZ), Cancun and Tijuana (1194, 773 and 668 respectively). PDR was estimated using the Stanford HIVdb tool from plasma HIV pol sequences.

Results

A higher proportion of females, lower education and lower employment rate were observed in Tijuana, while a higher proportion of MSM was observed in the CMZ (P < 0.0001, all cases). For 2012-16, PDR was 13.4%, 8.9% and 11.2% in the CMZ, Tijuana and Cancun respectively. NNRTI PDR was highest in the three regions (8.7%, 4.8% and 8.1% respectively, P < 0.05); nevertheless, NNRTI PDR in Tijuana was lower than in the CMZ (P = 0.01). For 2008-16, we observed increasing efavirenz resistance trends in all regions (P < 0.05, all cases), reaching 11.8%, 6.1% and 8.3% respectively in 2016. Increasing efavirenz resistance was mostly associated with increasing K103N frequency (P = 0.007 CMZ, P = 0.03 Tijuana, not significant for Cancun).

Conclusions

Our study suggests different NNRTI PDR prevalence and transmission dynamics in three geographical areas of Mexico. Even when increasing trends in efavirenz resistance were observed in the three areas, our observations support that, in a large country such as Mexico, subnational surveillance and locally tailored interventions to address drug resistance may be a reasonable option.

Molecular Epidemiology of the HIV Epidemic in Three German Metropolitan Regions - Cologne/Bonn, Munich and Hannover, 1999-2016

Using HIV sequence data to characterize clusters of HIV transmission may provide insight into the epidemic. Phylogenetic and network analyses were performed to infer putative relationships between HIV-1 partial pol sequences from 2,774 individuals receiving care in three German regions between 1999-2016. The regions have in common that they host some of the largest annual festivals in Europe (Carnival and Oktoberfest). Putative links with sequences (n = 150,396) from the Los Alamos HIV Sequence database were evaluated. A total of 595/2,774 (21.4%) sequences linked with at least one other sequence, forming 184 transmission clusters. Clustering individuals were significantly more likely to be younger, male, and report sex with men as their main risk factor (p < 0.001 each). Most clusters (77.2%) consisted exclusively of men; 41 (28.9%) of these included men reporting sex with women. Thirty-two clusters (17.4%) contained sequences from more than one region; clustering men were significantly more likely to be in a position bridging regional HIV epidemics than clustering women (p = 0.027). We found 236 clusters linking 547 sequences from our sample with sequences from the Los Alamos database (n = 1407; 31% from other German centres). These results highlight the pitfalls of focusing HIV prevention efforts on specific risk groups or specific locales.

Impact of Public Safety Policies on Human Immunodeficiency Virus Transmission Dynamics in Tijuana, Mexico

Background

North Tijuana, Mexico is home to many individuals at high risk for transmitting and acquiring human immunodeficiency virus (HIV). Recently, policy shifts by local government impacted how these individuals were handled by authorities. Here we examined how this affected regional HIV transmission dynamics.

Methods

HIV pol sequences and associated demographic information were collected from 8 research studies enrolling persons in Tijuana and were used to infer viral transmission patterns. To evaluate the impact of recent policy changes on HIV transmission dynamics, qualitative interviews were performed on a subset of recently infected individuals.

Results

Between 2004 and 2016, 288 unique HIV pol sequences were obtained from individuals in Tijuana, including 46.4% from men who have sex with men, 42.1% from individuals reporting transactional sex, and 27.8% from persons who inject drugs (some individuals had >1 risk factor). Forty-two percent of sequences linked to at least 1 other sequence, forming 37 transmission clusters. Thirty-two individuals seroconverted during the observation period, including 8 between April and July 2016. Three of these individuals were putatively linked together. Qualitative interviews suggested changes in policing led individuals to shift locations of residence and injection drug use, leading to increased risk taking (eg, sharing needles).

Conclusions

Near real-time molecular epidemiologic analyses identified a cluster of linked transmissions temporally associated with policy shifts. Interviews suggested these shifts may have led to increased risk taking among individuals at high risk for HIV acquisition. With all public policy shifts, downstream impacts need to be carefully considered, as even well-intentioned policies can have major public health consequences.

The Border Health Consortium of the Californias-Forming a Binational (California-Baja California) Entity to Address the Health of a Border Region: A Case Study

The California–Baja California border region is one of the most frequently traversed areas in the world with a shared population, environment, and health concerns. The Border Health Consortium of the Californias (the “Consortium”) was formed in 2013 to bring together leadership working in the areas of public health, health care, academia, government, and the non-profit sector, with the goal of aligning efforts to improve health outcomes in the region. The Consortium utilizes a Collective Impact framework which supports a shared vision for a healthy border region, mutually reinforcing activities among member organizations and work groups, and a binational executive committee that ensures continuous communication and progress toward meeting its goals. The Consortium is comprised of four binational work groups which address human immunodeficiency virus, tuberculosis, obesity, and mental health, all mutual priorities in the border region. The Consortium holds two general binational meetings each year alternating between California and Baja California. The work groups meet regularly to share information, resources and provide binational training opportunities. Since inception, the Consortium has been successful in strengthening binational communication, coordination, and collaboration by providing an opportunity for individuals to meet one another, learn about each other systems, and foster meaningful relationships. With binational leadership support and commitment, the Consortium could certainly be replicated in other border jurisdictions both nationally and internationally. The present article describes the background, methodology, accomplishments, challenges, and lessons learned in forming the Consortium.

Assessing police officers' attitudes and legal knowledge on behaviors that impact HIV transmission among people who inject drugs

BACKGROUND

Policing practices such as syringe confiscation and arrest can act as important social-structural drivers of HIV risk among people who inject drugs (PWID). However, police referral to treatment and other services may improve the health of PWID. Little is known about the role of modifiable attitudinal and knowledge factors in shaping officer behavior. Using baseline findings from a police education program (PEP), we assessed relationships between drug policy knowledge and attitudes towards public health interventions with self-reported syringe confiscation, drug arrest, and service referral among street-level police in Tijuana, Mexico.

METHODS

Between February, 2015 and May, 2016 we surveyed 1319 police officers who reported syringe contact. The self-administered survey focused on attitudes, knowledge, and behaviors related to drug policy, public health, and occupational safety. We used ordinal logistic regression to model the odds of syringe confiscation, arrest for heroin possession, and referring PWID to health/social programs.

RESULTS

The sample was mostly male (87%) and had at least a high school education (80%). In the last six months, a minority reported always/sometimes confiscating syringes (49%), arresting someone for heroin possession (43%), and referring PWID to health and social programs (37%). Those reporting needlestick injuries (NSI) had 1.38 (95% CI: 1.02-1.87) higher odds of reporting syringe confiscation. Officers who had favorable views on laws that treat addiction as a public health issue had lower odds (aOR=0.78; 95% CI: 0.59-1.03) of arresting PWID. Those agreeing that it was their role to refer PWID to health and social programs had higher odds of reporting such referrals (aOR: 3.32, 95% CI: 2.52-4.37). Legal knowledge was not associated with these practices.

CONCLUSION

Changing drug policy and knowledge may be insufficient in shifting police behavior. Modifying officers' occupational risks and attitudes towards harm reduction interventions can facilitate efforts to align police practices with PWID health.

Short Communication: HIV-1 Transmission Networks Across South Korea

Molecular epidemiology can help clarify the properties and dynamics of HIV-1 transmission networks in both global and regional scales. We studied 143 HIV-1-infected individuals recruited from four medical centers of three cities in South Korea between April 2013 and May 2014. HIV-1 env V3 sequence data were generated (337-793 bp) and analyzed using a pairwise distance-based clustering approach to infer putative transmission networks. Participants whose viruses were ≤2.0% divergent according to Tamura-Nei 93 genetic distance were defined as clustering. We collected demographic, risk, and clinical data and analyzed these data in relation to clustering. Among 143 participants, we identified nine putative transmission clusters of different sizes (range 2-4 participants). The reported risk factor of participants were concordant in only one network involving two participants, that is, both individuals reported homosexual sex as their risk factor. The participants in the other eight networks did not report concordant risk factors, although they were phylogenetically linked. About half of the participants refused to report their risk factor. Overall, molecular epidemiology provides more information to understand local transmission networks and the risks associated with these networks.

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.

A molecular transmission network of recent hepatitis C infection in people with and without HIV: Implications for targeted treatment strategies

Combining phylogenetic and network methodologies has the potential to better inform targeted interventions to prevent and treat infectious diseases. This study reconstructed a molecular transmission network for people with recent hepatitis C virus (HCV) infection and modelled the impact of targeting directly acting antiviral (DAA) treatment for HCV in the network. Participants were selected from three Australian studies of recent HCV from 2004 to 2014. HCV sequence data (Core-E2) from participants at the time of recent HCV detection were analysed to infer a network by connecting pairs of sequences whose divergence was ≤.03 substitutions/site. Logistic regression was used to identify factors associated with connectivity. Impact of targeting HCV DAAs at both HIV co-infected and random nodes was simulated (1 million replicates). Among 236 participants, 21% (n=49) were connected in the network. HCV/HIV co-infected participants (47%) were more likely to be connected compared to HCV mono-infected participants (16%) (OR 4.56; 95% CI; 2.13-9.74). Simulations targeting DAA HCV treatment to HCV/HIV co-infected individuals prevented 2.5 times more onward infections than providing DAAs to randomly selected individuals. Results demonstrate that genetic distance-based network analyses can be used to identify characteristics associated with HCV transmission, informing targeted prevention and treatment strategies.

Spatiotemporal dynamics of HIV-1 transmission in France (1999-2014) and impact of targeted prevention strategies

Background

Characterizing HIV-1 transmission networks can be important in understanding the evolutionary patterns and geospatial spread of the epidemic. We reconstructed the broad molecular epidemiology of HIV from individuals with primary HIV-1 infection (PHI) enrolled in France in the ANRS PRIMO C06 cohort over 15 years.

Results

Sociodemographic, geographic, clinical, biological and pol sequence data from 1356 patients were collected between 1999 and 2014. Network analysis was performed to infer genetic relationships, i.e. clusters of transmission, between HIV-1 sequences. Bayesian coalescent-based methods were used to examine the temporal and spatial dynamics of identified clusters from different regions in France. We also evaluated the use of network information to target prevention efforts. Participants were mostly Caucasian (85.9%) and men (86.7%) who reported sex with men (MSM, 71.4%). Overall, 387 individuals (28.5%) were involved in clusters: 156 patients (11.5%) in 78 dyads and 231 participants (17%) in 42 larger clusters (median size: 4, range 3–41). Compared to individuals with single PHI (n = 969), those in clusters were more frequently men (95.9 vs 83%, p < 0.01), MSM (85.8 vs 65.6%, p < 0.01) and infected with CRF02_AG (20.4 vs 13.4%, p < 0.01). Reconstruction of viral migrations across time suggests that Paris area was the major hub of dissemination of both subtype B and CRF02_AG epidemics. By targeting clustering individuals belonging to the identified active transmission network before 2010, 60 of the 143 onward transmissions could have been prevented.

Conclusion

These analyses support the hypothesis of a recent and rapid rise of CRF02_AG within the French HIV-1 epidemic among MSM. Combined with a short turnaround time for sample processing, targeting prevention efforts based on phylogenetic monitoring may be an efficient way to deliver prevention interventions but would require near real time targeted interventions on the identified index cases and their partners.

Electronic supplementary material

The online version of this article (doi:10.1186/s12977-017-0339-4) contains supplementary material, which is available to authorized users.

HIV surveillance combining an assay for identification of very recent infection and phylogenetic analyses on dried spots

BACKGROUND

Transmitted/founder viruses isolated at the early stage of infection are indicators of the variants that are spreading within a population. The French reporting system for new HIV diagnoses is linked to a virological surveillance using dried serum spots.

METHODS

We combined an immunoassay for very recent infection (less than 31 days) to a phylogenetic analysis of transmitted/founder viruses and sociodemographic information to analyze the dynamics of the HIV-1 epidemic during a 3-year period. Bayesian coalescent-based methods were used to explore the temporal and spatial dynamics of the identified clusters.

RESULTS

Of 17 010 dried serum spots collected, 549 very recent infections were identified for which both env sequences and sociodemographic data were available. Non-B transmitted/founder viruses were found in 196 cases (35.7%), belonging to six subtypes and seven circulating recombinant forms. Forty-three dyads/clusters were identified (range 2-11 cases), including 107 individuals (19.5%), mainly MSM. The largest cluster involved MSM infected by a CRF02_AG variant. Reconstruction of viral migrations across time suggests that Paris was the major hub of dissemination.

CONCLUSION

The study shows the feasibility of the surveillance of the HIV epidemic using this methodology. The observation of actively growing spatiotemporal clusters allows identification of specific networks that may be targets for intervention.

HIV Drug Resistance in Antiretroviral Treatment-Naïve Individuals in the Largest Public Hospital in Nicaragua, 2011-2015

Background

Increasing HIV pre-treatment drug resistance (PDR) levels have been observed in regions with increasing antiretroviral treatment (ART) coverage. However, data is lacking for several low/middle-income countries. We present the first PDR survey in Nicaragua since ART introduction in the country in 2003.

Methods

HIV-infected, ART-naïve Nicaraguan individuals were enrolled at Roberto Calderón Hospital, the largest national HIV referral center, from 2011 to 2015. HIV pol sequences were obtained at a WHO-accredited laboratory in Mexico by Sanger and next generation sequencing (NGS). PDR was assessed using the WHO surveillance drug resistance mutation (SDRM) list and the Stanford HIVdb tool.

Results

283 individuals were enrolled in the study. The overall PDR prevalence based on the list of SDRMs was 13.4%. Using the Stanford HIVdb tool, overall PDR reached 19.4%; with both nucleoside and non-nucleoside reverse transcriptase inhibitor (NRTI and NNRTI) PDR levels independently reaching moderate levels (6.7% and 11.3% respectively). Protease inhibitor PDR was low (2.8%). Using NGS with 2% threshold to detect SDRMs, PDR increased to 25.3%. K103N and M41L were the most frequent SDRMs and were present mostly in proportions >20% in each individual. A significant temporal increase in NNRTI PDR was observed (p = 0.0422), with no apparent trends for other drug classes. Importantly, PDR to zidovudine + lamivudine + efavirenz and tenofovir + emtricitabine + efavirenz, the most widely used first-line regimens in Nicaragua, reached 14.6% and 10.4% respectively in 2015. Of note, a higher proportion of females was observed among individuals with PDR compared to individuals without PDR (OR 14.2; 95% CI: 7.1–28.4; p<0.0001).

Conclusions

Overall PDR in the Nicaraguan cohort was high (19.4%), with a clear increasing temporal trend in NNRTI PDR. Current HIVDR to the most frequently used first-line ART regimens in Nicaragua reached levels >10%. These observations are worrisome and need to be evidenced to strengthen the national HIV program. Also, our observations warrant further nationally representative HIVDR surveillance studies and encourage other countries to perform national surveys. Cost-effectiveness studies are suggested to analyze the feasibility of implementation of baseline HIV genotyping as well as to review the choice of first-line ART regimens in Nicaragua.