HIV-1 Infection and Transmission Networks of Younger People in Chicago, Illinois, 2005-2011

Identifying the Key Nodes of HIV Molecular Transmission Network Among Men Who Have Sex with Men - Guangzhou, Guangdong Province, China, 2015-2017

What is already known about this topic?

Identifying the most influential spreaders in human immunodeficiency virus (HIV) transmission networks is crucial for developing effective prevention strategies.

What is added by this report?

This study identified key nodes of the HIV molecular transmission network among men who have sex with men (MSM) by utilizing linkages between sequences to reconstruct the transmission network at the molecular level.

What are the implications for public health practice?

This study could act as an important supplement of laboratory results to epidemiological studies and suggests that interdisciplinary research could inspire new ideas for finding breakthroughs on HIV/acquired immunodeficiency syndrome (AIDS) prevention and control.

Geographic Distribution of HIV Transmission Networks in the United States

BACKGROUND

Understanding geographic patterns of HIV transmission is critical to designing effective interventions. We characterized geographic proximity by transmission risk and urban-rural characteristics among people with closely related HIV strains suggestive of potential transmission relationships.

METHODS

We analyzed US National HIV Surveillance System data of people diagnosed between 2010 and 2016 with a reported HIV-1 partial polymerase nucleotide sequence. We used HIV TRAnsmission Cluster Engine (HIV-TRACE) to identify sequences linked at a genetic distance of ≤0.5%. For each linked person, we assessed median distances between counties of residence at diagnosis by transmission category and urban-rural classification, weighting observations to account for persons with multiple linked sequences.

RESULTS

There were 24,743 persons with viral sequence linkages to at least one other person included in this analysis. Overall, half (50.9%) of persons with linked viral sequences resided in different counties, and the median distance from persons with linked viruses was 11 km/7 miles [interquartile range (IQR), 0-145 km/90 miles]. Median distances were highest for men who have sex with men (MSM: 14 km/9 miles; IQR, 0-179 km/111 miles) and MSM who inject drugs, and median distances increased with increasing rurality (large central metro: 0 km/miles; IQR, 0-83 km/52 miles; nonmetro: 103 km/64 miles; IQR, 40 km/25 miles-316 km/196 miles).

CONCLUSION

Transmission networks in the United States involving MSM, MSM who inject drugs, or persons living in small metro and nonmetro counties may be more geographically dispersed, highlighting the importance of coordinated health department efforts for comprehensive follow-up and linkage to care.

Concordance of genotypic resistance interpretation algorithms in HIV-1 infected patients: An exploratory analysis in Greece

PURPOSE

Genotypic resistance-related mutations in HIV-1 disease are often difficult to interpret. Different algorithms have been developed to provide meaningful application into clinical context. We aimed to compare, for the first time in Greece, the results of genotypic resistance derived from three interpretation algorithms.

METHODS

The sequences of 120 HIV 1-infected patients were tested for genotypic resistance to 19 antiretroviral (ARV) drugs (n = 2280 sequences). The interpretation results of Rega, ANRS and ViroSeq algorithms were compared.

RESULTS

Complete concordance was found for 2/19 ARV drugs, namely lamivudine and emptricitabine. Concordance was high for nucleoside reverse transcriptase inhibitors (NRTIs) and low for protease inhibitors (PIs). In inter-algorithm pairs, agreement was high between Rega and ViroSeq (kappa = 0.701), especially by ARV class, namely NRTIs (k = 0.869) and NNRTIs (k = 0.562). The only exception was noted for rilpivirine, where agreement was higher between ANRS and Rega (k = 0.410) compared to other inter-algorithm pairs (k = 0.018-0.055). By contrast, for PIs all comparisons yielded concordance equivalent to chance (k = 0.000).

CONCLUSIONS

Our exploratory analysis provided evidence of significant inter-algorithm discordances, especially for PIs and NNRTIs highlighting the importance of matching the results of different algorithms to achieve optimized risk stratification. Ongoing research could assist clinical physicians in interpreting complex genotypic resistance patterns.

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.

Social Mixing and Clinical Features Linked With Transmission in a Network of Extensively Drug-resistant Tuberculosis Cases in KwaZulu-Natal, South Africa

BACKGROUND

Tuberculosis (TB) is the leading infectious cause of death globally, and drug-resistant TB strains pose a serious threat to controlling the global TB epidemic. The clinical features, locations, and social factors driving transmission in settings with high incidences of drug-resistant TB are poorly understood.

METHODS

We measured a network of genomic links using Mycobacterium tuberculosis whole-genome sequences.

RESULTS

Patients with 2-3 months of cough or who spent time in urban locations were more likely to be linked in the network, while patients with sputum smear-positive disease were less likely to be linked than those with smear-negative disease. Associations persisted using different thresholds to define genomic links and irrespective of assumptions about the direction of transmission.

CONCLUSIONS

Identifying factors that lead to many transmissions, including contact with urban areas, can suggest settings instrumental in transmission and indicate optimal locations and groups to target with interventions.

A cross-sectional study to characterize local HIV-1 dynamics in Washington, DC using next-generation sequencing

Washington, DC continues to experience a generalized HIV-1 epidemic. We characterized the local phylodynamics of HIV-1 in DC using next-generation sequencing (NGS) data. Viral samples from 68 participants from 2016 through 2017 were sequenced and paired with epidemiological data. Phylogenetic and network inferences, drug resistant mutations (DRMs), subtypes and HIV-1 diversity estimations were completed. Haplotypes were reconstructed to infer transmission clusters. Phylodynamic inferences based on the HIV-1 polymerase (pol) and envelope genes (env) were compared. Higher HIV-1 diversity (n.s.) was seen in men who have sex with men, heterosexual, and male participants in DC. 54.0% of the participants contained at least one DRM. The 40-49 year-olds showed the highest prevalence of DRMs (22.9%). Phylogenetic analysis of pol and env sequences grouped 31.9-33.8% of the participants into clusters. HIV-TRACE grouped 2.9-12.8% of participants when using consensus sequences and 9.0-64.2% when using haplotypes. NGS allowed us to characterize the local phylodynamics of HIV-1 in DC more broadly and accurately, given a better representation of its diversity and dynamics. Reconstructed haplotypes provided novel and deeper phylodynamic insights, which led to networks linking a higher number of participants. Our understanding of the HIV-1 epidemic was expanded with the powerful coupling of HIV-1 NGS data with epidemiological data.

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

Background

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

Methods

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

Results

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

Conclusion

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

A 28-Year History of HIV-1 Drug Resistance and Transmission in Washington, DC

Washington, DC consistently has one of the highest annual rates of new HIV-1 diagnoses in the United States over the last 10 years. To guide intervention and prevention strategies to combat DC HIV infection, it is helpful to understand HIV transmission dynamics in a historical context. Toward this aim, we conducted a retrospective study (years 1987–2015) of 3,349 HIV pol sequences (1,026 bp) from 1,995 individuals living in the DC area belonging to three different cohorts. We coupled HIV sequence data with clinical information (sex, risk factor, race/ethnicity, viral load, subtype, anti-retroviral regimen) to identify circulating drug resistant mutations (DRM) and transmission clusters and assess their persistence over time. Of the transmission clusters identified in the DC area, 78.0 and 31.7% involved MSM and heterosexuals, respectively. The longest spread of time for a single cluster was 5 years (2007–2012) using a distance-based network inference approach and 27 years (1987–2014) using a maximum likelihood phylogenetic approach. We found eight subtypes and nine recombinants. Genetic diversity increased steadily over time with a slight peak in 2009 and remained constant thereafter until 2015. Nucleotide diversity also increased over time while relative genetic diversity (BEAST) remained relatively steady over the last 28 years with slight increases since 2000 in subtypes B and C. Sequences from individuals on drug therapy contained the highest total number of DRMs (1,104–1,600) and unique DRMs (63–97) and the highest proportion (>20%) of resistant individuals. Heterosexuals (43.94%), MSM (40.13%), and unknown (44.26%) risk factors showed similar prevalence of DRMs, while injection drug users had a lower prevalence (33.33%). Finally, there was a 60% spike in the number of codons with DRMs between 2007 and 2010. Past patterns of HIV transmission and DRM accumulation over time described here will help to predict future efficacy of ART drugs based on DRMs persisting over time and identify risk groups of interest for prevention and intervention efforts within the DC population. Our results show how longitudinal data can help to understand the temporal dynamics of HIV-1 at the local level.

HIV-1 Transmission Clustering and Phylodynamics Highlight the Important Role of Young Men Who Have Sex with Men

More persons living with HIV reside in the Southern United States than in any other region, yet little is known about HIV molecular epidemiology in the South. We used cluster and phylodynamic analyses to evaluate HIV transmission patterns in middle Tennessee. We performed cross-sectional analyses of HIV-1 pol sequences and clinical data collected from 2001 to 2015 among persons attending the Vanderbilt Comprehensive Care Clinic. Transmission clusters were identified using maximum likelihood phylogenetics and patristic distance differences. Demographic, risk behavior, and clinical factors were assessed evaluating “active” clusters (clusters including sequences sampled 2011–2015) and associations estimated with logistic regression. Transmission risk ratios for men who have sex with men (MSM) were estimated with phylodynamic models. Among 2915 persons (96% subtype-B sequences), 963 (33%) were members of 292 clusters (distance ≤1.5%, size range 2–39). Most clusters (62%, n = 690 persons) were active, either being newly identified (n = 80) or showing expansion on existing clusters (n = 101). Correlates of active clustering among persons with sequences collected during 2011–2015 included MSM risk and ≤30 years of age. Active clusters were significantly more concentrated in MSM and younger persons than historical clusters. Young MSM (YMSM) (≤26.4 years) had high estimated transmission risk [risk ratio = 4.04 (2.85–5.65) relative to older MSM] and were much more likely to transmit to YMSM. In this Tennessee cohort, transmission clusters over time were more concentrated by MSM and younger age, with high transmission risk among and between YMSM, highlighting the importance of interventions among this group. Detecting active clusters could help direct interventions to disrupt ongoing transmission chains.

Sexual, Social, and Genetic Network Overlap: A Socio-Molecular Approach Toward Public Health Intervention of HIV

OBJECTIVES

To determine how network-level factors influence individual risk of HIV acquisition, which is key in preventing disease transmission.

METHODS

We recruited a cohort of young Black men who have sex with men (n = 618) in Chicago, Illinois, from 2013 to 2016. We identified potential molecular ties via pairwise genetic distance analysis of HIV pol sequences with links inferred between individuals whose sequences were 1.5% or less genetically distant. We defined clusters as 1 or more connections to another individual. We conducted entity resolution between confidant, sexual, referral, and Facebook network data between network types.

RESULTS

Of 266 (43.0%) participants identified as HIV-positive, we obtained 86 (32.3%) genetic sequences. Of these, 35 (40.7%) were linked to 1 or more other sequence; however, none of these were identified in first-, second-, or third-degree confidant and sexual networks. Minimal overlap existed between genetic and Facebook ties.

CONCLUSIONS

These results suggest that HIV transmissions may have occurred before elicitation of network data; future studies should expand the data collection timeframe to more accurately determine risk networks. Virtual network data, such as Facebook, may be particularly useful in developing one's risk environment.

Preferences for HIV test characteristics among young, Black Men Who Have Sex With Men (MSM) and transgender women: Implications for consistent HIV testing

BACKGROUND

Promoting consistent HIV testing is critical among young, Black Men Who Have Sex With Men (MSM) and transgender women who are overrepresented among new HIV cases in the United States. New HIV test options are available, including mobile unit testing, one-minute testing, at home or self-testing and couples HIV testing and counseling (CHTC). In the context of these newer options, the objective of this study was to explore whether and how preferences for specific characteristics of the tests acted as barriers to and/or facilitators of testing in general and consistent testing specifically among young Black MSM and transgender women aged 16 to 29.

METHODS

We conducted 30 qualitative, semi-structured, in-depth interviews with young, Black, gay, bisexual or MSM and transgender women in the New York City metropolitan area to identify preferences for specific HIV tests and aspects of HIV testing options. Participants were primarily recruited from online and mobile sites, followed by community-based, face-to-face recruitment strategies to specifically reach younger participants. Thematic coding was utilized to analyze the qualitative data based on a grounded theoretical approach.

RESULTS

We identified how past experiences, perceived test characteristics (e.g., accuracy, cost, etc.) and beliefs about the "fit" between the individual, and the test relate to preferred testing methods and consistent testing. Three major themes emerged as important to preferences for HIV testing methods: the perceived accuracy of the test method, venue characteristics, and lack of knowledge or experience with the newer testing options, including self-testing and CHTC.

CONCLUSIONS

These findings suggest that increasing awareness of and access to newer HIV testing options (e.g., free or reduced price on home or self-tests or CHTC available at all testing venues) is critical if these new options are to facilitate increased levels of consistent testing among young, Black MSM and transgender women. Addressing perceptions of test accuracy and supporting front line staff in creating welcoming and safe testing environments may be key intervention targets. Connecting young Black MSM and transgender women to the best test option, given preferences for specific characteristics, may support more and more consistent HIV testing.

Trends in HIV Risk, Testing, and Treatment among MSM in Chicago 2004-2014: Implications for HIV Elimination Planning

Men who have sex with men (MSM) in the USA continue to have high rates of HIV infection. Increasingly, in addition to behavioral factors, biomedical interventions have been found to play important roles in HIV prevention. In this analysis, we used four waves of cross-sectional data (2004, 2008, 2011, and 2014) from the National HIV Behavioral Surveillance System (NHBS) to examine trends in key behaviors and biomedical interventions among MSM in Chicago (N = 3298). Logistic regression was used to determine changes in behaviors and use of biomedical interventions. Condomless sex increased significantly in waves 3 and 4, compared to wave 1: wave 3 (AOR = 2.07; 95% CI 1.53, 2.78) and wave 4 (AOR = 2.19; 95% CI 1.62, 2.96). Compared to those aged 18-24, older participants were significantly less likely to be routinely tested for HIV: 30-39 (AOR = 0.63; 95% CI 0.48, 0.83), 40-49 (AOR = 0.40; 95% CI 0.29, 0.55), and >50 (AOR = 0.28; 95% CI 0.18, 0.43). Awareness of both post-exposure prophylaxis (PEP)(​AOR = 3.13; 95% CI 1.22, 8.03) and pre-exposure prophylaxis (PrEP)(​AOR = 10.02; 95% CI 2.95, 34.01) increased significantly in wave 4, compared to wave 3. These results suggest a potential increase in HIV rates among men with main and casual partners and should be monitored closely as PrEP becomes more widespread among MSM of all races and ethnicities in Chicago. This study also suggests that further analyses of the barriers to PEP and PreP uptake among high-risk populations are necessary.

Determinants of HIV Phylogenetic Clustering in Chicago Among Young Black Men Who Have Sex With Men From the uConnect Cohort

INTRODUCTION

Phylogenetic analysis determines similarities among HIV genetic sequences from persons infected with HIV, identifying clusters of transmission. We determined characteristics associated with both membership in an HIV transmission cluster and the number of clustered sequences among a cohort of young black men who have sex with men (YBMSM) in Chicago.

METHODS

Pairwise genetic distances of HIV-1 pol sequences were collected during 2013-2016. Potential transmission ties were identified among HIV-infected persons whose sequences were ≤1.5% genetically distant. Putative transmission pairs were defined as ≥1 tie to another sequence. We then determined demographic and risk attributes associated with both membership in an HIV transmission cluster and the number of ties to the sequences from other persons in the cluster.

RESULTS

Of 86 available sequences, 31 (36.0%) were tied to ≥1 other sequence. Through multivariable analyses, we determined that those who reported symptoms of depression and those who had a higher number of confidants in their network had significantly decreased odds of membership in transmission clusters. We found that those who had unstable housing and who reported heavy marijuana use had significantly more ties to other individuals within transmission clusters, whereas those identifying as bisexual, those participating in group sex, and those with higher numbers of sexual partners had significantly fewer ties.

CONCLUSIONS

This study demonstrates the potential for combining phylogenetic and individual and network attributes to target HIV control efforts to persons with potentially higher transmission risk, as well as suggesting some unappreciated specific predictors of transmission risk among YBMSM in Chicago for future study.