Sources of HIV infection among men having sex with men and implications for prevention

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.

Sources of Human Immunodeficiency Virus Infections Among Men Who Have Sex With Men With a Migration Background: A Viral Phylogenetic Case Study in Amsterdam, The Netherlands

BACKGROUND

Men and women with a migration background comprise an increasing proportion of incident human immunodeficiency virus (HIV) cases across Western Europe.

METHODS

To characterize sources of transmission in local transmission chains, we used partial HIV consensus sequences with linked demographic and clinical data from the opt-out AIDS Therapy Evaluation in the Netherlands (ATHENA) cohort of people with HIV in the Netherlands and identified phylogenetically and epidemiologically possible HIV transmission pairs in Amsterdam. We interpreted these in the context of estimated infection dates, and quantified population-level sources of transmission to foreign-born and Dutch-born Amsterdam men who have sex with men (MSM) within Amsterdam transmission chains.

RESULTS

We estimate that Dutch-born MSM were the predominant sources of infections among all Amsterdam MSM who acquired their infection locally in 2010-2021, and among almost all foreign-born Amsterdam MSM subpopulations. Stratifying by 2-year intervals indicated time trends in transmission dynamics, with a majority of infections originating from foreign-born MSM since 2016, although uncertainty ranges remained wide.

CONCLUSIONS

Native-born MSM have predominantly driven HIV transmissions in Amsterdam in 2010-2021. However, in the context of rapidly declining incidence in Amsterdam, the contribution from foreign-born MSM living in Amsterdam is increasing, with some evidence that most local transmissions have been from foreign-born Amsterdam MSM since 2016.

Prioritization of ethical concerns regarding HIV molecular epidemiology by public health practitioners and researchers

BACKGROUND

HIV molecular epidemiology (HIV ME) can support the early detection of emerging clusters of new HIV infections by combining HIV sequence data routinely obtained during the clinical treatment of people living with HIV with behavioral, geographic, and sociodemographic information. While information about emerging clusters promises to facilitate HIV prevention and treatment efforts, the use of this data also raises several ethical concerns. We sought to assess how those working on the frontlines of HIV ME, specifically public health practitioners (PHPs) and researchers, prioritized these issues.

METHODS

Ethical issues were identified through literature review, qualitative in-depth interviews, and stakeholder engagement. PHPs and researchers using HIV ME prioritized the issues using best-worst scaling (BWS). A balanced incomplete block design was used to generate 11 choice tasks each consisting of a sub-set of 5 ethical concerns. In each task, respondents were asked to assess the most and least concerning issue. Data were analyzed using conditional logit, with a Swait-Louviere test of poolability. Latent class analysis was then used to explore preference heterogeneity.

RESULTS

In total, 57 respondents completed the BWS experiment May-June 2023 with the Swait-Louviere test indicating that researchers and PHPs could be pooled (p = 0.512). Latent class analysis identified two classes, those highlighting "Harms" (n = 29) (prioritizing concerns about potential risk of legal prosecution, individual harm, and group stigma) and those highlighting "Utility" (n = 28) (prioritizing concerns about limited evidence, resource allocation, non-disclosure of data use for HIV ME, and the potential to infer the directionality of HIV transmission). There were no differences in the characteristics of members across classes.

CONCLUSIONS

The ethical issues of HIV ME vary in importance among stakeholders, reflecting different perspectives on the potential impact and usefulness of the data. Knowing these differences exist can directly inform the focus of future deliberations about the policies and practices of HIV ME in the United States.

Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda

HIV incidence in eastern and southern Africa has historically been concentrated among girls and women aged 15-24 years. As new cases decline with HIV interventions, population-level infection dynamics may shift by age and gender. Here, we integrated population-based surveillance of 38,749 participants in the Rakai Community Cohort Study and longitudinal deep-sequence viral phylogenetics to assess how HIV incidence and population groups driving transmission have changed from 2003 to 2018 in Uganda. We observed 1,117 individuals in the incidence cohort and 1,978 individuals in the transmission cohort. HIV viral suppression increased more rapidly in women than men, however incidence declined more slowly in women than men. We found that age-specific transmission flows shifted: whereas HIV transmission to girls and women (aged 15-24 years) from older men declined by about one-third, transmission to women (aged 25-34 years) from men that were 0-6 years older increased by half in 2003 to 2018. Based on changes in transmission flows, we estimated that closing the gender gap in viral suppression could have reduced HIV incidence in women by half in 2018. This study suggests that HIV programmes to increase HIV suppression in men are critical to reduce incidence in women, close gender gaps in infection burden and improve men's health in Africa.

Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda

HIV incidence in eastern and southern Africa has historically been concentrated among girls and women aged 15-24 years. As new cases decline with HIV interventions, population-level infection dynamics may shift by age and gender. Here, we integrated population-based surveillance of 38,749 participants in the Rakai Community Cohort Study and longitudinal deep sequence viral phylogenetics to assess how HIV incidence and population groups driving transmission have changed from 2003 to 2018 in Uganda. We observed 1,117 individuals in the incidence cohort and 1,978 individuals in the transmission cohort. HIV viral suppression increased more rapidly in women than men, however incidence declined more slowly in women than men. We found that age-specific transmission flows shifted, while HIV transmission to girls and women (aged 15-24 years) from older men declined by about one third, transmission to women (aged 25-34 years) from men that were 0-6 years older increased by half in 2003 to 2018. Based on changes in transmission flows, we estimated that closing the gender gap in viral suppression could have reduced HIV incidence in women by half in 2018. This study suggests that HIV programs to increase HIV suppression in men are critical to reduce incidence in women, close gender gaps in infection burden and improve men's health in Africa.

A 95% decline in estimated newly acquired HIV infections, Amsterdam, 2010 to 2022

The infrastructure in cities provides unique opportunities to eliminate HIV. Since 2014, the HIV Transmission Elimination AMsterdam Initiative, a consortium involved in HIV prevention and care, has employed an integrated approach to curb HIV incidence in Amsterdam. This effort contributed to the 95% decline in estimated newly acquired infections and the 79% decline in observed new HIV diagnoses in Amsterdam from 2010 to 2022. In 2022, Amsterdam reached and exceeded the 95-95-95 UNAIDS treatment cascade goals (98-95%-96%).

Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies

Within-host Human immunodeficiency virus (HIV) evolution involves several features that may disrupt standard phylogenetic reconstruction. One important feature is reactivation of latently integrated provirus, which has the potential to disrupt the temporal signal, leading to variation in the branch lengths and apparent evolutionary rates in a tree. Yet, real within-host HIV phylogenies tend to show clear, ladder-like trees structured by the time of sampling. Another important feature is recombination, which violates the fundamental assumption that evolutionary history can be represented by a single bifurcating tree. Thus, recombination complicates the within-host HIV dynamic by mixing genomes and creating evolutionary loop structures that cannot be represented in a bifurcating tree. In this paper, we develop a coalescent-based simulator of within-host HIV evolution that includes latency, recombination, and effective population size dynamics that allows us to study the relationship between the true, complex genealogy of within-host HIV evolution, encoded as an ancestral recombination graph (ARG), and the observed phylogenetic tree. To compare our ARG results to the familiar phylogeny format, we calculate the expected bifurcating tree after decomposing the ARG into all unique site trees, their combined distance matrix, and the overall corresponding bifurcating tree. While latency and recombination separately disrupt the phylogenetic signal, remarkably, we find that recombination recovers the temporal signal of within-host HIV evolution caused by latency by mixing fragments of old, latent genomes into the contemporary population. In effect, recombination averages over extant heterogeneity, whether it stems from mixed time signals or population bottlenecks. Furthermore, we establish that the signals of latency and recombination can be observed in phylogenetic trees despite being an incorrect representation of the true evolutionary history. Using an approximate Bayesian computation method, we develop a set of statistical probes to tune our simulation model to nine longitudinally sampled within-host HIV phylogenies. Because ARGs are exceedingly difficult to infer from real HIV data, our simulation system allows investigating effects of latency, recombination, and population size bottlenecks by matching decomposed ARGs to real data as observed in standard phylogenies.

HIV transmission among acutely infected participants of a Dutch cohort study 2015-2021 is not associated with large, clustered outbreaks

OBJECTIVE

Timely identification of acute or early HIV infection (AEHI) is important to help prevent onward transmission, and understanding the number of secondary infections resulting from individuals with AEHI is key to planning HIV prevention services and case finding.

DESIGN

We performed a phylogenetic investigation of a dense sample of individuals with AEHI who took part in the Netherlands Cohort Study on Acute HIV infection (NOVA) in the Netherlands during 2015-2021.

METHODS

Transmission clusters were identified using phylogenetic analyses based on HIV pol sequences. The Tamura-Nei model was used to estimate genetic distance. A number of 1000 bootstraps was used to check the reliability of clustering using maximum likelihood. A cluster was defined as having a bootstrap value of at least 95% and a genetic distance of at most 1.5%. Sensitivity analyses using different values for the bootstrap and genetic distance were performed to study the reproducibility of the clustering.

RESULTS

Of the 156 participants included in NOVA between July 2015 and April 2021, 134 individuals for whom baseline characteristics and genotypic resistance data at baseline were available could be included. We identified 10 clusters, but the majority of persons (111/134) were not part of a cluster, suggesting mainly independent transmission events.

CONCLUSION

Mainly independent transmission events among a study population consisting predominantly of MSM in a low-incidence high-resource setting is likely the result of active AEHI case finding and direct start of treatment, and the roll-out over recent years of preventive measures such as preexposure prophylaxis.

Improving provider-initiated testing for HIV and other STI in the primary care setting in Amsterdam, the Netherlands: Results from a multifaceted, educational intervention programme

BACKGROUND

In the Netherlands, general practitioners (GPs) play a key role in HIV testing. However, the proportion of people diagnosed with late-stage HIV remains high, and opportunities for earlier diagnosis are being missed. We implemented an educational intervention to improve HIV and STI testing in primary care in Amsterdam, the Netherlands.

METHODS

GPs were invited to participate in an educational program between 2015 and 2020, which included repeat sessions using audit and feedback and quality improvement plans. Data on HIV, chlamydia and gonorrhoea testing by GPs were collected from 2011 through 2020. The primary outcome was HIV testing frequency, which was compared between GPs before and after participation using Poisson regression. Secondary outcomes were chlamydia and gonorrhoea testing frequencies, and positive test proportions. Additional analyses stratified by patient sex and age were done.

FINDINGS

GPs after participation performed 7% more HIV tests compared to GPs before participation (adjusted relative ratio [aRR] 1.07, 95%CI 1.04-1.09); there was no change in the proportion HIV positive tests (aRR 0.87, 95%CI 0.63-1.19). HIV testing increased most among patients who were female and ≤19 or 50-64 years old. After participation, HIV testing continued to increase (aRR 1.02 per quarter, 95%CI 1.01-1.02). Chlamydia testing by GPs after participation increased by 6% (aRR 1.06, 95%CI 1.05-1.08), while gonorrhoea testing decreased by 2% (aRR 0.98, 95%CI 0.97-0.99). We observed increases specifically in extragenital chlamydia and gonorrhoea testing.

CONCLUSIONS

The intervention was associated with a modest increase in HIV testing among GPs after participation, while the proportion positive HIV tests remained stable. Our results suggest that the intervention yielded a sustained effect.

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.

Improving indicator-condition guided testing for HIV in the hospital setting (PROTEST 2·0): A multicenter, interrupted time-series analysis

BACKGROUND

Indicator-condition (IC) guided HIV testing is a feasible and cost-effective strategy to identify undiagnosed people living with HIV (PLHIV), but remains insufficiently implemented. We aimed to promote IC-guided HIV testing in seven ICs.

METHODS

Relevant departments in five hospitals of the Amsterdam region participated. HIV testing among adult patients without known HIV infection but with an IC was assessed using electronic health records during pre-intervention (January 2015-June 2020) and intervention (July 2020-June 2021) periods. The multifaceted intervention included audit and feedback. The primary endpoint was HIV testing ≤3 months before or after IC diagnosis and the effect of the intervention was evaluated using segmented Poisson regression.

FINDINGS

Data from 7986 patients were included, of whom 6730 (84·3%) were diagnosed with an IC in the pre-intervention period and 1256 (15·7%) in the intervention period. The proportion HIV tested ≤3 months before or after IC diagnosis increased from 36.8% to 47.0% (adjusted risk ratio [RR]= 1.16, 95% CI=1.03-1.30, p=0.02). For individual ICs, we observed significant increases in HIV testing among patients with cervical cancer or intraepithelial neoplasia grade 3 (adjusted RR=3.62, 95% CI=1.93-6.79) and peripheral neuropathy (adjusted RR=2.27 95% CI=1.48-3.49), but not the other ICs. Eighteen of 3068 tested patients were HIV positive (0.6%).

INTERPRETATION

Overall IC-guided testing improved after the intervention, but not for all ICs. Variations in effect by IC may have been due to variations in implemented developments, but the effect of separate elements could not be assessed.

FUNDING

HIV Transmission Elimination Amsterdam (H-TEAM) initiative, Aidsfonds (grant number: P-42702).

Undiagnosed HIV Infections May Drive HIV Transmission in the Era of "Treat All": A Deep-Sampling Molecular Network Study in Northeast China during 2016 to 2019

Universal antiretroviral therapy (ART, “treat all”) was recommended by the World Health Organization in 2015; however, HIV-1 transmission is still ongoing. This study characterizes the drivers of HIV transmission in the “treat all” era. Demographic and clinical information and HIV pol gene were collected from all newly diagnosed cases in Shenyang, the largest city in Northeast China, during 2016 to 2019. Molecular networks were constructed based on genetic distance and logistic regression analysis was used to assess potential transmission source characteristics. The cumulative ART coverage in Shenyang increased significantly from 77.0% (485/630) in 2016 to 93.0% (2598/2794) in 2019 (p < 0.001). Molecular networks showed that recent HIV infections linked to untreated individuals decreased from 61.6% in 2017 to 28.9% in 2019, while linking to individuals with viral suppression (VS) increased from 9.0% to 49.0% during the same time frame (p < 0.001). Undiagnosed people living with HIV (PLWH) hidden behind the links between index cases and individuals with VS were likely to be male, younger than 25 years of age, with Manchu nationality (p < 0.05). HIV transmission has declined significantly in the era of “treat all”. Undiagnosed PLWH may drive HIV transmission and should be the target for early detection and intervention.

Genetic network analysis of human immunodeficiency virus sexual transmission in rural Southwest China after the expansion of antiretroviral therapy: A population-based study

Background

This study is used to analyze the genetic network of HIV sexual transmission in rural areas of Southwest China after expanding antiretroviral therapy (ART) and to investigate the factors associated with HIV sexual transmission through the genetic network.

Materials and methods

This was a longitudinal genetic network study in Guangxi, China. The baseline survey and follow-up study were conducted among patients with HIV in 2015, and among those newly diagnosed from 2016 to 2018, respectively. A generalized estimating equation model was employed to explore the factors associated with HIV transmission through the genetic linkage between newly diagnosed patients with HIV (2016-2018) and those at baseline (2015-2017), respectively.

Results

Of 3,259 identified HIV patient sequences, 2,714 patients were at baseline, and 545 were newly diagnosed patients with HIV at follow-up. A total of 8,691 baseline objectives were observed by repeated measurement analysis. The prevention efficacy in HIV transmission for treated HIV patients was 33% [adjusted odds ratio (AOR): 0.67, 95% confidence interval (CI): 0.48-0.93]. Stratified analyses indicated the prevention efficacy in HIV transmission for treated HIV patients with a viral load (VL) of <50 copies/ml and those treated for 4 years with a VL of <50 copies/ml to be 41 [AOR: 0.59, 95% CI: 0.43-0.82] and 65% [AOR: 0.35, 95% CI: 0.24-0.50], respectively. No significant reduction in HIV transmission occurred among treated HIV patients with VL missing or treated HIV patients on dropout. Some factors were associated with HIV transmission, including over 50 years old, men, Zhuang and other nationalities, with less than secondary schooling, working as a farmer, and heterosexual transmission.

Conclusion

This study reveals the role of ART in reducing HIV transmission, and those older male farmers with less than secondary schooling are at high risk of HIV infection at a population level. Improvements to ART efficacy for patients with HIV and precision intervention on high-risk individuals during the expansion of ART are urgently required.

Estimating the potential to prevent locally acquired HIV infections in a UNAIDS Fast-Track City, Amsterdam

Background:

More than 300 cities including the city of Amsterdam in the Netherlands have joined the UNAIDS Fast-Track Cities initiative, committing to accelerate their HIV response and end the AIDS epidemic in cities by 2030. To support this commitment, we aimed to estimate the number and proportion of Amsterdam HIV infections that originated within the city, from Amsterdam residents. We also aimed to estimate the proportion of recent HIV infections during the 5-year period 2014–2018 in Amsterdam that remained undiagnosed.

Methods:

We located diagnosed HIV infections in Amsterdam using postcode data (PC4) at time of registration in the ATHENA observational HIV cohort, and used HIV sequence data to reconstruct phylogeographically distinct, partially observed Amsterdam transmission chains. Individual-level infection times were estimated from biomarker data, and used to date the phylogenetically observed transmission chains as well as to estimate undiagnosed proportions among recent infections. A Bayesian Negative Binomial branching process model was used to estimate the number, size, and growth of the unobserved Amsterdam transmission chains from the partially observed phylogenetic data.

Results:

Between 1 January 2014 and 1 May 2019, there were 846 HIV diagnoses in Amsterdam residents, of whom 516 (61%) were estimated to have been infected in 2014–2018. The rate of new Amsterdam diagnoses since 2014 (104 per 100,000) remained higher than the national rates excluding Amsterdam (24 per 100,000), and in this sense Amsterdam remained a HIV hotspot in the Netherlands. An estimated 14% [12–16%] of infections in Amsterdan MSM in 2014–2018 remained undiagnosed by 1 May 2019, and 41% [35–48%] in Amsterdam heterosexuals, with variation by region of birth. An estimated 67% [60–74%] of Amsterdam MSM infections in 2014–2018 had an Amsterdam resident as source, and 56% [41–70%] in Amsterdam heterosexuals, with heterogeneity by region of birth. Of the locally acquired infections, an estimated 43% [37–49%] were in foreign-born MSM, 41% [35–47%] in Dutch-born MSM, 10% [6–18%] in foreign-born heterosexuals, and 5% [2–9%] in Dutch-born heterosexuals. We estimate the majority of Amsterdam MSM infections in 2014–2018 originated in transmission chains that pre-existed by 2014.

Conclusions:

This combined phylogenetic, epidemiologic, and modelling analysis in the UNAIDS Fast-Track City Amsterdam indicates that there remains considerable potential to prevent HIV infections among Amsterdam residents through city-level interventions. The burden of locally acquired infection remains concentrated in MSM, and both Dutch-born and foreign-born MSM would likely benefit most from intensified city-level interventions.

Funding:

This study received funding as part of the H-TEAM initiative from Aidsfonds (project number P29701). The H-TEAM initiative is being supported by Aidsfonds (grant number: 2013169, P29701, P60803), Stichting Amsterdam Dinner Foundation, Bristol-Myers Squibb International Corp. (study number: AI424-541), Gilead Sciences Europe Ltd (grant number: PA-HIV-PREP-16-0024), Gilead Sciences (protocol numbers: CO-NL-276-4222, CO-US-276-1712, CO-NL-985-6195), and M.A.C AIDS Fund.

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

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

Phylogeographic Assessment Reveals Geographic Sources of HIV-1 Dissemination Among Men Who Have Sex With Men in Kenya

HIV-1 transmission dynamics involving men who have sex with men (MSM) in Africa are not well understood. We investigated the rates of HIV-1 transmission between MSM across three regions in Kenya: Coast, Nairobi, and Nyanza. We analyzed 372 HIV-1 partial pol sequences sampled during 2006-2019 from MSM in Coast (N = 178, 47.9%), Nairobi (N = 137, 36.8%), and Nyanza (N = 57, 15.3%) provinces in Kenya. Maximum-likelihood (ML) phylogenetics and Bayesian inference were used to determine HIV-1 clusters, evolutionary dynamics, and virus migration rates between geographic regions. HIV-1 sub-subtype A1 (72.0%) was most common followed by subtype D (11.0%), unique recombinant forms (8.9%), subtype C (5.9%), CRF 21A2D (0.8%), subtype G (0.8%), CRF 16A2D (0.3%), and subtype B (0.3%). Forty-six clusters (size range 2-20 sequences) were found-half (50.0%) of which had evidence of extensive HIV-1 mixing among different provinces. Data revealed an exponential increase in infections among MSM during the early-to-mid 2000s and stable or decreasing transmission dynamics in recent years (2017-2019). Phylogeographic inference showed significant (Bayes factor, BF > 3) HIV-1 dissemination from Coast to Nairobi and Nyanza provinces, and from Nairobi to Nyanza province. Strengthening HIV-1 prevention programs to MSM in geographic locations with higher HIV-1 prevalence among MSM (such as Coast and Nairobi) may reduce HIV-1 incidence among MSM in Kenya.

Quantifying rates of HIV-1 flow between risk groups and geographic locations in Kenya: A country-wide phylogenetic study

In Kenya, HIV-1 key populations including men having sex with men (MSM), people who inject drugs (PWID) and female sex workers (FSW) are thought to significantly contribute to HIV-1 transmission in the wider, mostly heterosexual (HET) HIV-1 transmission network. However, clear data on HIV-1 transmission dynamics within and between these groups are limited. We aimed to empirically quantify rates of HIV-1 flow between key populations and the HET population, as well as between different geographic regions to determine HIV-1 'hotspots' and their contribution to HIV-1 transmission in Kenya. We used maximum-likelihood phylogenetic and Bayesian inference to analyse 4058 HIV-1 pol sequences (representing 0.3 per cent of the epidemic in Kenya) sampled 1986-2019 from individuals of different risk groups and regions in Kenya. We found 89 per cent within-risk group transmission and 11 per cent mixing between risk groups, cyclic HIV-1 exchange between adjoining geographic provinces and strong evidence of HIV-1 dissemination from (i) West-to-East (i.e. higher-to-lower HIV-1 prevalence regions), and (ii) heterosexual-to-key populations. Low HIV-1 prevalence regions and key populations are sinks rather than major sources of HIV-1 transmission in Kenya. Targeting key populations in Kenya needs to occur concurrently with strengthening interventions in the general epidemic.

Dating the Origin and Estimating the Transmission Rates of the Major HIV-1 Clusters in Greece: Evidence about the Earliest Subtype A1 Epidemic in Europe

Our aim was to estimate the date of the origin and the transmission rates of the major local clusters of subtypes A1 and B in Greece. Phylodynamic analyses were conducted in 14 subtype A1 and 31 subtype B clusters. The earliest dates of origin for subtypes A1 and B were in 1982.6 and in 1985.5, respectively. The transmission rate for the subtype A1 clusters ranged between 7.54 and 39.61 infections/100 person years (IQR: 9.39, 15.88), and for subtype B clusters between 4.42 and 36.44 infections/100 person years (IQR: 7.38, 15.04). Statistical analysis revealed that the average difference in the transmission rate between the PWID and the MSM clusters was 6.73 (95% CI: 0.86 to 12.60; p = 0.026). Our study provides evidence that the date of introduction of subtype A1 in Greece was the earliest in Europe. Transmission rates were significantly higher for PWID than MSM clusters due to the conditions that gave rise to an extensive PWID HIV-1 outbreak ten years ago in Athens, Greece. Transmission rate can be considered as a valuable measure for public health since it provides a proxy of the rate of epidemic growth within a cluster and, therefore, it can be useful for targeted HIV prevention programs.

Cohort profile: the Netherlands Cohort Study on Acute HIV infection (NOVA), a prospective cohort study of people with acute or early HIV infection who immediately initiate HIV treatment

PURPOSE

Initiation of combination antiretroviral therapy (cART) during acute or early HIV-infection (AEHI) limits the size of the viral reservoir and preserves immune function. This renders individuals who started cART during AEHI promising participants in HIV-cure trials. Therefore, we established a multicentre prospective cohort study in the Netherlands that enrols people with AEHI. In anticipation of future cure trials, we will longitudinally investigate the properties of the viral reservoir size and HIV-specific immune responses among cohort participants.

PARTICIPANTS

Participants immediately initiate intensified cART: dolutegravir, emtricitabine/tenofovir and darunavir/ritonavir (DRV/r). After 4 weeks, once baseline resistance data are available, DRV/r is discontinued. Three study groups are assembled based on the preparedness of individuals to participate in the extensiveness of sampling. Participants accepting immediate treatment and follow-up but declining additional sampling are included in study group 1 ('standard') and routine diagnostic procedures are performed. Participants willing to undergo blood, leukapheresis and semen sampling are included in study group 2 ('less invasive'). In study group 3 ('extended'), additional tissue (gut-associated lymphoid tissue, peripheral lymph node) and cerebrospinal fluid sampling are performed.

FINDINGS TO DATE

Between 2015 and 2020, 140 individuals with AEHI have been enrolled at nine study sites. At enrolment, median age was 36 (IQR 28-47) years, and 134 (95.7%) participants were men. Distribution of Fiebig stages was as follows: Fiebig I, 3 (2.1%); II, 20 (14.3%); III, 7 (5.0%); IV, 49 (35.0%); V, 39 (27.9%); VI, 22 (15.7%). Median plasma HIV RNA was 5.9 (IQR 4.7-6.7) log10 copies/mL and CD4 count 510 (IQR 370-700) cells/mm3. Median time from cART initiation to viral suppression was 8.0 (IQR 4.0-16.0) weeks.

FUTURE PLANS

The Netherlands Cohort Study on Acute HIV infection remains open for participant enrolment and for additional sites to join the network. This cohort provides a unique nationwide platform for conducting future in-depth virological, immunological, host genetic and interventional studies investigating HIV-cure strategies.

Community-based point-of-care testing to identify new HIV infections: A cross-sectional study from Pune, India

ABSTRACT

The World Health Organization recommends point-of-care testing (POCT) to detect human immunodeficiency virus (HIV) infected individuals in the community. This will help improve treatment coverage through detection of HIV infection among those who are unaware of their status.This study was planned with an objective to investigate the feasibility and acceptability of POCT for HIV in the community.A community-based cross-sectional study was conducted in rural and peri-urban areas of Pune, India. These sites were selected based on the distance from the nearest HIV testing center. Testing locations were identified in consultation with the local stakeholders and grass-root health workers to identify and capture the priority population. The POCT was performed on blood samples collected by the finger-prick method.The proportion of participants seeking HIV tests for the first time was 79.6% that signifies the feasibility of POCT. The acceptability in the peri-urban and rural areas was 70.2% and 69.7%, respectively. POCT was performed at construction sites (24.9%), nearby industries (16.1%) and parking areas of long-distance trucks (8.1%) in the peri-urban area. Three newly diagnosed HIV-infected participants (0.1%) were detected from the peri-urban areas but none from the rural areas. Two of the newly diagnosed participants and their spouses were linked to care.There was a high acceptability of POCT and wider coverage of priority population with a strategy of testing at places preferable to the study population. Therefore, we believe that community-based POCT is a promising tool for improving HIV testing coverage even in low prevalence settings with the concentrated HIV epidemic.

A simple algorithm for selecting cases to investigate acute and early HIV infections in low- and middle-income countries

We documented the outcome of an over 10-year (2011-2021) effort to diagnose acute and early HIV infections (AEHI) in an Infectious Diseases Outpatient Clinic with limited resources. Of a total of 132, 119 HIV-RNA tests were performed from 2017 to 2020, 12 cases were identified, using a simple algorithm: risk exposure of 6 weeks or less before the visit and/or symptoms compatible with acute retroviral syndrome 7-30 days after exposure and/or undetermined 3rd generation rapid diagnostic test or serology. AEHI diagnoses varied from 2.4% among asymptomatic to 25% for undetermined serology cases using this simple screening applicable to different settings.

Decreased Time to Viral Suppression After Implementation of Targeted Testing and Immediate Initiation of Treatment of Acute Human Immunodeficiency Virus Infection Among Men Who Have Sex With Men in Amsterdam

BACKGROUND

Men who have sex with men (MSM) with acute human immunodeficiency virus (HIV) infection (AHI) are a key source of new infections. To curb transmission, we implemented a strategy for rapid AHI diagnosis and immediate initiation of combination antiretroviral therapy (cART) in Amsterdam MSM. We assessed its effectiveness in diagnosing AHI and decreasing the time to viral suppression.

METHODS

We included 63 278 HIV testing visits in 2008-2017, during which 1013 MSM were diagnosed. Standard of care (SOC) included HIV diagnosis confirmation in < 1 week and cART initiation in < 1 month. The AHI strategy comprised same-visit diagnosis confirmation and immediate cART. Time from diagnosis to viral suppression was assessed for 3 cART initiation periods: (1) 2008-2011: cART initiation if CD4 < 500 cells/μL (SOC); (2) January 2012-July 2015: cART initiation if CD4 < 500 cells/μL, or if AHI or early HIV infection (SOC); and (3a) August 2015-June 2017: universal cART initiation (SOC) or (3b) August 2015-June 2017 (the AHI strategy).

RESULTS

Before implementation of the AHI strategy, the proportion of AHI among HIV diagnoses was 0.6% (5/876); after implementation this was 11.0% (15/137). Median time (in days) to viral suppression during periods 1, 2, 3a, and 3b was 584 (interquartile range [IQR], 267-1065), 230 (IQR, 132-480), 95 (IQR, 63-136), and 55 (IQR, 31-72), respectively (P < .001).

CONCLUSIONS

Implementing the AHI strategy was successful in diagnosing AHI and significantly decreasing the time between HIV diagnosis and viral suppression.

HIV-1 Transmission linkages among persons with incident infection to inform public health surveillance

BACKGROUND

We evaluated features of HIV transmission networks involving persons diagnosed during incident HIV infection (IHI) to assess network-based opportunities to curtail onward transmission.

METHODS

Transmission networks were constructed using partial pol sequences reported to North Carolina surveillance among persons with recent (2014-2018) and past (<2014) HIV diagnoses. IHI were defined as documented acute infections or seroconversion. Demographic and virologic features of HIV genetic clusters (<1.5% pairwise genetic distance) involving ≥ 1 IHI were assessed. Persons with viral genetic links and who had diagnoses >90 days prior to an IHI were further characterized. We assessed named partner outcomes among IHI index persons using contact tracing data.

FINDINGS

Of 4,405 HIV diagnoses 2014-2018 with sequences, there were 323 (7%) IHI index persons; most were male (88%), Black (65%), young (68% <30 years), and reported sex with men (MSM) risk (79%). Index persons were more likely to be cluster members compared to non-index persons diagnosed during the same period (72% vs. 49%). In total, 162 clusters were identified involving 233 IHI, 577 recent diagnoses, and 163 past diagnoses. Most IHI cases (53%) had viral linkages to ≥1 previously diagnosed person without evidence of HIV viral suppression in the year prior to the diagnosis of the IHI index. In contact tracing, only 53% IHI cases named an HIV-positive contact, resulting in 0.5 previously diagnosed persons detected per IHI investigated. When combined with viral analyses, the detection rate of viremic previously diagnosed persons increased to 1.3.

INTERPRETATION

Integrating public health with molecular epidemiology, revealed that more than half of IHI have viral links to persons with previously diagnosed unsuppressed HIV infection which was largely unrecognized by traditional contact tracing. Enhanced partner services to support engagement and retention in HIV care and improved case finding supported by rapid phylogenetic analysis are tools to substantially reduce onward HIV transmission.

The Role of Phylogenetics in Discerning HIV-1 Mixing among Vulnerable Populations and Geographic Regions in Sub-Saharan Africa: A Systematic Review

To reduce global HIV-1 incidence, there is a need to understand and disentangle HIV-1 transmission dynamics and to determine the geographic areas and populations that act as hubs or drivers of HIV-1 spread. In Sub-Saharan Africa (sSA), the region with the highest HIV-1 burden, information about such transmission dynamics is sparse. Phylogenetic inference is a powerful method for the study of HIV-1 transmission networks and source attribution. In this review, we assessed available phylogenetic data on mixing between HIV-1 hotspots (geographic areas and populations with high HIV-1 incidence and prevalence) and areas or populations with lower HIV-1 burden in sSA. We searched PubMed and identified and reviewed 64 studies on HIV-1 transmission dynamics within and between risk groups and geographic locations in sSA (published 1995-2021). We describe HIV-1 transmission from both a geographic and a risk group perspective in sSA. Finally, we discuss the challenges facing phylogenetic inference in mixed epidemics in sSA and offer our perspectives and potential solutions to the identified challenges.

HIV-1 Infection Alters the Viral Composition of Plasma in Men Who Have Sex with Men

Altered gut virome and expanded abundance of certain viruses were found in HIV-1-infected individuals. It remains largely unknown how plasma virus composition changes during HIV-1 infection and antiretroviral therapy (ART). We performed viral metagenomic analysis on viral particles enriched from human plasma from 101 men who have sex with men (MSM) with or without HIV-1 infection and whether or not on ART and compared the differences in the plasma virome. An increased plasma viral abundance of main eukaryotic viruses was observed during HIV-1 infection in MSM, especially in AIDS patients (CD4⁺ T cell counts of <200). Anellovirus, pegivirus and hepatitis B virus (HBV) were the most abundant blood-borne viruses detected among MSM and HIV-1-infected individuals, and anellovirus and pegivirus were closely related to HIV-1 infection. High diversity of anelloviruses was found mostly in HIV-1-infected MSM, and their abundance was positively correlated with the HIV-1 viral load, but negatively correlated with both CD4⁺ T cell counts and CD4⁺/CD8⁺ ratio; in contrast, the abundance of pegivirus showed opposite correlations. ART usage could restore the plasma virome toward that of HIV-1-negative individuals. These data showed an expansion in abundance of certain viruses during HIV-1 infection, indicating the higher risk of shedding some blood-borne viruses in these individuals. These investigations indicate that both anellovirus and pegivirus may play certain roles in HIV disease progression.IMPORTANCE Though an increasing number of studies have indicated the existence of an interaction between the virome and human health or disease, the specific role of these plasma viral components remains largely unsolved. We provide evidence here that an altered plasma virome profile is associated with different immune status of HIV-1 infection. Specific resident viruses, such as anellovirus and pegivirus, may directly or indirectly participate in the disease progression of HIV-1 infection. These results can help to determine their clinical relevance and design potential therapies.

Transmission dynamics and molecular characterization of HIV-1 epidemic among therapeutic failure patients in Santa Catarina state, southern Brazil

The HIV-1 epidemic in southern Brazil is mostly caused by subtype C, which contrasts the dominance of subtype B in the other regions of the country. Santa Catarina (SC), although the smallest state in the southern region, presents one of the highest incidences and mortality rates in Brazil due to AIDS. This work investigated the HIV-1 molecular diversity and phylogenetic transmission networks in SC state by analyzing a database of 3070 sequences of the national genotyping service. HIV-1C proved to be the most frequent subtype, with a significant increase in prevalence over time. HIV-1B was observed to be associated with highly educated men, suggesting a compartmentalization from other subtypes. Such observation was confirmed by the high frequency of HIV-1B circulating in MSM transmission networks. Identified transmission clusters were majority composed by individuals living up to 25 km away and interstate linkages were mainly between southern neighbor states. In general, individuals between 25 and 40 years old and sequences sampled after 2014 were more likely to be in transmission chains, in agreement with the universal treatment protocol launched in 2014. The present study brings new insights about HIV-1 transmission dynamics in southern Brazil.

Sustained, Low Prevalence of Undiagnosed HIV Among Gay and Bisexual Men in Sydney, Australia Coincident With Increased Testing and Pre-exposure Prophylaxis Use: Results From Repeated, Bio-Behavioral Studies 2014-2018

BACKGROUND

Gay and bisexual men with undiagnosed HIV contribute disproportionately to HIV transmission in Australia.

METHODS

In 2014 and 2018, we recruited men at gay venues and events in Sydney. Participants self-completed surveys and provided oral fluid samples for HIV testing. We calculated the prevalence of HIV and undiagnosed infection, and assessed changes in behavior, HIV testing, and the use of pre-exposure prophylaxis. We weighted the samples to adjust for differences in where participants were recruited between rounds. Two-sample tests of proportion were used to compare prevalence estimates and χ tests to assess differences between the samples.

RESULTS

In 2014, 944 men were recruited, and 890 men were recruited in 2018. In 2014, the weighted estimate of HIV prevalence was 6.1% [95% confidence intervals (CI): 4.6 to 7.6], of which 13.8% (95% CI: 5.0 to 22.7) was undiagnosed. In 2018, weighted HIV prevalence was 6.4% (95% CI: 4.8 to 8.0), of which 5.3% (95% CI: 0.5 to 11.1) was undiagnosed. Between 2014 and 2018 among all participants, men reporting at least 10 recent casual partners increased from 22.3% to 27.7% (P = 0.008), condomless anal intercourse with casual partners in the previous 6 months increased from 23.9% to 37.3% (P < 0.001), and sexually transmitted infection diagnoses in the previous year increased from 14.4% to 27.5% (P < 0.001). HIV testing and the use of pre-exposure prophylaxis in the previous 6 months increased from 49.6% to 56.3% (P = 0.004) and 2.0%-21.0% (P < 0.001), respectively.

CONCLUSIONS

Repeated, bio-behavioral surveillance suggests the prevalence of undiagnosed HIV remains low in Sydney, despite gay and bisexual men reporting more casual sex partners, condomless sex, and sexually transmitted infections.

Monitoring Recently Acquired HIV Infections in Amsterdam, The Netherlands: The Attribution of Test Locations

Background: Surveillance of recent HIV infections (RHI) using an avidity assay has been implemented at Dutch sexual health centres (SHC) since 2014, but data on RHI diagnosed at other test locations is lacking.

Setting: Implementation of the avidity assay in HIV treatment clinics for the purpose of studying RHI among HIV patients tested at different test locations.

Methods: We retrospectively tested leftover specimens from newly diagnosed HIV patients in care in 2013–2015 in Amsterdam. Avidity Index (AI) values ≤0.80 indicated recent infection (acquired ≤6 months prior to diagnosis), and AI > 0.80 indicated established infection (acquired >6 months prior to diagnosis). An algorithm for RHI was applied to correct for false recency. Recency based on this algorithm was compared with recency based on epidemiological data only. Multivariable logistic regression analysis was used to identify factors associated with RHI among men who have sex with men (MSM).

Results: We tested 447 specimens with avidity; 72% from MSM. Proportions of RHI were 20% among MSM and 10% among heterosexuals. SHC showed highest proportions of RHI (27%), followed by GPs (15%), hospitals (5%), and other/unknown locations (11%) (p < 0.001). Test location was the only factor associated with RHI among MSM. A higher proportion of RHI was found based on epidemiological data compared to avidity testing combined with the RHI algorithm.

Conclusion: SHC identify more RHI infections compared to other test locations, as they serve high-risk populations and offer frequent HIV testing. Using avidity-testing for surveillance purposes may help targeting prevention programs, but the assay lacks robustness and its added value may decline with improved, repeat HIV testing and data collection.

Evaluation of Phylogenetic Methods for Inferring the Direction of Human Immunodeficiency Virus (HIV) Transmission: HIV Prevention Trials Network (HPTN) 052

BACKGROUND

Phylogenetic analysis can be used to assess human immunodeficiency virus (HIV) transmission in populations. We inferred the direction of HIV transmission using whole-genome HIV sequences from couples with known linked infection and known transmission direction.

METHODS

Complete next-generation sequencing (NGS) data were obtained for 105 unique index-partner sample pairs from 32 couples enrolled in the HIV Prevention Trials Network (HPTN) 052 study (up to 2 samples/person). Index samples were obtained up to 5.5 years before partner infection; partner samples were obtained near the time of seroconversion. The bioinformatics method, phyloscanner, was used to infer transmission direction. Analyses were performed using samples from individual sample pairs, samples from all couples (1 sample/person; group analysis), and all available samples (multisample group analysis). Analysis was also performed using NGS data from defined regions of the HIV genome (gag, pol, env).

RESULTS

Using whole-genome NGS data, transmission direction was inferred correctly (index to partner) for 98 of 105 (93.3%) of the individual sample pairs, 99 of 105 (94.3%) sample pairs using group analysis, and 31 of the 32 couples (96.9%) using multisample group analysis. There were no cases where the incorrect transmission direction (partner to index) was inferred. The accuracy of the method was higher with greater time between index and partner sample collection. Pol region sequences performed better than env or gag sequences for inferring transmission direction.

CONCLUSIONS

We demonstrate the potential of a phylogenetic method to infer the direction of HIV transmission between 2 individuals using whole-genome and pol NGS data.

Human Immunodeficiency Virus Type 1 Phylodynamics to Detect and Characterize Active Transmission Clusters in North Carolina

BACKGROUND

Human immunodeficiency virus type 1 (HIV-1) phylodynamics can be used to monitor epidemic trends and help target prevention through identification and characterization of transmission clusters.

METHODS

We analyzed HIV-1 pol sequences sampled in North Carolina from 1997 to 2014. Putative clusters were identified using maximum-likelihood trees and dated using Bayesian Markov Chain Monte Carlo inference. Active clusters were defined as clusters including internal nodes from 2009 to 2014. Effective reproductive numbers (Re) were estimated using birth-death models for large clusters that expanded ≥2-fold from 2009 to 2014.

RESULTS

Of 14 921 persons, 7508 (50%) sequences were identified in 2264 clusters. Only 288 (13%) clusters were active from 2009 to 2014; 37 were large (10-36 members). Compared to smaller clusters, large clusters were increasingly populated by men and younger persons; however, nearly 60% included ≥1 women. Clusters with ≥3 members demonstrated assortative mixing by sex, age, and sample region. Of 15 large clusters with ≥2-fold expansion, nearly all had Re approximately 1 by 2014.

CONCLUSIONS

Phylodynamics revealed transmission cluster expansion in this densely sampled region and allowed estimates of Re to monitor active clusters, showing the propensity for steady, onward propagation. Associations with clustering and cluster characteristics vary by cluster size. Harnessing sequence-derived epidemiologic parameters within routine surveillance could allow refined monitoring of local subepidemics.

Molecular epidemiology in the HIV and SARS-CoV-2 pandemics

PURPOSE OF REVIEW

The aim of this review was to compare and contrast the application of molecular epidemiology approaches for the improved management and understanding of the HIV versus SARS-CoV-2 epidemics.

RECENT FINDINGS

Molecular biology approaches, including PCR and whole genome sequencing (WGS), have become powerful tools for epidemiological investigation. PCR approaches form the basis for many high-sensitivity diagnostic tests and can supplement traditional contact tracing and surveillance strategies to define risk networks and transmission patterns. WGS approaches can further define the causative agents of disease, trace the origins of the pathogen, and clarify routes of transmission. When coupled with clinical datasets, such as electronic medical record data, these approaches can investigate co-correlates of disease and pathogenesis. In the ongoing HIV epidemic, these approaches have been effectively deployed to identify treatment gaps, transmission clusters and risk factors, though significant barriers to rapid or real-time implementation remain critical to overcome. Likewise, these approaches have been successful in addressing some questions of SARS-CoV-2 transmission and pathogenesis, but the nature and rapid spread of the virus have posed additional challenges.

SUMMARY

Overall, molecular epidemiology approaches offer unique advantages and challenges that complement traditional epidemiological tools for the improved understanding and management of epidemics.

Acute and early HIV infection screening among men who have sex with men, a systematic review and meta-analysis

INTRODUCTION

Screening for acute and early HIV infections (AEHI) among men who have sex with men (MSM) remains uncommon in sub-Saharan Africa (SSA). Yet, undiagnosed AEHI among MSM and subsequent failure to link to care are important drivers of the HIV epidemic. We conducted a systematic review and meta-analysis of AEHI yield among MSM mobilized for AEHI testing; and assessed which risk factors and/or symptoms could increase AEHI yield in MSM.

METHODS

We systematically searched four databases from their inception through May 2020 for studies reporting strategies of mobilizing MSM for testing and their AEHI yield, or risk and/or symptom scores targeting AEHI screening. AEHI yield was defined as the proportion of AEHI cases among the total number of visits. Study estimates for AEHI yield were pooled using random effects models. Predictive ability of risk and/or symptom scores was expressed as the area under the receiver operator curve (AUC).

RESULTS

Twenty-two studies were identified and included a variety of mobilization strategies (eight studies) and risk and/or symptom scores (fourteen studies). The overall pooled AEHI yield was 6.3% (95% CI, 2.1 to 12.4; I2  = 94.9%; five studies); yield varied between studies using targeted strategies (11.1%; 95% CI, 5.9 to 17.6; I2  = 83.8%; three studies) versus universal testing (1.6%; 95% CI, 0.8 to 2.4; two studies). The AUC of risk and/or symptom scores ranged from 0.69 to 0.89 in development study samples, and from 0.51 to 0.88 in validation study samples. AUC was the highest for scores including symptoms, such as diarrhoea, fever and fatigue. Key risk score variables were age, number of sexual partners, condomless receptive anal intercourse, sexual intercourse with a person living with HIV, a sexually transmitted infection, and illicit drug use. No studies were identified that assessed AEHI yield among MSM in SSA and risk and/or symptom scores developed among MSM in SSA lacked validation.

CONCLUSIONS

Strategies mobilizing MSM for targeted AEHI testing resulted in substantially higher AEHI yields than universal AEHI testing. Targeted AEHI testing may be optimized using risk and/or symptom scores, especially if scores include symptoms. Studies assessing AEHI yield and validation of risk and/or symptom scores among MSM in SSA are urgently needed.

Is reaching 90-90-90 enough to end AIDS? Lessons from Amsterdam

PURPOSE OF REVIEW

Although cities present opportunities for infectious pathogens such as HIV to spread, public health infrastructure within these cities also provides opportunities to design effective approaches to eliminate transmission of these pathogens. The HIV Transmission Elimination AMsterdam (H-TEAM) Initiative, a consortium of relevant stakeholders involved in HIV prevention and care, designed an integrated approach to curb the HIV epidemic in Amsterdam, including providing preexposure prophylaxis (PrEP), increasing awareness of acute HIV infection, offering same-day test and treat, and improving indicator disease-driven HIV testing.

RECENT FINDINGS

In 2013, approximately 230 people in Amsterdam were newly diagnosed with HIV, largely belonging to one of two key affected populations, namely MSM and people with a migration background. Since the start of H-TEAM in 2014, a decrease in new diagnoses was observed (130 in 2017), with an increasing proportion of MSM who had been diagnosed with a recent infection.

SUMMARY

The H-TEAM shows that a city-based concerted effort is feasible. However, major challenges remain, such as reducing the number of late HIV diagnoses, and identifying and providing appropriate services to a diminishing group of individuals who are likely the source of transmission.

HIV-1 Transmission Patterns Within and Between Risk Groups in Coastal Kenya

HIV-1 transmission patterns within and between populations at different risk of HIV-1 acquisition in Kenya are not well understood. We investigated HIV-1 transmission networks in men who have sex with men (MSM), injecting drug users (IDU), female sex workers (FSW) and heterosexuals (HET) in coastal Kenya. We used maximum-likelihood and Bayesian phylogenetics to analyse new (N = 163) and previously published (N = 495) HIV-1 polymerase sequences collected during 2005-2019. Of the 658 sequences, 131 (20%) were from MSM, 58 (9%) IDU, 109 (17%) FSW, and 360 (55%) HET. Overall, 206 (31%) sequences formed 61 clusters. Most clusters (85%) consisted of sequences from the same risk group, suggesting frequent within-group transmission. The remaining clusters were mixed between HET/MSM (7%), HET/FSW (5%), and MSM/FSW (3%) sequences. One large IDU-exclusive cluster was found, indicating an independent sub-epidemic among this group. Phylodynamic analysis of this cluster revealed a steady increase in HIV-1 infections among IDU since the estimated origin of the cluster in 1987. Our results suggest mixing between high-risk groups and heterosexual populations and could be relevant for the development of targeted HIV-1 prevention programmes in coastal Kenya.

Phylogenetics applied to the human immunodeficiency virus type 1 (HIV-1): from the cross-species transmissions to the contact network inferences

Phylogenetic analyses were crucial to elucidate the origin and spread of the pandemic human immunodeficiency virus type 1 (HIV-1) group M virus, both during the pre-epidemic period of cryptic dissemination in human populations as well as during the epidemic phase of spread. The use of phylogenetics and phylodynamics approaches has provided important insights to track the founder events that resulted in the spread of HIV-1 strains across vast geographic areas, specific countries and within geographically restricted communities. In the recent years, the use of phylogenetic analysis combined with the huge availability of HIV sequences has become an increasingly important approach to reconstruct HIV transmission networks and understand transmission dynamics in concentrated and generalised epidemics. Significant efforts to obtain viral sequences from newly HIV-infected individuals could certainly contribute to detect rapidly expanding HIV-1 lineages, identify key populations at high-risk and understand what public health interventions should be prioritised in different scenarios.

'Break the Chains 2015' community-based HIV prevention campaign for men who have sex with men in Switzerland: non-randomised evaluation and cost analysis

OBJECTIVES

To study the implementation, effects and costs of Break the Chains, a community-based HIV prevention campaign for men who have sex with men (MSM) in Switzerland, from March to May 2015, which aimed to reduce early HIV transmission by promoting the campaign message to adopt short-term risk reduction followed by HIV testing.

DESIGN

Non-randomised evaluation and cost analysis.

SETTING

Gay venues in 11 of 26 cantons in Switzerland and national online media campaign.

PARTICIPANTS

MSM in online surveys (precampaign n=834, postcampaign n=688) or attending HIV testing centres (n=885); campaign managers (n=9); and campaign staff (n=38) or further intermediaries (n=80) in an online survey.

PRIMARY AND SECONDARY OUTCOME MEASURES

The primary outcome measure was the proportion of MSM at risk of HIV acquisition or transmission who adhered to the campaign message. Secondary outcomes were postcampaign test uptake, knowledge about HIV primary infection and sense of belonging to the gay community.

RESULTS

Campaign staff estimated that they contacted 17 145 MSM in 11 cantons. Among 688 respondents to the postcampaign survey, 311 (45.2%) were categorised as MSM at risk. Of 402/688 (58.5%) MSM who had heard about Break the Chains 2015, MSM categorised as being at risk were less likely to report adherence to the campaign message than MSM not at risk (adjusted OR 0.24; 95% CI 0.14 to 0.42). Twenty per cent of MSM with a defined risk of HIV acquisition or transmission who adopted risk reduction declared having done so because of the campaign. Costs for one MSM at risk to adhere to the campaign message were estimated at USD purchasing power parity 36-55. The number of HIV tests in the month after the campaign was twice the monthly average.

CONCLUSION

Break the Chains increased HIV testing, implying that community-based campaigns are useful HIV prevention strategies for MSM. Additional interventions are needed to reach MSM at the highest risk of infection more effectively.

Public health in genetic spaces: a statistical framework to optimize cluster-based outbreak detection

Genetic clustering is a popular method for characterizing variation in transmission rates for rapidly evolving viruses, and could potentially be used to detect outbreaks in 'near real time'. However, the statistical properties of clustering are poorly understood in this context, and there are no objective guidelines for setting clustering criteria. Here, we develop a new statistical framework to optimize a genetic clustering method based on the ability to forecast new cases. We analysed the pairwise Tamura-Nei (TN93) genetic distances for anonymized HIV-1 subtype B pol sequences from Seattle (n = 1,653) and Middle Tennessee, USA (n = 2,779), and northern Alberta, Canada (n = 809). Under varying TN93 thresholds, we fit two models to the distributions of new cases relative to clusters of known cases: 1, a null model that assumes cluster growth is strictly proportional to cluster size, i.e. no variation in transmission rates among individuals; and 2, a weighted model that incorporates individual-level covariates, such as recency of diagnosis. The optimal threshold maximizes the difference in information loss between models, where covariates are used most effectively. Optimal TN93 thresholds varied substantially between data sets, e.g. 0.0104 in Alberta and 0.016 in Seattle and Tennessee, such that the optimum for one population would potentially misdirect prevention efforts in another. For a given population, the range of thresholds where the weighted model conferred greater predictive accuracy tended to be narrow (±0.005 units), and the optimal threshold tended to be stable over time. Our framework also indicated that variation in the recency of HIV diagnosis among clusters was significantly more predictive of new cases than sample collection dates (ΔAIC > 50). These results suggest that one cannot rely on historical precedence or convention to configure genetic clustering methods for public health applications, especially when translating methods between settings of low-level and generalized epidemics. Our framework not only enables investigators to calibrate a clustering method to a specific public health setting, but also provides a variable selection procedure to evaluate different predictive models of cluster growth.

Prevalence of Non-B HIV-1 Subtypes in North Italy and Analysis of Transmission Clusters Based on Sequence Data Analysis

HIV-1 diversity is increasing in European countries due to immigration flows, as well as travels and human mobility, leading to the circulation of both new viral subtypes and new recombinant forms, with important implications for public health. We analyzed 710 HIV-1 sequences comprising protease and reverse-transcriptase (PR/RT) coding regions, sampled from 2011 to 2017, from naive patients in Spedali Civili Hospital, Brescia, Italy. Subtyping was performed by using a combination of different tools; the phylogenetic analysis with a structured coalescence model and Makarov Chain Monte Carlo was used on the datasets, to determine clusters and evolution. We detected 304 (43%) patients infected with HIV-1 non-B variants, of which only 293 sequences were available, with four pure subtypes and five recombinant forms; subtype F1 (17%) and CRF02_AG (51.1%) were most common. Twenty-five transmission clusters were identified, three of which included >10 patients, belonging to subtype CRF02_AG and subtype F. Most cases of alleged transmission were between heterosexual couples. Probably due to strong migratory flows, we have identified different subtypes with particular patterns of recombination or, as in the case of the subtype G (18/293, 6.1%), to a complete lack of relationship between the sequenced strains, revealing that they are all singletons. Continued HIV molecular surveillance is most important to analyze the dynamics of the boost of transmission clusters in order to implement public health interventions aimed at controlling the HIV epidemic.

Exploring HIV-1 Transmission Dynamics by Combining Phylogenetic Analysis and Infection Timing

HIV-1 pol sequences obtained through baseline drug resistance testing of patients newly diagnosed between 2013 and 2017 were analyzed for genetic similarity. For 927 patients the information on genetic similarity was combined with demographic data and with information on the recency of infection. Overall, 48.3% of the patients were genetically linked with 11.4% belonging to a pair and 36.9% involved in a cluster of ≥3 members. The percentage of early diagnosed (≤4 months after infection) was 28.6%. Patients of Belgian origin were more frequently involved in transmission clusters (49.7% compared to 15.3%) and diagnosed earlier (37.4% compared to 12.2%) than patients of Sub-Saharan African origin. Of the infections reported to be locally acquired, 69.5% were linked (14.1% paired and 55.4% in a cluster). Equal parts of early and late diagnosed individuals (59.9% and 52.4%, respectively) were involved in clusters. The identification of a genetically linked individual for the majority of locally infected patients suggests a high rate of diagnosis in this population. Diagnosis however is often delayed for >4 months after infection increasing the opportunities for onward transmission. Prevention of local infection should focus on earlier diagnosis and protection of the still uninfected members of sexual networks with human immunodeficiency virus (HIV)-infected members.

Ethical issues associated with HIV molecular epidemiology: a qualitative exploratory study using inductive analytic approaches

Background

HIV molecular epidemiology is increasingly recognized as a vital source of information for understanding HIV transmission dynamics. Despite extensive use of these data-intensive techniques in both research and public health settings, the ethical issues associated with this science have received minimal attention. As the discipline evolves, there is reasonable concern that existing ethical and legal frameworks and standards might lag behind the rapid methodological developments in this field. This is a follow-up on our earlier work that applied a predetermined analytical framework to examine the perspectives of a sample of scientists from the fields of epidemiology, public health, virology and bioethics on key ethical issues associated with HIV molecular epidemiology in HIV network research.

Methods

Fourteen in-depth interviews were conducted with scientists from the fields of molecular epidemiology, public health, virology and bioethics. Inductive analytical approaches were applied to identify key themes that emerged from the data.

Results

Our interviewees acknowledged the potential positive impact of molecular epidemiology in the fight against HIV. However, they were concerned that HIV phylogenetics research messages may be incorrectly interpreted if not presented at the appropriate level. There was consensus that HIV phylogenetics research presents a potential risk to privacy, but the probability and magnitude of this risk was less obvious. Although participants acknowledged the social value that could be realized from the analysis of HIV genetic sequences, there was a perceived fear that the boundaries for use of HIV sequence data were not clearly defined.

Conclusions

Our findings highlight distinct ethical issues arising from HIV molecular epidemiology. As the discipline evolves and HIV sequence data become increasingly available, it is critical to ensure that ethical standards keep pace with biomedical advancements. We argue that the ethical issues raised in this study, whether real or perceived, require further conceptual and empirical examination.

Motives for choosing, switching and stopping daily or event-driven pre-exposure prophylaxis - a qualitative analysis

INTRODUCTION

In settings where both daily and event-driven pre-exposure prophylaxis (PrEP) are offered to men who have sex with men (MSM), a clear understanding of the motives to choose between the different dosing-regimens can facilitate more effective PrEP implementation. We therefore studied the motives for choosing for, switching between, and stopping daily or event-driven PrEP.

METHODS

We used data (August 2015-June 2017) from the prospective, longitudinal, open-label Amsterdam PrEP demonstration study, in which daily (dPrEP) and event-driven PrEP (edPrEP) were offered to 374 HIV-negative MSM and two transgender persons. Participants self-selected the preferred PrEP-regimen at baseline and could switch regimens at three-monthly follow-up visits. We measured motives for choosing PrEP-regimen at baseline and for switching and stopping PrEP at follow-up visits. Open- and closed-end items were combined and qualitatively analysed.

RESULTS

Choices of PrEP-regimens were determined by personal and contextual factors, involving the perceived self-efficacy concerning adherence, the risk-context, and the anticipated impact of PrEP on physical and sexual wellbeing. dPrEP was preferred because of the anticipated better adherence and the fear of side-effects relating to edPrEP re-initiations. Moreover, dPrEP was perceived to be more effective than edPrEP. Motives to choose edPrEP were the expected physical burden of dPrEP, anticipated side-effects of dPrEP, and fear to forget daily doses. Regarding the risk-context: dPrEP was preferred for unplanned and/or frequent sex, while edPrEP was chosen when risk was predictable and/or less frequent. While some chose for dPrEP to gain more sexual freedom, others chose for edPrEP to minimize sexual risk episodes. Changes in the above factors, such as changing risk patterns, changing relationships or changing physical conditions, resulted in switching regimens. Choices to stop PrEP were related to lower sexual risk, adherence issues and side-effects.

CONCLUSIONS

The great diversity of motives illustrates the importance of offering a choice of PrEP-regimens. In counselling of MSM starting PrEP, choices for PrEP-regimens may be addressed as a continuum of flexible and changeable options over time. This may help individuals choose the PrEP-regimen that best fits their current sexual context, priorities and personal capabilities and therefore will be more easily adhered to.

Efficacy and cost-effectiveness of early antiretroviral therapy and partners' pre-exposure prophylaxis among men who have sex with men in Shenyang, China: a prospective cohort and costing study

BACKGROUND

Biomedical interventions such as antiretroviral therapy (ART) and pre-exposure prophylaxis (PrEP) are highly effective for prevention of human immunodeficiency virus (HIV) infection. However, China has not released national PrEP guidelines, and HIV incidence among men who have sex with men (MSM) is unchanged despite substantial scale-up of ART. We evaluated reductions in HIV transmission that may be achieved through early initiation of ART plus partners' PrEP.

METHODS

Six intervention scenarios were evaluated in terms of their impact on HIV transmission and their cost-effectiveness for 36 months post-infection. Three scenarios were based on observed data: non-ART, standard-ART, and early-ART. Another three scenarios were based on observed and hypothetical data: non-ART plus partners' PrEP, standard-ART plus partners' PrEP, and early-ART plus partners' PrEP. The number of onward transmissions was calculated according to viral load and self-reported sexual behaviors, and calibrated by the prevalence and incidence of HIV among Chinese MSM. Cost-effectiveness outcomes were quality-adjusted life-years (QALYs) and cost-utility ratio (CUR).

RESULTS

The estimated number of onward transmissions by every 100 HIV-positive cases 36 months post-infection was 41.83 (95% credible interval: 30.75-57.69) in the non-ART scenario, 7.95 (5.85-10.95) in the early-ART scenario, and 0.79 (0.58-1.09) in the early-ART plus partners' PrEP scenario. Compared with non-ART, the early-ART and early-ART plus partners' PrEP scenarios were associated with an 81.0 and 98.1% reduction in HIV transmission, and had a CUR of $12,864/QALY and $16,817/QALY, respectively.

CONCLUSIONS

Integrated delivery of early ART and sexual partners' PrEP could nearly eliminate HIV transmission and reduce costs during the first 36 months of HIV infection. Our results suggest a feasible and cost-effective strategy for reversing the HIV epidemic among MSM in China.

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

The multidimensional nature and continued evolution of HIV epidemics among men who have sex with men (MSM) requires innovative intervention approaches. Strategies are needed that recognise the individual, social and structural factors driving HIV transmission; that can pinpoint networks with heightened transmission risk; and that can help target intervention in real time. HIV phylogenetics is a rapidly evolving field with strong promise for informing innovative responses to the HIV epidemic among MSM. Currently, HIV phylogenetic insights are providing new understandings of characteristics of HIV epidemics involving MSM, social networks influencing transmission, characteristics of HIV transmission clusters involving MSM, targets for antiretroviral and other prevention strategies and dynamics of emergent epidemics. Maximising the potential of HIV phylogenetics for HIV responses among MSM will require attention to key methodological challenges and ethical considerations, as well as resolving key implementation and scientific questions. Enhanced and integrated use of HIV surveillance, sociobehavioural and phylogenetic data resources are becoming increasingly critical for informing public health approaches to HIV among MSM.

Genetic Cluster Analysis for HIV Prevention

PURPOSE OF REVIEW

This review summarizes the use of genetic similarity clusters to understand HIV transmission and inform prevention efforts.

RECENT FINDINGS

Recent emphases include the development of real-time cluster identification in order to interrupt transmission chains, the use of clusters to estimate rates of transmission along the HIV care cascade, and the extension of cluster analyses to understand transmission in the generalized epidemics of sub-Saharan Africa. Importantly, this recent empirical work has been accompanied by theoretical work that elucidates the processes that underlie HIV genetic similarity clusters; multiple studies suggest that clusters are not necessarily enriched with individuals with high transmission rates, but rather can reflect variation in sampling times within a population, with individuals sampled early in infection more likely to cluster. Analyses of genetic similarity clusters have great promise to inform HIV epidemiology and prevention. Future emphases should include the collection of additional sequence data from underrepresented populations, such as those in sub-Saharan Africa, and further development and evaluation of clustering methods.