HIV transmission networks among transgender women in Los Angeles County, CA, USA: a phylogenetic analysis of surveillance data

Application of molecular epidemiology in revealing HIV-1 transmission network and recombination patterns in Tianjin, China

Using a comprehensive molecular epidemiological approach, we characterized the transmission dynamics of HIV-1 among the MSM population in Tianjin, China. Our findings revealed that 38.56% (386/1001) of individuals clustered across 109 molecular transmission clusters (TCs), with MSM aged 50 and below being the group most commonly transmitting HIV-1. Among the identified TCs, CRF01_AE predominated, followed by CRF07_BC. Notably, CRF07_BC demonstrated a higher propensity for forming large clusters compared to CRF01_AE. Birth-death skyline analyses of the two largest clusters indicated that the HIV/AIDS transmission may be at a critical point, nearly all had Re approximately 1 by now. A retrospective analysis revealed that the rapid expansion of these large clusters was primarily driven by the introduction of viruses in 2021, highlighting the crucial importance of continuous molecular surveillance in identifying newly emerging high-risk transmission chains and adapting measures to address evolving epidemic dynamics. Furthermore, we detected the transmission of drug-resistant mutations (DRMs) within the TCs, particularly in the CRF07_BC clusters (K103N, Y181C, and K101E) and CRF01_AE clusters (P225H and K219R), emphasizing the importance of monitoring to support the continued efficacy of first-line therapies and pre-exposure prophylaxis (PrEP). Recombination analyses indicated that complex recombinant patterns, associated with increased amino acid variability, could confer adaptive traits to the viruses, potentially providing a competitive advantage in certain host populations or regions. Our study highlights the potential of integrating molecular epidemiological and phylodynamic approaches to inform targeted interventions.

Characteristics of Subtype and Molecular Transmission Networks among Newly Diagnosed HIV-1 Infections in Patients Residing in Taiyuan City, Shanxi Province, China, from 2021 to 2023

The HIV-1 pandemic, spanning four decades, presents a significant challenge to global public health. This study aimed to understand the molecular transmission characteristics of newly reported HIV infections in Taiyuan, Shanxi Province, China, to analyze the characteristics of subtypes and the risk factors of the transmission network, providing a scientific basis for precise prevention and intervention measures. A total of 720 samples were collected from newly diagnosed HIV-1 patients residing in Taiyuan between 2021 and 2023. Sequencing of partial genes of the HIV-1 pol gene resulted in multiple sequence acquisitions and was conducted to analyze their subtypes and molecular transmission networks. Out of the samples, 584 pol sequences were obtained, revealing 17 HIV-1 subtypes, with CRF07_BC (48.29%), CRF01_AE (31.34%), and CRF79_0107 (7.19%) being the dominant subtypes. Using a genetic distance threshold of 1.5%, 49 molecular transmission clusters were generated from the 313 pol gene sequences. Univariate analysis showed significant differences in the HIV transmission molecular network in terms of HIV subtype and household registration (p < 0.05). Multivariate logistic regression analysis showed that CRF79_0107 subtype and its migrants were associated with higher proportions of sequences in the HIV transmission network. These findings provide a scientific foundation for the development of localized HIV-specific intervention strategies.

Prevalence of Sexually Transmitted Infections Among Transgender Women With and Without HIV in the Eastern and Southern United States

BACKGROUND

Data on the epidemiology of sexually transmitted infections (STIs) among transgender women (TGW) with and without human immunodeficiency virus (HIV) are limited.

METHODS

We analyzed baseline data collected from a cohort of adult TGW across 6 eastern and southern US cities between March 2018 and August 2020 (n = 1018). Participants completed oral HIV screening, provided self-collected rectal and urogenital specimens for chlamydia and gonorrhea testing, and provided sera specimens for syphilis testing. We assessed associations with ≥1 prevalent bacterial STI using modified Poisson regression.

RESULTS

Bacterial STI prevalence was high and differed by HIV status: 32% among TGW with HIV and 11% among those without HIV (demographic-adjusted prevalence ratio = 1.91; 95% confidence interval = 1.39-2.62). Among TGW without HIV, bacterial STI prevalence differed by geographic region, race and ethnicity, and gender identity, and was positively associated with reporting >1 sexual partner, hazardous alcohol use, homelessness, having safety concerns regarding transit to health care, and no prior receipt of gender-affirming health services. Among TGW with HIV, older age was inversely associated with bacterial STI.

CONCLUSIONS

TGW had a high prevalence of bacterial STIs. The prevalence and correlates of bacterial STI differed by HIV status, highlighting the unique needs and risks of TGW with and without HIV. Tailored interventions may reduce sexual health-related inequities.

Exploring Dynamic Changes in HIV-1 Molecular Transmission Networks and Key Influencing Factors: Cross-Sectional Study

BACKGROUND

The HIV-1 molecular network is an innovative tool, using gene sequences to understand transmission attributes and complementing social and sexual network studies. While previous research focused on static network characteristics, recent studies' emphasis on dynamic features enhances our understanding of real-time changes, offering insights for targeted interventions and efficient allocation of public health resources.

OBJECTIVE

This study aims to identify the dynamic changes occurring in HIV-1 molecular transmission networks and analyze the primary influencing factors driving the dynamics of HIV-1 molecular networks.

METHODS

We analyzed and compared the dynamic changes in the molecular network over a specific time period between the baseline and observed end point. The primary factors influencing the dynamic changes in the HIV-1 molecular network were identified through univariate analysis and multivariate analysis.

RESULTS

A total of 955 HIV-1 polymerase fragments were successfully amplified from 1013 specimens; CRF01_AE and CRF07_BC were the predominant subtypes, accounting for 40.8% (n=390) and 33.6% (n=321) of the specimens, respectively. Through the analysis and comparison of the basic and terminal molecular networks, it was discovered that 144 sequences constituted static molecular networks, and 487 sequences contributed to the formation of dynamic molecular networks. The findings of the multivariate analysis indicated that the factors occupation as a student, floating population, Han ethnicity, engagement in occasional or multiple sexual partnerships, participation in anal sex, and being single were independent risk factors for the dynamic changes observed in the HIV-1 molecular network, and the odds ratio (OR; 95% CIs) values were 2.63 (1.54-4.47), 1.83 (1.17-2.84), 2.91 (1.09-7.79), 1.75 (1.06-2.90), 4.12 (2.48-6.87), 5.58 (2.43-12.80), and 2.10 (1.25-3.54), respectively. Heterosexuality and homosexuality seem to exhibit protective effects when compared to bisexuality, with OR values of 0.12 (95% CI 0.05-0.32) and 0.26 (95% CI 0.11-0.64), respectively. Additionally, the National Eight-Item score and sex education experience were also identified as protective factors against dynamic changes in the HIV-1 molecular network, with OR values of 0.12 (95% CI 0.05-0.32) and 0.26 (95% CI 0.11-0.64), respectively.

CONCLUSIONS

The HIV-1 molecular network analysis showed 144 sequences in static networks and 487 in dynamic networks. Multivariate analysis revealed that occupation as a student, floating population, Han ethnicity, and risky sexual behavior were independent risk factors for dynamic changes, while heterosexuality and homosexuality were protective compared to bisexuality. A higher National Eight-Item score and sex education experience were also protective factors. The identification of HIV dynamic molecular networks has provided valuable insights into the characteristics of individuals undergoing dynamic alterations. These findings contribute to a better understanding of HIV-1 transmission dynamics and could inform targeted prevention strategies.

Sexual Health Care for Transgender and Gender Diverse People

The proportion of people who identify as transgender and gender diverse (TGD) is increasing. Health care for TGD people, including sexual health care, must affirm and respect patients' gender identities and expressions. Here, the authors outline strategies to make health care settings more welcoming to and inclusive of TGD people and describe concrete steps to improve sexual health care for TGD populations.

HIV transmission and associated factors under the scale-up of HIV antiretroviral therapy: a population-based longitudinal molecular network study

OBJECTIVES

To evaluate the prevention efficacy of scaling up HIV/AIDS antiretroviral therapy (ART) on HIV transmission at the population level and determine associated factors of HIV secondary transmission.

METHODS

We used HIV longitudinal molecular networks to assess the genetic linkage between baseline and newly diagnosed cases. A generalized estimating equation was applied to determine the associations between demographic, clinical characteristics and HIV transmission.

RESULTS

Patients on ART had a 32% lower risk of HIV transmission than those not on ART. A 36% reduction in risk was also seen if ART-patients maintained their HIV viral load lower than 50 copies/mL. A 71% lower risk occurred when patients sustained ART for at least 3 years and kept HIV viral load less than 50 copies/mL. Patients who discontinued ART had a similar HIV transmission risk as those not on ART. Patients who were older, male, non-Han, not single, retired, infected via a heterosexual route of transmission and those who possessed higher CD4 counts had a higher risk of HIV transmission. HIV-1 subtype of CRF01_AE was less transmissible than other subtypes.

CONCLUSIONS

The efficacy of ART in a real-world setting was supported by this longitudinal molecular network study. Promoting adherence to ART is crucial to reduce HIV transmission.

Characteristics of the different HIV-1 risk populations based on the genetic transmission network of the newly diagnosed HIV cases in Jiangsu, Eastern China

Introduction

The HIV-1 prevalence has been steadily increasing in Jiangsu, China. HIV-1 genetic transmission network can be used to explore the transmission kinetics and precision intervention in high-risk populations. Thus, we generated an HIV-1 genetic transmission network, explored key risk populations based on different risk factors and found out the risk factors for HIV-1 prevention and control among the newly-diagnosed HIV-1 cases from 2017 to 2018.

Method

We amplified the HIV-1 pol sequences from the plasma samples of the newly-diagnosed HIV-1 cases from 2017 to 2018 and obtained the infection data from The National HIV/AIDS Surveillance System. HIV-Trace and Cytoscape Software were both used to construct the HIV-1 genetic network with a gene distance of <0.005. The R software was used to analyze the risk factors for inclusion into the network.

Results

We obtained 3362 sequences with the pol gene region, of which 3316 contained detailed individual information. CRF01_AE accounted for 42.3 % of the HIV-1 subtypes in the samples. The median CD4+T lymphocyte count was 329 cells/μL in 2017 and 313 cells/μL in 2018. At the gene distance threshold of 0.005, 481 sequences were incorporated into the HIV-1 gene network, constructing 202 clusters. Age over 60 years old, heterosexual transmission route, subtype (CRF105_0107, CRF55_01 B, and CRF67_01 B) and CD4+T lymphocyte count (>200) were the risk factors influencing inclusion into the HIV-1 gene network. Moreover, south Jiangsu cities had higher inclusion in the network. Thus, key risk populations in the clusters with different transmission routes, new emerging subtypes, drug resistance nodes, and individuals above 60 years of age in the network represented the critical risk populations that should be focused more on for intervention.

Conclusion

The HIV-1 genetic transmission network is adept at discovering undiagnosed HIV-infected cases and linking all diagnosed cases for determination of risk infections. Therefore we should pay more attention to these risk infections with further investigation and intervention, helping to achieve the goal of 95 % use combination prevention from the World Health Organization, and push to end AIDS epidemic.

Molecular Transmission Network of Newly Reported HIV Infections in Pengzhou, Sichuan Province: A Study Based on Genomics and Spatial Epidemiology

OBJECTIVE

The objective of this study was to understand the molecular transmission characteristics of newly reported HIV infections in the city of Pengzhou, Sichuan Province, to analyze the risk factors of transmission network and spatial clustering and the transmission characteristics, and to provide a scientific basis for precision prevention and intervention.

METHODS

Anticoagulated whole blood was collected from newly reported HIV infections in Pengzhou from March 2019 to August 2021. After the plasma was isolated, the HIV-1 pol gene was amplified and sequenced by reverse transcriptase polymerase chain reaction (PCR). The obtained gene sequences were used to construct a maximum likelihood phylogenetic tree for the analysis of virus subtypes, and a molecular transmission network was constructed using the genetic distance method to evaluate the transmission pattern of people living with HIV/AIDS in Pengzhou. A logistic regression model was used to find out the potential risk factors for entering the molecular transmission network with the number of nodes ≥ 2. Spatial analysis is used to show the geographical pattern of the proportion of newly reported HIV infections entering the molecular transmission network, and a flow map is used to show the intensity of transmission within and between townships.

RESULTS

A total of 463 newly reported HIV-infection sequences were obtained in this study, including 237 cases (51.19%) of CRF01_ AE, 159 cases (34.34%) of CRF07_BC, 45 cases (9.72%) of B, 15 cases (3.24%) of CRF08_BC and 7 cases (1.5%) of others. The number of clusters was the highest when the gene distance was 0.009, with a total of 246 sequences entering the network, forming 54 clusters, and the network entry rate was 55.36%. There were 170 sequences with more than two nodes in the network sequence. The logistic regression showed that compared with age < 50 years old, age ≥ 50 years old has a higher risk of transmission (OR = 3.43, 95% CI = 2.06-5.71); compared with farmers, the risk of transmission within industry is lower (OR = 0.046, 95% CI = 0.25-0.87); and compared with CRF07_BC, CRF01_AE (OR = 6.09, 95% CI = 3.60-10.30) and B (OR = 20.31, 95% CI = 8.94-46.13) had a higher risk of transmission. Men aged ≥ 50 years are mainly clustered with women between 50 and 70 years of age. In addition to being clustered with gay men, there are nine (50%) and three (16.7%) chains of transmission between gay men and heterosexual men and women, respectively. In the geographical space, there is no hot spot clustering of the molecular propagation network. The subtype B was mainly distributed in the town of Tianpeng and formed transmission networks in eastern Pengzhou;0020CRF01_AE is mainly distributed in the town of Lichun and formed transmission networks in the west and north of Pengzhou.

CONCLUSION

This study reveals the characteristics and influencing factors of molecular network transmission in the region, as well as the spatial transmission characteristics of newly reported HIV infections in recent years, and reveals the geographical differences in HIV-1 transmission. The results provide a scientific basis for the development of local AIDS-specific intervention measures.

From components to communities: bringing network science to clustering for molecular epidemiology

Defining clusters of epidemiologically related infections is a common problem in the surveillance of infectious disease. A popular method for generating clusters is pairwise distance clustering, which assigns pairs of sequences to the same cluster if their genetic distance falls below some threshold. The result is often represented as a network or graph of nodes. A connected component is a set of interconnected nodes in a graph that are not connected to any other node. The prevailing approach to pairwise clustering is to map clusters to the connected components of the graph on a one-to-one basis. We propose that this definition of clusters is unnecessarily rigid. For instance, the connected components can collapse into one cluster by the addition of a single sequence that bridges nodes in the respective components. Moreover, the distance thresholds typically used for viruses like HIV-1 tend to exclude a large proportion of new sequences, making it difficult to train models for predicting cluster growth. These issues may be resolved by revisiting how we define clusters from genetic distances. Community detection is a promising class of clustering methods from the field of network science. A community is a set of nodes that are more densely inter-connected relative to the number of their connections to external nodes. Thus, a connected component may be partitioned into two or more communities. Here we describe community detection methods in the context of genetic clustering for epidemiology, demonstrate how a popular method (Markov clustering) enables us to resolve variation in transmission rates within a giant connected component of HIV-1 sequences, and identify current challenges and directions for further work.

Characterization of HIV-1 Transmission Clusters Inferred from the Brazilian Nationwide Genotyping Service Database

The study of HIV-1 transmission networks inferred from viral genetic data can be used to clarify important factors about the dynamics of HIV-1 transmission, such as network growth rate and demographic composition. In Brazil, HIV transmission has been stable since the early 2000s and the study of transmission clusters can provide valuable data to understand the drivers of virus spread. In this work, we analyzed a nation-wide database of approximately 53,000 HIV-1 nucleotide pol sequences sampled from genotyped patients from 2008-2017. Phylogenetic trees were reconstructed for the HIV-1 subtypes B, C and F1 in Brazil and transmission clusters were inferred by applying genetic distances thresholds of 1.5%, 3.0% and 4.5%, as well as high (>0.9) cluster statistical support. An odds ratio test revealed that young men (15-24 years) and individuals with more years of education presented higher odds to cluster. The assortativity coefficient revealed that individuals with similar demographic features tended to cluster together, with emphasis on features, such as place of residence and age. We also observed that assortativity weakens as the genetic distance threshold increases. Our results indicate that the phylogenetic clusters identified here are likely representative of the contact networks that shape HIV transmission, and this is a valuable tool even in sites with low sampling density, such as Brazil.

Exploring HIV risk behavior and sexual/gender identities among transgender women and their sexual partners in Peru using respondent-driven sampling

HIV prevalence is high among transgender women, but little is known about cisgender men who have sex with transgender women (MSTW). The objective of this study was to investigate characteristics and behavior of MSTW compared to transgender women and men who have sex with men (MSM) using a modified respondent-driven sampling design. Seed participants completed a survey and invited up to three sex partners. Forward recruitment continued in waves through the referral of sex partners. Cross-sectional data were assessed using mixed effects models. From February to July 2018, 479 participants in Lima, Peru enrolled (n = 199 transgender women, n = 196 MSTW, and n = 45 MSM). MSTW behavior and identity differed significantly from that of transgender women and MSM. MSTW primarily identified as bisexual (69%) or heterosexual (15%) and only 6% reported male partners. Insertive condomless anal intercourse was reported by 61% of MSTW; 46% did not know their HIV serostatus. Compared to MSTW without male partners, those with recent male partners were more likely to sell sex (OR 15.7, 95% CI 4.1-60.5), and report condomless receptive anal intercourse (OR 89.0, 95% CI 19.1-414.8). This evidence suggests that MSTW are a distinct population from MSM, and highlights the critical need to include MSTW in HIV research and interventions.

In Their Own Words: How Trans Women Acquired HIV Infection

Despite high HIV prevalence, the reasons trans women acquire HIV are not well understood. Trans women are often mis-classified or aggregated with men who have sex with men (MSM) in epidemiologic studies and HIV surveillance data. Trans women enrolled in the 2019/2020 National HIV Behavioral Surveillance Study in San Francisco were asked an open-ended question about how they were infected with HIV. The most common responses were "Sex with a straight cisgender man partner when the respondent identified as a trans woman" (43.0%); "Sexual assault" (13.9%); "Injection drug use (IDU)" (10.1%); "IDU or sexual contact" (7.6%) and "Sex with a partner who injected drugs" (7.6%). Sex with a cisgender man partner prior to identifying as a trans women (MSM contact) was not mentioned by any respondent. HIV prevention strategies targeting MSM will fail to reach trans women and many of their cisgender men partners.

HIV transmission patterns among transgender women, their cisgender male partners, and cisgender MSM in Lima, Peru: A molecular epidemiologic and phylodynamic analysis

BACKGROUND

Transgender women (TW) in Peru are disproportionately affected by HIV. The role that cisgender men who have sex with TW (MSTW) and their sexual networks play in TW's risk of acquiring HIV is not well understood. We used HIV sequences from TW, MSTW, and cisgender men who have sex with men (MSM) to examine transmission dynamics between these groups.

METHODS

We used HIV-1 pol sequences and epidemiologic data collected through three Lima-based studies from 2013 to 2018 (n = 139 TW, n = 25 MSTW, n = 303 MSM). We identified molecular clusters based on pairwise genetic distance and used structured coalescent phylodynamic modeling to estimate transmission patterns between groups.

FINDINGS

Among 200 participants (43%) found in 62 clusters, the probability of clustering did not differ by group. Both MSM and TW were more likely to cluster with members of their own group than would be expected based on random mixing. Phylodynamic modeling estimated that there was frequent transmission from MSTW to TW (67·9% of transmission from MSTW; 95%CI = 52·8-83·2%) and from TW to MSTW (76·5% of transmissions from TW; 95%CI = 65·5-90·3%). HIV transmission between MSM and TW was estimated to comprise a small proportion of overall transmissions (4·9% of transmissions from MSM, and 11·8% of transmissions from TW), as were transmissions between MSM and MSTW (7·2% of transmissions from MSM, and 32·0% of transmissions from MSTW).

INTERPRETATION

These results provide quantitative evidence that MSTW play an important role in TW's HIV vulnerability and that MSTW have an HIV transmission network that is largely distinct from MSM.

Non-student young men put students at high risk of human immunodeficiency virus acquisition in Guangxi, China: a phylogenetic analysis of surveillance data

Background

We sought to identify students and their sexual partners in a molecular transmission network.

Methods

We obtained 5996 HIV protease and reverse transcriptase gene sequences in Guangxi (165 from students and 5831 from the general populations) and the relevant demographic data. We constructed a molecular transmission network and introduced a permutation test to assess the robust genetic linkages. We calculated the centrality measures to describe the transmission patterns in clusters.

Results

At the network level, 68 (41.2%) students fell within the network across 43 (8.1%) clusters. Of 141 genetic linkages between students and their partners, only 25 (17.7%) occurred within students. Students were more likely than random permutations to link to other students (odds ratio [OR], 7.2; P < .001), private company employees aged 16–24 years (OR, 3.3; P = .01), private company or government employees aged 25–49 years (OR, 1.7; P = .03), and freelancers or unemployed individuals aged 16–24 years (OR, 5.0; P < .001). At the cluster level, the median age of nonstudents directly linked to students (interquartile range) was 25 (22–30) years, and 80.3% of them had a high school or higher education background. Compared with students, they showed a significantly higher median degree (4.0 vs 2.0; P < .001) but an equivalent median Eigenvector Centrality (0.83 vs 0.81; P = .60).

Conclusions

The tendency of genetic linkage between students and nonstudent young men and their important position in the HIV transmission network emphasizes the urgent need for 2-pronged public health interventions based on both school and society.

HIV-1 genetic transmission networks among people living with HIV/AIDS in Sichuan, China: a genomic and spatial epidemiological analysis

BACKGROUND

Spatialized HIV genetic transmission networks can help understand dynamic changes of HIV-1 at the regional level. This study aimed to combine genomic, epidemiological, and spatial data to investigate the patterns of the HIV-1 epidemic at both individual and regional levels among people living with HIV (PLWH) with virological failure of antiretroviral therapy (ART).

METHODS

We evaluated the transmission patterns of 5,790 PLWH with identified pol sequences of the five main HIV-1 subtypes (B, CRF08_BC, CRF85_BC, CRF07_BC, and CRF01_AE) in Sichuan Province, China. A phylogenetic cluster was defined as a group of sequences with genetically similar HIV strains, with all phylogenetic clusters forming an HIV-1 genetic transmission network for each subtype. Logistic regression was used to identify the potential risk factors for phylogenetic clustering. Spatial analysis was applied to demonstrate the geographic patterns of phylogenetic clustering rates; intensity matrices and flow maps were made to demonstrate the intensity of transmission within and between cities.

FINDINGS

There were 2,159 (37.3%) of 5,790 PLWH, distributed in 452 phylogenetic clusters. Some individual clinical and behavioral factors were associated with phylogenetic clustering, including a viral load of >50,000 copies/ml (OR=1.16, 95%CI=1.02-1.33), infection of other sexually transmitted diseases (OR=1.38, 95%CI=1.12-1.69), and ≥5 non-marital sexual partners (OR=1.25, 95%CI=1.03-1.51), while >3 years of treatment since the initial ART was associated with less likelihood of phylogenetic clustering (OR=0.82, 95%CI=0.70-0.97). The phylogenetic clustering rates varied regionally and were highest in the central region of Sichuan, especially for subtype CRF08_BC. The significant spatial clusters of high and low phylogenetic clustering rates were detected in the east (Dazhou for B; Zigong and Luzhou for CFR08_BC) and west (Yaan and Ganzi for CRF07_BC), respectively. The proportion of intercity transmission varied across cities from 0.14 (Yibin) and 1.00 (Ganzi). Stronger intercity transmission than average existed between some cities, e.g., between Deyang and Neijiang. CRF07_BC was the most widespread subtype between cities, and CRF85_BC (a novel HIV-1 subtype) showed strong intercity transmission (e.g., between Yibin and Guangan).

INTERPRETATION

The phylogenetic clustering rates and intercity connections of HIV-1 have varied geographically, possibly due to varying human mobility, traffic convenience, and economic activities. Our findings enhanced the understanding of the dynamics of HIV-1 transmission from individual to city level, and demonstrated a novel cross-disciplinary (epidemiological, genetic, and spatial) approach by which we identified high-risk populations and areas. Our approach could be adapted to other regions for precision public health interventions.

FUNDING

The National Natural Science Foundation of China, Sichuan Science and Technology Program, Project of Sichuan Provincial Health Committee, Science and Technology Project of Sichuan Provincial Health Committee, Wuhan University 351 Talent Program, 2020, and the International Institute of Spatial Lifecourse Epidemiology (ISLE).

Characteristics and growth of the genetic HIV transmission network of Mexico City during 2020

INTRODUCTION

Molecular surveillance systems could provide public health benefits to focus strategies to improve the HIV care continuum. Here, we infer the HIV genetic network of Mexico City in 2020, and identify actively growing clusters that could represent relevant targets for intervention.

METHODS

All new diagnoses, referrals from other institutions, as well as persons returning to care, enrolling at the largest HIV clinic in Mexico City were invited to participate in the study. The network was inferred from HIV pol sequences, using pairwise genetic distance methods, with a locally hosted, secure version of the HIV-TRACE tool: Seguro HIV-TRACE. Socio-demographic, clinical and behavioural metadata were overlaid across the network to design focused prevention interventions.

RESULTS

A total of 3168 HIV sequences from unique individuals were included. One thousand and one-hundred and fifty (36%) sequences formed 1361 links within 386 transmission clusters in the network. Cluster size varied from 2 to 14 (63% were dyads). After adjustment for covariates, lower age (adjusted odds ratio [aOR]: 0.37, p<0.001; >34 vs. <24 years), being a man who has sex with men (MSM) (aOR: 2.47, p = 0.004; MSM vs. cisgender women), having higher viral load (aOR: 1.28, p<0.001) and higher CD4+ T cell count (aOR: 1.80, p<0.001; ≥500 vs. <200 cells/mm3 ) remained associated with higher odds of clustering. Compared to MSM, cisgender women and heterosexual men had significantly lower education (none or any elementary: 59.1% and 54.2% vs. 16.6%, p<0.001) and socio-economic status (low income: 36.4% and 29.0% vs. 18.6%, p = 0.03) than MSM. We identified 10 (2.6%) clusters with constant growth, for prioritized intervention, that included intersecting sexual risk groups, highly connected nodes and bridge nodes between possible sub-clusters with high growth potential.

CONCLUSIONS

HIV transmission in Mexico City is strongly driven by young MSM with higher education level and recent infection. Nevertheless, leveraging network inference, we identified actively growing clusters that could be prioritized for focused intervention with demographic and risk characteristics that do not necessarily reflect the ones observed in the overall clustering population. Further studies evaluating different models to predict growing clusters are warranted. Focused interventions will have to consider structural and risk disparities between the MSM and the heterosexual populations.

"That same stigma...that same hatred and negativity:" a qualitative study to understand stigma and medical mistrust experienced by people living with HIV diagnosed with COVID-19

BACKGROUND

The COVID-19 and HIV epidemics have exacerbated existing inequities among vulnerable groups and severely impacted communities of color. People living with HIV (PLWH), who may already face stigma or discrimination, are at risk of experiencing further stigma as a result of COVID-19, which can result in medical mistrust.

METHODS

We performed qualitative interviews between June and August 2020 among 32 PLWH, including 10 individuals diagnosed with COVID-19. A majority of participants perceived themselves as having an increased risk of contracting COVID-19 due to their HIV status.

RESULTS

Of those who tested positive for COVID-19, the majority regarded their HIV diagnosis as having a more profound impact on their lives but found similarities between COVID-19 stigma and HIV-related stigma. Many participants also expressed mistrust.

CONCLUSIONS

These results can be used to better understand the perspectives of PLWH during the COVID-19 pandemic and have important implications for potential COVID-19 vaccine hesitancy and future health crises.

Sorting by Race/Ethnicity Across HIV Genetic Transmission Networks in Three Major Metropolitan Areas in the United States

An important component underlying the disparity in HIV risk between race/ethnic groups is the preferential transmission between individuals in the same group. We sought to quantify transmission between different race/ethnicity groups and measure racial assortativity in HIV transmission networks in major metropolitan areas in the United States. We reconstructed HIV molecular transmission networks from viral sequences collected as part of HIV surveillance in New York City, Los Angeles County, and Cook County, Illinois. We calculated assortativity (the tendency for individuals to link to others with similar characteristics) across the network for three candidate characteristics: transmission risk, age at diagnosis, and race/ethnicity. We then compared assortativity between race/ethnicity groups. Finally, for each race/ethnicity pair, we performed network permutations to test whether the number of links observed differed from that expected if individuals were sorting at random. Transmission networks in all three jurisdictions were more assortative by race/ethnicity than by transmission risk or age at diagnosis. Despite the different race/ethnicity proportions in each metropolitan area and lower proportions of clustering among African Americans than other race/ethnicities, African Americans were the group most likely to have transmission partners of the same race/ethnicity. This high level of assortativity should be considered in the design of HIV intervention and prevention strategies.

Heterosexual Cisgender Men Partnered with Transgender Women Exhibit Higher HIV/STI Sexual Risk than Their Gay, Bisexual, and Queer Counterparts: Findings from a U.S.-Based Convenience Sample Recruited Online

Cisgender men are frequently vectors for HIV transmission among transgender women. Despite this, the correlates of sexual risk among these men remain under-examined. The purpose of the present study was to explore potential differences in relationship characteristics, sexual risk-taking, and risk-reduction strategies among cisgender men partnered with transgender women. The study utilized secondary screening data provided by adult cis men who reported being in a primary relationship with a trans woman (N = 710). Gay men (18%) were comparatively older, and most likely to report both HIV seropositivity and committed pairings. Heterosexual men (14%) were more likely to report exchange sex, briefer relationships, extra-dyadic sex, lesser serostatus awareness or PrEP uptake. Queer men (7%) were youngest, and most likely to access PrEP. Heterosexual cis men with trans women partners may be subject to unique socio-cultural drivers of sexual risk, such as heteronormative pressures and relationship stigma.

Self-Identity, Beliefs, and Behavior Among Men Who Have Sex with Transgender Women: Implications for HIV Research and Interventions

While transgender women have been identified as a global priority population for HIV prevention and treatment, little is known about the cisgender male partners of transgender women, including their sexual behavior and HIV prevalence. Previous research has suggested that these male partners have varied identities and sexual behavior, which make identifying and engaging them in research difficult. This paper describes interviews conducted with fifteen cisgender men who reported recent sexual activity with transgender women in Lima, Peru. The purpose of this research was to explore how these men reported their identities and sexual behavior, to better understand how they would interact with HIV outreach, research, and care. The major themes were sexual orientation and identity; view of transgender partners; social ties to transgender women and other men with transgender women partners; disclosure of relationships; HIV knowledge and risk perception; and attitudes toward interventions. We found that language used to assess sexual orientation was problematic in this population, due to lack of consistency between orientation and reported behavior, and unfamiliarity with terms used to describe sexual orientation. In addition, stigma, lack of knowledge of HIV prevention methods, and fear of disclosure of sexual behavior were identified as barriers that could impact engagement in HIV research, prevention, and care. However, participants reported social relationships with both transgender women and other men who have transgender partners, presenting possible avenues for recruitment into HIV research and healthcare services.

Drug resistance mutations in HIV: new bioinformatics approaches and challenges

Drug resistance mutations appear in HIV under treatment pressure. Resistant variants can be transmitted to treatment-naive individuals, which can lead to rapid virological failure and can limit treatment options. Consequently, quantifying the prevalence, emergence and transmission of drug resistance is critical to effectively treating patients and to shape health policies. We review recent bioinformatics developments and in particular describe: (1) the machine learning approaches intended to predict and explain the level of resistance of HIV variants from their sequence data; (2) the phylogenetic methods used to survey the emergence and dynamics of resistant HIV transmission clusters; (3) the impact of deep sequencing in studying within-host and between-host genetic diversity of HIV variants, notably regarding minority resistant variants.

Scale-Free Spanning Trees and Their Application in Genomic Epidemiology

We study the algorithmic problem of finding the most “scale-free-like” spanning tree of a connected graph. This problem is motivated by the fundamental problem of genomic epidemiology: given viral genomes sampled from infected individuals, reconstruct the transmission network (“who infected whom”). We use two possible objective functions for this problem and introduce the corresponding algorithmic problems termedm-SF (-scale free) ands-SF Spanning Tree problems. We prove that those problems are APX- and NP-hard, respectively, even in the classes of cubic and bipartite graphs. We propose two integer linear programming (ILP) formulations for thes-SF Spanning Tree problem, and experimentally assess its performance using simulated and experimental data. In particular, we demonstrate that the ILP-based approach allows for accurate reconstruction of transmission histories of several hepatitis C outbreaks.

HIV-1 molecular transmission network among sexually transmitted populations in Liaoning Province, China

INTRODUCTION

In recent years, with the development of molecular epidemiology, molecular transmission networks based on evolutionary theory and sequence analysis have been widely used in research on human immunodeficiency virus (HIV)-1 transmission dynamics and precise intervention for high-risk populations. The HIV-1 molecular transmission network is a new method to study the population's access to the network, the characteristics of clustering, and the characteristics of interconnection in the network. Here, we analyzed the characteristics of the HIV-1 molecular transmission network of sexually transmitted people in Liaoning Province.

METHODS

A study of HIV-infected persons who were sexually transmitted in Liaoning Province from 2003 to 2019. HIV-1 RNA was extracted, amplified and sequenced, and a phylogenetic tree was constructed to determine the subtype using the well matched pol gene region sequence. The gene distance between sequences was calculated, the threshold was determined, and the molecular transmission network was constructed.

RESULTS

109 samples of pol gene region were obtained. The main subtype of HIV-1 was CRF01_AE, followed by B, CRF07_BC, etc. 12.8% of them were resistant to HIV. At the threshold of 0.55 gene distance, 60.6% of them entered the HIV-1 molecular transmission network. Workers, sample source voluntary counseling and testing, other testing, subtype B and drug resistance are the factors influencing the access to HIV-1 molecular transmission network. The subtype of CRF01_AE formed 6 clusters in the molecular transmission network. In the network, the difference of connection degree between different subtypes was statistically significant.

DISCUSSION

The three subtypes CRF01_AE, CRF07_BC and B that enter the molecular transmission network do not have interconnections, and they form clusters with each other. It shows that the risk of transmission among the three subtypes is less than the risk of transmission within each subtype. The factors affecting HIV-1 entry into the molecular transmission network were occupation, sample source, genotype and drug resistance. The L33F mutation at the HIV-1 resistance mutation site constitutes the interconnection in the largest transmission cluster in the network. The epidemiological characteristics of HIV-infected persons in each molecular transmission cluster show that 97% of the study subjects come from the same area and have a certain spatial aggregation.

CONCLUSION

Constructing a molecular transmission network and conducting long-term monitoring, while taking targeted measures to block the spread of HIV can achieve precise prevention and control.

Interplay Between Geography and HIV Transmission Clusters in Los Angeles County

BACKGROUND

Clusters of HIV diagnoses in time and space and clusters of genetically linked cases can both serve as alerts for directing prevention and treatment activities. We assessed the interplay between geography and transmission across the Los Angeles County (LAC) HIV genetic transmission network.

METHODS

Deidentified surveillance data reported for 8186 people with HIV residing in LAC from 2010 through 2016 were used to construct a transmission network using HIV-TRACE. We explored geographic assortativity, the tendency for people to link within the same geographic region; concordant time-space pairs, the proportion of genetically linked pairs from the same geographic region and diagnosis year; and Jaccard coefficient, the overlap between geographical and genetic clusters.

RESULTS

Geography was assortative in the genetic transmission network but less so than either race/ethnicity or transmission risk. Only 18% of individuals were diagnosed in the same year and location as a genetically linked partner. Jaccard analysis revealed that cis-men and younger age at diagnosis had more overlap between genetic clusters and geography; the inverse association was observed for trans-women and Blacks/African Americans.

CONCLUSIONS

Within an urban setting with endemic HIV, genetic clustering may serve as a better indicator than time-space clustering to understand HIV transmission patterns and guide public health action.

HIV Care Prioritization Using Phylogenetic Branch Length

BACKGROUND

The structure of the HIV transmission networks can be dictated by just a few individuals. Public health intervention, such as ensuring people living with HIV adhere to antiretroviral therapy and remain virally suppressed, can help control the spread of the virus. However, such intervention requires using limited public health resource allocations. Determining which individuals are most at risk of transmitting HIV could allow public health officials to focus their limited resources on these individuals.

SETTING

Molecular epidemiology can help prioritize people living with HIV by patterns of transmission inferred from their sampled viral sequences. Such prioritization has been previously suggested and performed by monitoring cluster growth. In this article, we introduce Prioritization using AnCesTral edge lengths (ProACT), a phylogenetic approach for prioritizing individuals living with HIV.

METHODS

ProACT starts from a phylogeny inferred from sequence data and orders individuals according to their terminal branch length, breaking ties using ancestral branch lengths. We evaluated ProACT on a real data set of 926 HIV-1 subtype B pol data obtained in San Diego between 2005 and 2014 and a simulation data set modeling the same epidemic. Prioritization methods are compared by their ability to predict individuals who transmit most after the prioritization.

RESULTS

Across all simulation conditions and most real data sampling conditions, ProACT outperformed monitoring cluster growth for multiple metrics of prioritization efficacy.

CONCLUSION

The simple strategy used by ProACT improves the effectiveness of prioritization compared with state-of-the-art methods that rely on monitoring the growth of transmission clusters defined based on genetic distance.

Methodological synthesis of Bayesian phylodynamics, HIV-TRACE, and GEE: HIV-1 transmission epidemiology in a racially/ethnically diverse Southern U.S. context

This study introduces an innovative methodological approach to identify potential drivers of structuring HIV-1 transmission clustering patterns between different subpopulations in the culturally and racially/ethnically diverse context of Houston, TX, the largest city in the Southern United States. Using 6332 HIV-1 pol sequences from persons newly diagnosed with HIV during the period 2010–2018, we reconstructed HIV-1 transmission clusters, using the HIV-TRAnsmission Cluster Engine (HIV-TRACE); inferred demographic and risk parameters on HIV-1 transmission dynamics by jointly estimating viral transmission rates across racial/ethnic, age, and transmission risk groups; and modeled the degree of network connectivity by using generalized estimating equations (GEE). Our results indicate that Hispanics/Latinos are most vulnerable to the structure of transmission clusters and serve as a bridge population, acting as recipients of transmissions from Whites (3.0 state changes/year) and from Blacks (2.6 state changes/year) as well as sources of transmissions to Whites (1.8 state changes/year) and to Blacks (1.2 state changes/year). There were high rates of transmission and high network connectivity between younger and older Hispanics/Latinos as well as between younger and older Blacks. Prevention and intervention efforts are needed for transmission clusters that involve younger racial/ethnic minorities, in particular Hispanic/Latino youth, to reduce onward transmission of HIV in Houston.

Structural modeling and phylogenetic analysis for infectious disease transmission pattern based on maximum likelihood tree approach

The contagious disease transmission pattern outbreak caused a massive human casualty and became a pandemic, as confirmed by the World Health Organization (WHO). The present research aims to understand the infectious disease transmission pattern outbreak due to molecular epidemiology. Hence, infected patients over time can spread infectious disease. The virus may develop further mutations, and that there might be a more toxic virulent strain, which leads to several environmental risk factors. Therefore, it is essential to monitor and characterize patient profiles, variants, symptoms, geographic locations, and treatment responses to analyze and evaluate infectious disease patterns among humans. This research proposes the Evolutionary tree analysis (ETA) for the molecular evolutionary genetic analysis to reduce medical risk factors. Furthermore, The Maximum likelihood tree method (MLTM) has been used to analyze the selective pressure, which is examined to identify a mutation that may influence the infectious disease transmission pattern's clinical progress. This study also utilizes ETA with Markov Chain Bayesian Statistics (MCBS) approach to reconstruct transmission trees with sequence information. The experimental shows that the proposed ETA-MCBS method achieves a 97.55% accuracy, prediction of 99.56%, and 98.55% performance compared to other existing methods.

The Relationship Between the Human Immunodeficiency Virus-1 Transmission Network and the HIV Care Continuum in Los Angeles County

BACKGROUND

Public health action combating human immunodeficiency virus (HIV) includes facilitating navigation through the HIV continuum of care: timely diagnosis followed by linkage to care and initiation of antiretroviral therapy to suppress viral replication. Molecular epidemiology can identify rapidly growing HIV genetic transmission clusters. How progression through the care continuum relates to transmission clusters has not been previously characterized.

METHODS

We performed a retrospective study on HIV surveillance data from 5226 adult cases in Los Angeles County diagnosed from 2010 through 2014. Genetic transmission clusters were constructed using HIV-TRACE. Cox proportional hazard models were used to estimate the impact of transmission cluster growth on the time intervals between care continuum events. Gamma frailty models incorporated the effect of heterogeneity associated with genetic transmission clusters.

RESULTS

In contrast to our expectations, there were no differences in time to the care continuum events among individuals in clusters with different growth dynamics. However, upon achieving viral suppression, individuals in high growth clusters were slower to experience viral rebound (hazard ratio 0.83, P = .011) compared with individuals in low growth clusters. Heterogeneity associated with cluster membership in the timing to each event in the care continuum was highly significant (P < .001), with and without adjustment for transmission risk and demographics.

CONCLUSIONS

Individuals within the same transmission cluster have more similar trajectories through the HIV care continuum than those across transmission clusters. These findings suggest molecular epidemiology can assist public health officials in identifying clusters of individuals who may benefit from assistance in navigating the HIV care continuum.

Dynamics of HIV-1 Molecular Networks Reveal Effective Control of Large Transmission Clusters in an Area Affected by an Epidemic of Multiple HIV Subtypes

This study reconstructed molecular networks of human immunodeficiency virus (HIV) transmission history in an area affected by an epidemic of multiple HIV-1 subtypes and assessed the efficacy of strengthened early antiretroviral therapy (ART) and regular interventions in preventing HIV spread. We collected demographic and clinical data of 2221 treatment-naïve HIV-1–infected patients in a long-term cohort in Shenyang, Northeast China, between 2008 and 2016. HIV pol gene sequencing was performed and molecular networks of CRF01_AE, CRF07_BC, and subtype B were inferred using HIV-TRACE with separate optimized genetic distance threshold. We identified 168 clusters containing ≥ 2 cases among CRF01_AE-, CRF07_BC-, and subtype B-infected cases, including 13 large clusters (≥ 10 cases). Individuals in large clusters were characterized by younger age, homosexual behavior, more recent infection, higher CD4 counts, and delayed/no ART (P < 0.001). The dynamics of large clusters were estimated by proportional detection rate (PDR), cluster growth predictor, and effective reproductive number (R_e). Most large clusters showed decreased or stable during the study period, indicating that expansion was slowing. The proportion of newly diagnosed cases in large clusters declined from 30 to 8% between 2008 and 2016, coinciding with an increase in early ART within 6 months after diagnosis from 24 to 79%, supporting the effectiveness of strengthened early ART and continuous regular interventions. In conclusion, molecular network analyses can thus be useful for evaluating the efficacy of interventions in epidemics with a complex HIV profile.

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

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

What Should Health Departments Do with HIV Sequence Data?

Many countries and US states have mandatory statues that require reporting of HIV clinical data including genetic sequencing results to the public health departments. Because genetic sequencing is a part of routine care for HIV infected persons, health departments have extensive sequence collections spanning years and even decades of the HIV epidemic. How should these data be used (or not) in public health practice? This is a complex, multi-faceted question that weighs personal risks against public health benefit. The answer is neither straightforward nor universal. However, to make that judgement—of how genetic sequence data should be used in describing and combating the HIV epidemic—we need a clear image of what a phylogenetically enhanced HIV surveillance system can do and what benefit it might provide. In this paper, we present a positive case for how up-to-date analysis of HIV sequence databases managed by health departments can provide unique and actionable information of how HIV is spreading in local communities. We discuss this question broadly, with examples from the US, as it is globally relevant for all health authorities that collect HIV genetic data.

Molecular surveillance of methicillin-susceptible Staphylococcus aureus (MSSA) isolated over a one-year period from a Malaysian Teaching Hospital

Introduction

We report the results of a molecular surveillance study carried out on methicillin-susceptible Staphylococcus aureus (MSSA) isolated in a one-year duration from Hospital Canselor Tuanku Muhriz (HCTM), a tertiary hospital located in Kuala Lumpur, Malaysia.

Methods

The first strain isolated from each MSSA infection in HCTM during the year 2009 was included into the study. Antimicrobial susceptibility testing and agr group typing were carried out for all strains; virulence gene (cna, seh, TSST-1 and PVL) typing results of the strains were obtained from a previous study. Pulsed-field gel electrophoresis (PFGE) was done on selected strains from the orthopedic ward. Relationship(s) between different typing methods used in the study was investigated, where a p value of <0.05 indicated significant association between typing methods.

Results

A total of 880 MSSA strains were included into the study. The strains were generally susceptible to most antibiotics, with most of them carrying cna and agr-I (51.6%, n=454; 39.8%, n=350, respectively). A total of 17 PFGE pulsotypes were identified using an 80% similarity cut-off value, where the main pulsotype (pulsotype E) consisted of 24 isolates (23.5%). agr-III strains were found to be usually positive for both cna and seh (p<0.05). In addition, some PFGE pulsotypes were also characteristic of certain virulence genes or agr groups.

Conclusions

We did not identify a dominant MSSA clone circulating in HCTM in 2009. Nevertheless, results from this molecular surveillance will provide good baseline data for the hospital's second S. aureus surveillance planned for the year 2020.

Strategies for engaging transgender populations in HIV prevention and care

PURPOSE OF REVIEW

Transgender (trans) populations are heavily impacted by HIV, yet face structural, social, and individual barriers to engagement in HIV prevention and care. In this review, we summarize the data on barriers and facilitators and discuss evidence-informed strategies to facilitate access to and engagement in HIV prevention and care by trans communities.

RECENT FINDINGS

Intersectional stigma and discrimination at structural, community, individual levels present substantial impediments to HIV prevention and optimal care. Access to gender-affirming health care is a priority for trans communities. Where trans communities are highly networked, these networks may provide a strong infrastructure for disseminating HIV innovations and reaching individuals who are not engaged in HIV services. Efforts to engage trans people in HIV prevention and care must address stigma, provide gender-affirming services, and build on community strengths and priorities to ensure trans populations achieve maximum benefit from advances in HIV prevention and care.

SUMMARY

Combination approaches that respond to the complex drivers of HIV in trans communities represent promising strategies for engaging trans people and their partners in HIV prevention and care.

Global transmission network of SARS-CoV-2: from outbreak to pandemic

Background

The COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is straining health systems around the world. Although the Chinese government implemented a number of severe restrictions on people's movement in an attempt to contain its local and international spread, the virus had already reached many areas of the world in part due to its potent transmissibility and the fact that a substantial fraction of infected individuals develop little or no symptoms at all. Following its emergence, the virus started to generate sustained transmission in neighboring countries in Asia, Western Europe, Australia, Canada and the United States, and finally in South America and Africa. As the virus continues its global spread, a clear and evidence-based understanding of properties and dynamics of the global transmission network of SARS-CoV-2 is essential to design and put in place efficient and globally coordinated interventions.

Methods

We employ molecular surveillance data of SARS-CoV-2 epidemics for inference and comprehensive analysis of its global transmission network before the pandemic declaration. Our goal was to characterize the spatial-temporal transmission pathways that led to the establishment of the pandemic. We exploited a network-based approach specifically tailored to emerging outbreak settings. Specifically, it traces the accumulation of mutations in viral genomic variants via mutation trees, which are then used to infer transmission networks, revealing an up-to-date picture of the spread of SARS-CoV-2 between and within countries and geographic regions.

Results and Conclusions

The analysis suggest multiple introductions of SARS-CoV-2 into the majority of world regions by means of heterogeneous transmission pathways. The transmission network is scale-free, with a few genomic variants responsible for the majority of possible transmissions. The network structure is in line with the available temporal information represented by sample collection times and suggest the expected sampling time difference of few days between potential transmission pairs. The inferred network structural properties, transmission clusters and pathways and virus introduction routes emphasize the extent of the global epidemiological linkage and demonstrate the importance of internationally coordinated public health measures.

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.

Understanding HIV risk and vulnerability among cisgender men with transgender partners

In the HIV pandemic, cisgender (ie, non-transgender) men with transgender partners are an underserved population. Complexities of sexuality and gender affect HIV vulnerability for this group, including not identifying with conventional sexual orientation categories (eg, bisexual, heterosexual, or gay) and having attractions based on gender role or expression rather than genital anatomy. Only one HIV prevention interventional study in this population was identified, and one study that assessed the perceived acceptability of an intervention. We found no data for interventions using pre-exposure prophylaxis, interventions for cisgender men with transgender men partners, or cisgender men with casual or transactional sexual partnerships with transgender people. Cisgender men with transgender partners are not easily categorised using traditional HIV risk categories. Additional research is needed to understand stigma and other structural drivers of HIV vulnerability, sexual networks and practices, substance use patterns, and biomedical prevention interest and uptake for this group. Studies that use an intersectional lens and syndemic framework could offer key insights.

Contribution of transgender sex workers to the complexity of the HIV-1 epidemic in the metropolitan area of Milan

OBJECTIVES

Transgender people are disproportionately affected by the HIV-1 epidemic. We evaluated the origin of HIV-1 variants carried by South American transgenders living in Milan by combining accurate phylogenetic methods and epidemiological data.

METHODS

We collected 156 HIV-1 pol sequences obtained from transgender patients engaged in sex work (TSWs) followed between 1999 and 2015 at L. Sacco Hospital, Milan, Italy. Phylogenetic analyses were conducted by HIV-TRACE, MrBayes, MacClade and Beast programs. Reference sequences were retrieved from Los Alamos and local databases. Last negative testing or proxy data from clinical records of infected individuals were used to investigate the country of infection.

RESULTS

Among South American TSWs, the most represented HIV-1 subtypes were B (70.5%), F1 (12.8%) and C (4.4%). Gene flow migrations of B subtype indicated significant fluxes from TSWs to Italians (21.3%) belonging to all risk groups (26.4% to heterosexuals (HEs), 18.9% to men who have sex with men (MSM), 15.1% to injecting drug users). The largest proportion of bidirectional fluxes were observed between Italians and TSWs (24.6%). For F1 subtype, bidirectional viral fluxes involved TSWs and Italians (7.1% and 14.3%), and a similar proportion of fluxes linked TSWs and Italian HEs or MSM (both 15.8%). Significant fluxes were detected from Italians to TSWs for subtype C involving both MSM (30%) and HEs (40%). Country of HIV-1 acquisition was identified for 72 subjects; overall, the largest proportion of patients with B subtype (73.5%) acquired HIV-1 infection in South America.

CONCLUSIONS

Our results indicated that South American transgenders largely contribute to the heterogeneity of HIV-1 variants in our country. The high number of clusters based on all subtypes indicated numerous transmission chains in which TSWs were constantly intermixed with HEs and MSM. Our results strongly advocate interventions to facilitate prevention, diagnosis and HIV-1 care continuum among transgender people.

Natural selection favoring more transmissible HIV detected in United States molecular transmission network

HIV molecular epidemiology can identify clusters of individuals with elevated rates of HIV transmission. These variable transmission rates are primarily driven by host risk behavior; however, the effect of viral traits on variable transmission rates is poorly understood. Viral load, the concentration of HIV in blood, is a heritable viral trait that influences HIV infectiousness and disease progression. Here, we reconstruct HIV genetic transmission clusters using data from the United States National HIV Surveillance System and report that viruses in clusters, inferred to be frequently transmitted, have higher viral loads at diagnosis. Further, viral load is higher in people in larger clusters and with increased network connectivity, suggesting that HIV in the United States is experiencing natural selection to be more infectious and virulent. We also observe a concurrent increase in viral load at diagnosis over the last decade. This evolutionary trajectory may be slowed by prevention strategies prioritized toward rapidly growing transmission clusters.

Characteristics of a cohort of high-risk men who have sex with men on pre-exposure prophylaxis reporting transgender sexual partners

Transgender people continue to be at high-risk for HIV acquisition, but little is known about the characteristics of their sexual partners. To address this gap, we examined sociodemographic and sexual characteristics of cisgender men who have sex with men (MSM) on pre-exposure prophylaxis (PrEP) reporting transgender sexual partners.A cohort of 392 MSM in southern California in a randomized clinical trial for PrEP adherence were followed from 2013 to 2016. Multivariable generalized estimating equation and logistic models identified characteristics of MSM reporting transgender sexual partners and PrEP adherence.Only 14 (4%) MSM reported having transgender sexual partners. MSM were more likely to report transgender partners if they were African American, had incident chlamydia, reported injection drug-using sexual partners, or received items for sex. Most associations remained significant in the multivariable model: African American (adjusted odds ratio [AOR] 11.20, P = .01), incident chlamydia (AOR 3.71, P = .04), and receiving items for sex (AOR 5.29, P = .04). There were no significant differences in PrEP adherence between MSM reporting transgender partners and their counterpart.MSM who report transgender sexual partners share characteristics associated with individuals with high HIV prevalence. Identifying this group distinct from larger cohorts of MSM could offer new HIV prevention opportunities for this group of MSM and the transgender community.

A View of Human Immunodeficiency Virus Infections in the North-West Region of Romania

Background and objectives: In Romania, the human immunodeficiency virus (HIV) epidemic is almost the same as it is in Central Europe, with some differences; particularity the following one: people with nosocomial HIV infection, also known as Romanian cohort. Aim: The study aimed to present a local view of HIV infection in the North-West part of Romania, and to identify the particularities of patients under medical care in the Cluj AIDS Center. Materials and Methods: The demographic characteristics (age and gender), and medical and epidemiological data (stage of HIV infection and mode of transmission) of patients in a medical care in the Cluj Acquired Immunodeficiency Syndrome (AIDS) Center were evaluated. Data from the first patients admitted between 1989 and 2018, and the statuses of the infected persons as per 31 December 2018 were analyzed. Results: Nine hundred and fourteen patients were included in the study. The patients' ages varied from 0 (newborns from HIV-infected mothers) to 72 years old, and most patients were men (596 men vs. 318 women). The main mode of transmission was sexual (>50%), with an increased number of men who have sex with men (MSM) in the last years (from two cases in 2006 to thirty-four cases in 2018), and a very small percentage of intravenous drug users (IDU; <1%). The patients from the Romanian cohort were more frequently women as compared with men (p-value <0.0001), women were more frequently later presenters than men (p-value <0.0001), and the women more frequently had candidosis (p-value = 0.0372), cerebral toxoplasmosis (p-value = 0.0404), and co-infection with hepatitis B virus (p-value = 0.0018). One hundred and sixty patients died by the end of 2018 (17.5%). Sixty-eight children had been born from HIV-infected mothers, and 17 were HIV infected (25%). Conclusion: The main mode of HIV transmission in our sample was sexual, with an increased number of MSM over the last years and a low number of cases of intravenous drug users. A quarter of children borne from HIV-infected mothers were HIV infected.

American Cohort to Study HIV Acquisition Among Transgender Women in High-Risk Areas (The LITE Study): Protocol for a Multisite Prospective Cohort Study in the Eastern and Southern United States

BACKGROUND

In the United States, transgender women (TW) are disproportionately burdened by HIV infection. Cohort studies are needed to evaluate factors driving HIV acquisition among TW over time. These will require implementation strategies that are acceptable to the TW community and feasible to implement.

OBJECTIVE

This study aims to investigate the rate and correlates of HIV acquisition and other health outcomes among TW in eastern and southern United States.

METHODS

LITE is a multisite prospective cohort in 6 eastern and southern US cities, which will be followed across 24 months of technology-enhanced biobehavioral follow-up. Adult TW, regardless of HIV status, are recruited via convenience sampling (eg, peer referrals, social media, and dating apps). Participants are enrolled in a baseline study visit, complete a sociobehavioral survey, and test for HIV and sexually transmitted infections. Participants who are not living with HIV at baseline are offered enrollment into the cohort (N=1100); follow-up assessments occur quarterly.

RESULTS

Cohort assembly was informed by synchronous Web-based focus group discussions with TW (n=41) and by continuing engagement with community advisory board members from each site. Enrollment launched in March 2018. The study is underway in the Atlanta; Baltimore; Boston; Miami; New York City; and Washington, DC, metro areas. As of March 2019, 795 TW completed a baseline visit (mean age 35 years). The majority of the participants are racial/ethnic minorities, with 45% of the TW identifying as black and 28% of the TW identifying as Hispanic/Latinx. More than one-quarter (28%) of the TW are living with HIV infection (laboratory-confirmed). Online recruitment methods support engagement with TW, although peer referral and referral through trusted health facilities and organizations remain most effective.

CONCLUSIONS

This study is responsive to increasing research interest in technology-enhanced methods for cohort research, particularly for hard-to-reach populations. Importantly, the diversity of literacy, technology use, and overall socioeconomic situations in this sample of TW highlights the need to leverage technology to permit a flexible, adaptive methodology that enhances engagement of potential participants living in marginalized contexts while still ensuring rigorous and sound study design.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

DERR1-10.2196/14704.

The HIV-Related Risk Factors of the Cisgender Male Sexual Partners of Transgender Women (MSTW) in the United States: A Systematic Review of the Literature

Cisgender male sexual partners of transgender women (MSTW) may be at risk for HIV infection. We performed a review of HIV risk factors among MSTW. We searched PubMed database for empirical quantitative U.S.-based studies that included MSTW and were published in English up to November 2018. Of the 4,680 total papers identified, 6 unique studies were included. MSTW displayed heterogeneity in HIV risk factors (e.g., condom use, sexual partners, sexual positions, substance use). In our exploratory meta-analyses, estimated prevalence of self-reported HIV positive status among MSTW was 30.6%, HIV unknown status was 8.8%, and self-reported condomless anal sex with transgender women was 46.1%. Reports of sexual health communication with transgender women was low. More research on MSTW populations is needed to better understand this population's unique needs in the context of recent advancements in HIV prevention.