Phylogenetic inferences on HIV-1 transmission: implications for the design of prevention and treatment interventions

Prevention of Viral Hepatitis and HIV Infection among People Who Inject Drugs: A Systematic Review and Meta-Analysis

This study aimed to explore the current evidence on preventing blood-borne virus infections among people who inject drugs (PWID). We conducted a comprehensive search across three databases (PubMed, Embase, Cochrane Library) for relevant articles published in English between 2014 and 2023. We followed the Preferred Reporting Items for Systematic Reviews and Meta Analysis (PRISMA) guidelines, assessed the quality of the paper using the revised Cochrane Risk of Bias Tool (ROB 2), and conducted a meta-analysis using RevMan 5.3. Completing the harm reduction program (HRP) participation and receiving all three vaccine doses resulted in a 28% reduction in the risk of HBV infection (OR: 0.72, 95% CI: 0.37-1.42). Various interventions increased the willingness of PWIDs to undergo HCV treatment (OR: 5.91, 95% CI: 2.46-14.24) and promoted treatment adherence (OR: 15.04, 95% CI: 2.80-80.61). Taking PrEP, participating in HRP, and modifying risky behaviors were associated with a 33% reduction in the risk of HIV infection (OR: 0.67, 95% CI: 0.61-0.74). Conducting referrals, providing counseling, and implementing antiretroviral therapy resulted in a 44% reduction in the risk of viral transmission (OR: 0.56, 95% CI: 0.47-0.66). Co-infection may potentially compromise effectiveness, so it is important to consider drug resistance.

Non-B subtypes account for a large proportion of clustered primary HIV-1 infections in Italy

OBJECTIVES AND DESIGN

Using pol sequences obtained for routine resistance testing, we characterised the molecular patterns of HIV-1 transmission and factors associated with being part of a transmission cluster among individuals who in 2008-2014 presented with primary HIV-1 infection (PHI) at 11 urban centres across Italy.

METHODS

Pol sequences were obtained by Sanger sequencing. Transmission clusters were identified by phylogenetic analysis (maximum likelihood method, confirmed by Bayesian analysis). Multivariable logistic regression explored factors associated with a participant being part of a transmission cluster.

RESULTS

The PHI cohort comprised 186 participants (159/186, 85.5% males) with median age 44 years, median CD4 count 464 cells/mm³ and median plasma HIV-1 RNA 5.6 log₁₀ copies/mL. Drug resistance associated mutations were found in 16/186 (8.6%). A diversity of non-B subtypes accounted for 60/186 (32.3%) of all infections. A total of 17 transmission clusters were identified, including 44/186 (23.7%) participants. Each cluster comprised 2-6 sequences. Non-B subtypes accounted for seven clusters and 22/44 (50%) of clustered sequences. In multivariable logistic regression analysis, factors associated with being part of a transmission cluster comprised harbouring a non-B subtype (adjusted OR (adjOR) 2.28; 95% CI 1.03 to 5.05; p=0.04) and showing a lower plasma HIV-1 RNA (adjOR 0.80, 95% CI 0.64 to 0.99; p=0.04).

CONCLUSIONS

There was a large contribution of diverse non-B subtypes to transmission clusters among people presenting with acute or recent HIV-1 infection in this cohort, illustrating the evolving dynamics of the HIV-1 epidemic in Italy, where subtype B previously dominated.

Similar But Different: Integrated Phylogenetic Analysis of Austrian and Swiss HIV-1 Sequences Reveal Differences in Transmission Patterns of the Local HIV-1 Epidemics

OBJECTIVES

Phylogenetic analyses of 2 or more countries allow to detect differences in transmission dynamics of local HIV-1 epidemics beyond differences in demographic characteristics.

METHODS

A maximum-likelihood phylogenetic tree was built using pol -sequences of the Swiss HIV Cohort Study (SHCS) and the Austrian HIV Cohort Study (AHIVCOS), with international background sequences. Three types of phylogenetic cherries (clusters of size 2) were analyzed further: (1) domestic cherries; (2) international cherries; and (3) SHCS/AHIVCOS-cherries. Transmission group and ethnicities observed within the cherries were compared with the respective distribution expected from a random distribution of patients on the phylogeny.

RESULTS

The demographic characteristics of the AHIVCOS (included patients: 3'141) and the SHCS (included patients: 12'902) are very similar. In the AHIVCOS, 36.5% of the patients were in domestic cherries, 8.3% in international cherries, and 7.0% in SHCS/AHIVCOS cherries. Similarly, in the SHCS, 43.0% of the patients were in domestic cherries, 8.2% in international cherries, and 1.7% in SHCS/AHIVCOS cherries. Although international cherries in the SHCS were dominated by heterosexuals with men who have sex with men being underrepresented, the opposite was the case for the AHIVCOS. In both cohorts, cherries with one patient belonging to the transmission group intravenous drug user and the other one non-intravenous drug user were underrepresented.

CONCLUSIONS

In both cohorts, international HIV transmission plays a major role in the local epidemics, mostly driven by men who have sex with men in the AHIVOS, and by heterosexuals in the SHCS, highlighting the importance of international collaborations to understand global HIV transmission links on the way to eliminate HIV.

Transmission Clusters, Predominantly Associated With Men Who Have Sex With Men, Play a Main Role in the Propagation of HIV-1 in Northern Spain (2013–2018)

Viruses of HIV-1-infected individuals whose transmission is related group phylogenetically in transmission clusters (TCs). The study of the phylogenetic relations of these viruses and the factors associated with these individuals is essential to analyze the HIV-1 epidemic. In this study, we examine the role of TCs in the epidemiology of HIV-1 infection in Galicia and the Basque County, two regions of northern Spain. A total of 1,158 HIV-1-infected patients from both regions with new diagnoses (NDs) in 2013–2018 were included in the study. Partial HIV-1 pol sequences were analyzed phylogenetically by approximately maximum-likelihood with FastTree 2. In this analysis, 10,687 additional sequences from samples from HIV-1-infected individuals collected in Spain in 1999–2019 were also included to assign TC membership and to determine TCs’ sizes. TCs were defined as those which included viruses from ≥4 individuals, at least 50% of them Spaniards, and with ≥0.95 Shimodaira-Hasegawa-like node support in the phylogenetic tree. Factors associated to TCs were evaluated using odds ratios (OR) and their 95% CI. Fifty-one percent of NDs grouped in 162 TCs. Male patients (OR: 2.6; 95% CI: 1.5–4.7) and men having sex with men (MSM; OR: 2.1; 95% CI: 1.4–3.2) had higher odds of belonging to a TC compared to female and heterosexual patients, respectively. Individuals from Latin America (OR: 0.3; 95% CI: 0.2–0.4), North Africa (OR: 0.4; 95% CI: 0.2–1.0), and especially Sub-Saharan Africa (OR: 0.02; 95% CI: 0.003–0.2) were inversely associated to belonging to TCs compared to native Spaniards. Our results show that TCs are important components of the HIV-1 epidemics in the two Spanish regions studied, where transmission between MSM is predominant. The majority of migrants were infected with viruses not belonging to TCs that expand in Spain. Molecular epidemiology is essential to identify local peculiarities of HIV-1 propagation. The early detection of TCs and prevention of their expansion, implementing effective control measures, could reduce HIV-1 infections.

The role of high-risk geographies in the perpetuation of the HIV epidemic in rural South Africa: A spatial molecular epidemiology study

In this study, we hypothesize that HIV geographical clusters (geospatial areas with significantly higher numbers of HIV positive individuals) can behave as the highly connected nodes in the transmission network. Using data come from one of the most comprehensive demographic surveillance systems in Africa, we found that more than 70% of the HIV transmission links identified were directly connected to an HIV geographical cluster located in a peri-urban area. Moreover, we identified a single central large community of highly connected nodes located within the HIV cluster. This module was composed by nodes highly connected among them, forming a central structure of the network that was also connected with the small sparser modules located outside of the HIV geographical cluster. Our study supports the evidence of the high level of connectivity between HIV geographical high-risk populations and the entire community.

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

BACKGROUND

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

METHODS

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

FINDINGS

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

INTERPRETATION

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

FUNDING

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

The Role of Phylogenetics in Unravelling Patterns of HIV Transmission towards Epidemic Control: The Quebec Experience (2002-2020)

Phylogenetics has been advanced as a structural framework to infer evolving trends in the regional spread of HIV-1 and guide public health interventions. In Quebec, molecular network analyses tracked HIV transmission dynamics from 2002-2020 using MEGA10-Neighbour-joining, HIV-TRACE, and MicrobeTrace methodologies. Phylogenetics revealed three patterns of viral spread among Men having Sex with Men (MSM, n = 5024) and heterosexuals (HET, n = 1345) harbouring subtype B epidemics as well as B and non-B subtype epidemics (n = 1848) introduced through migration. Notably, half of new subtype B infections amongst MSM and HET segregating as solitary transmissions or small cluster networks (2-5 members) declined by 70% from 2006-2020, concomitant to advances in treatment-as-prevention. Nonetheless, subtype B epidemic control amongst MSM was thwarted by the ongoing genesis and expansion of super-spreader large cluster variants leading to micro-epidemics, averaging 49 members/cluster at the end of 2020. The growth of large clusters was related to forward transmission cascades of untreated early-stage infections, younger at-risk populations, more transmissible/replicative-competent strains, and changing demographics. Subtype B and non-B subtype infections introduced through recent migration now surpass the domestic epidemic amongst MSM. Phylodynamics can assist in predicting and responding to active, recurrent, and newly emergent large cluster networks, as well as the cryptic spread of HIV introduced through migration.

Molecular Transmission Dynamics of Primary HIV Infections in Lazio Region, Years 2013-2020

Molecular investigation of primary HIV infections (PHI) is crucial to describe current dynamics of HIV transmission. Aim of the study was to investigate HIV transmission clusters (TC) in PHI referred during the years 2013–2020 to the National Institute for Infectious Diseases in Rome (INMI), that is the Lazio regional AIDS reference centre, and factors possibly associated with inclusion in TC. These were identified by phylogenetic analysis, based on population sequencing of pol; a more in depth analysis was performed on TC of B subtype, using ultra-deep sequencing (UDS) of env. Of 270 patients diagnosed with PHI during the study period, 229 were enrolled (median follow-up 168 (IQR 96–232) weeks). Median age: 39 (IQR 32–48) years; 94.8% males, 86.5% Italians, 83.4% MSM, 56.8% carrying HIV-1 subtype B. Of them, 92.6% started early treatment within a median of 4 (IQR 2–7) days after diagnosis; median time to sustained suppression was 20 (IQR 8–32) weeks. Twenty TC (median size 3, range 2–9 individuals), including 68 patients, were identified. A diagnosis prior to 2015 was the unique factor associated with inclusion in a TC. Added value of UDS was the identification of shared quasispecies components in transmission pairs within TC.

Mapping of HIV-1C Transmission Networks Reveals Extensive Spread of Viral Lineages Across Villages in Botswana Treatment-as-Prevention Trial

BACKGROUND

Phylogenetic mapping of HIV-1 lineages circulating across defined geographical locations is promising for better understanding HIV transmission networks to design optimal prevention interventions.

METHODS

We obtained near full-length HIV-1 genome sequences from people living with HIV (PLWH), including participants on antiretroviral treatment in the Botswana Combination Prevention Project, conducted in 30 Botswana communities in 2013-2018. Phylogenetic relationships among viral sequences were estimated by maximum likelihood.

RESULTS

We obtained 6078 near full-length HIV-1C genome sequences from 6075 PLWH. We identified 984 phylogenetically distinct HIV-1 lineages (molecular HIV clusters) circulating in Botswana by mid-2018, with 2-27 members per cluster. Of these, dyads accounted for 62%, approximately 32% (n = 316) were found in single communities, and 68% (n = 668) were spread across multiple communities. Men in clusters were approximately 3 years older than women (median age 42 years, vs 39 years; P < .0001). In 65% of clusters, men were older than women, while in 35% of clusters women were older than men. The majority of identified viral lineages were spread across multiple communities.

CONCLUSIONS

A large number of circulating phylogenetically distinct HIV-1C lineages (molecular HIV clusters) suggests highly diversified HIV transmission networks across Botswana communities by 2018.

Evaluation of HIV Transmission Clusters among Natives and Foreigners Living in Italy

We aimed at evaluating the characteristics of HIV-1 molecular transmission clusters (MTCs) among natives and migrants living in Italy, diagnosed between 1998 and 2018. Phylogenetic analyses were performed on HIV-1 polymerase (pol) sequences to characterise subtypes and identify MTCs, divided into small (SMTCs, 2–3 sequences), medium (MMTCs, 4–9 sequences) and large (LMTCs, ≥10 sequences). Among 3499 drug-naïve individuals enrolled in the Italian Cohort Naive Antiretroviral (ICONA) cohort (2804 natives; 695 migrants), 726 (20.8%; 644 natives, 82 migrants) were involved in 228 MTCs (6 LMTCs, 36 MMTCs, 186 SMTCs). Migrants contributed 14.4% to SMTCs, 7.6% to MMTCs and 7.1% to LMTCs, respectively. HIV-1 non-B subtypes were found in 51 MTCs; noteworthy was that non-B infections involved in MTCs were more commonly found in natives (n = 47) than in migrants (n = 4). Factors such as Italian origin, being men who have sex with men (MSM), younger age, more recent diagnosis and a higher CD4 count were significantly associated with MTCs. Our findings show that HIV-1 clustering transmission among newly diagnosed individuals living in Italy is prevalently driven by natives, mainly MSM, with a more recent diagnosis and frequently infected with HIV-1 non-B subtypes. These results can contribute to monitoring of the HIV epidemic and guiding the public health response to prevent new HIV infections.

Molecular Epidemiology of the HIV-1 Subtype B Sub-Epidemic in Bulgaria

HIV-1 subtype B is the predominant strain in Bulgaria, yet little is known about the molecular epidemiology of these infections, including its origin and transmissibility. We used a phylodynamics approach by combining and analyzing 663 HIV-1 polymerase (pol) sequences collected from persons diagnosed with HIV/AIDS between 1988-2018 and associated epidemiologic data to better understand this sub-epidemic in Bulgaria. Using network analyses at a 1.5% genetic distance threshold (d) we found several large phylogenetic clusters composed mostly of men who have sex with men (MSM) and male heterosexuals (HET). However, at d = 0.5%, used to identify more recent transmission, the largest clusters dissociated to become smaller in size. The majority of female HET and persons with other transmission risks were singletons or pairs in the network. Phylogenetic analysis of the Bulgarian pol sequences with publicly available global sequences showed that subtype B was likely introduced into Bulgaria from multiple countries, including Israel and several European countries. Our findings indicate that subtype B was introduced into Bulgaria multiple times since 1988 and then infections rapidly spread among MSM and non-disclosed MSM. These high-risk behaviors continue to spread subtype B infection in Bulgaria as evidenced by the large clusters at d = 0.5%. Relatively low levels of antiretroviral drug resistance were observed in our study. Prevention strategies should continue to include increased testing and linkage to care and treatment, as well as expanded outreach to the MSM communities.

Incorporation of information diffusion model for enhancing analyses in HIV molecular surveillance

Molecular surveillance of infections is essential in monitoring their transmission in the population. In this study, newly diagnosed HIV patients' phylogenetic, clinical and behavioural data were integrated, and an information diffusion model was incorporated in analysing transmission dynamics. A genetic network was constructed from HIV sequences, from which transmission cascades were extracted. From the transmission cascades, CRF01_AE had higher values of information diffusion metrics, including scale, speed and range, than that of B, signifying the distinct transmission patterns of two circulating subtypes in Hong Kong. Patients connected in the network, were more likely male, younger, of main circulating subtypes, to have acquired HIV infection locally, and a higher CD4 level at diagnosis. Genetic connections varied among men who have sex with men (MSM) who used different channels of sex networking and varied in their engagement in risk behaviours. MSM using recreational drugs for sex held positions of greater importance within the network. Significant differences in network metrics were observed among MSM as differentiated by their mobile apps usage patterns, evidencing the impact of social network on transmission networks. The applied model in the presence of consistently collected longitudinal data could enhance HIV molecular epidemiologic surveillance for informing future intervention planning.

Leveraging Phylogenetics to Understand HIV Transmission and Partner Notification Networks

BACKGROUND

Partner notification is an important component of public health test and treat interventions. To enhance this essential function, we assessed the potential for molecular methods to supplement routine partner notification and corroborate HIV networks.

METHODS

All persons diagnosed with HIV infection in Wake County, NC, during 2012-2013 and their disclosed sexual partners were included in a sexual network. A data set containing HIV-1 pol sequences collected in NC during 1997-2014 from 15,246 persons was matched to HIV-positive persons in the network and used to identify putative transmission clusters. Both networks were compared.

RESULTS

The partner notification network comprised 280 index cases and 383 sexual partners and high-risk social contacts (n = 131 HIV-positive). Of the 411 HIV-positive persons in the partner notification network, 181 (44%) did not match to a HIV sequence, 61 (15%) had sequences but were not identified in a transmission cluster, and 169 (41%) were identified in a transmission cluster. More than half (59%) of transmission clusters bridged sexual network partnerships that were not recognized in the partner notification; most of these clusters were dominated by men who have sex with men.

CONCLUSIONS

Partner notification and HIV sequence analysis provide complementary representations of the existent partnerships underlying the HIV transmission network. The partner notification network components were bridged by transmission clusters, particularly among components dominated by men who have sex with men. Supplementing the partner notification network with phylogenetic data highlighted avenues for intervention.

A Short-Term Assessment of Nascent HIV-1 Transmission Clusters Among Newly Diagnosed Individuals Using Envelope Sequence-Based Phylogenetic Analyses

The identification of transmission clusters (TCs) of HIV-1 using phylogenetic analyses can provide insights into viral transmission network and help improve prevention strategies. We compared the use of partial HIV-1 envelope fragment of 1,070 bp with its loop 3 (108 bp) to determine its utility in inferring HIV-1 transmission clustering. Serum samples of recently (n = 106) and chronically (n = 156) HIV-1-infected patients with status confirmed were sequenced. HIV-1 envelope nucleotide-based phylogenetic analyses were used to infer HIV-1 TCs. Those were constructed using ClusterPickerGUI_1.2.3 considering a pairwise genetic distance of ≤10% threshold. Logistic regression analyses were used to examine the relationship between the demographic factors that were likely associated with HIV-1 clustering. Ninety-eight distinct consensus envelope sequences were subjected to phylogenetic analyses. Using a partial envelope fragment sequence, 42 sequences were grouped into 15 distinct small TCs while the V3 loop reproduces 10 clusters. The agreement between the partial envelope and the V3 loop fragments was significantly moderate with a Cohen's kappa (κ) coefficient of 0.59, p < .00001. The mean age (<38.8 years) and HIV-1 B subtype are two factors identified that were significantly associated with HIV-1 transmission clustering in the cohort, odds ratio (OR) = 0.25, 95% confidence interval (CI, 0.04–0.66), p = .002 and OR: 0.17, 95% CI (0.10–0.61), p = .011, respectively. The present study confirms that a partial fragment of the HIV-1 envelope sequence is a better predictor of transmission clustering. However, the loop 3 segment may be useful in screening purposes and may be more amenable to integration in surveillance programs.

Drivers of HIV-1 transmission: The Portuguese case

Background

Portugal has one of the most severe HIV-1 epidemics in Western Europe. Two subtypes circulate in parallel since the beginning of the epidemic. Comparing their transmission patterns and its association with transmitted drug resistance (TDR) is important to pinpoint transmission hotspots and to develop evidence-based treatment guidelines.

Methods

Demographic, clinical and genomic data were collected from 3599 HIV-1 naive patients between 2001 and 2014. Sequences obtained from drug resistance testing were used for subtyping, TDR determination and transmission clusters (TC) analyses.

Results

In Portugal, transmission of subtype B was significantly associated with young males, while transmission of subtype G was associated with older heterosexuals. In Portuguese originated people, there was a decreasing trend both for prevalence of subtype G and for number of TCs in this subtype. The active TCs that were identified (i.e. clusters originated after 2008) were associated with subtype B-infected males residing in Lisbon. TDR was significantly different when comparing subtypes B (10.8% [9.5–12.2]) and G (7.6% [6.4–9.0]) (p = 0.001).

Discussion

TC analyses shows that, in Portugal, the subtype B epidemic is active and fueled by young male patients residing in Lisbon, while transmission of subtype G is decreasing. Despite similar treatment rates for both subtypes in Portugal, TDR is significantly different between subtypes.

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.

Comparative analysis of HIV sequences in real time for public health

PURPOSE OF REVIEW

The purpose of this study is to summarize recent advances in public health applications of comparative methods for HIV-1 sequence analysis in real time, including genetic clustering methods.

RECENT FINDINGS

Over the past 2 years, several groups have reported the deployment of established genetic clustering methods to guide public health decisions for HIV prevention in 'near real time'. However, it remains unresolved how well the readouts of comparative methods like clusters translate to events that are actionable for public health. A small number of recent studies have begun to elucidate the linkage between clusters and HIV-1 incidence, whereas others continue to refine and develop new comparative methods for such applications.

SUMMARY

Although the use of established methods to cluster HIV-1 sequence databases has become a widespread activity, there remains a critical gap between clusters and public health value.

Integration of Contact Tracing and Phylogenetics in an Investigation of Acute HIV Infection

BACKGROUND

The integration of traditional contact tracing with HIV sequence analyses offers opportunities to mitigate some of the barriers to effective network construction. We used combined analyses during an outbreak investigation of spatiotemporally clustered acute HIV infections to evaluate if the observed clustering was the product of a single outbreak.

METHODS

We investigated acute and recent HIV index cases reported in North Carolina from 2013 to 2014 and their reported contacts. Contact tracing networks were constructed with surveillance data and compared with phylogenetic transmission clusters involving an index case using available HIV-1 pol sequences including 1672 references. Clusters were defined as clades of 2 or more sequences with a less than 1.5% genetic distance and a bootstrap of at least 98% on maximum-likelihood phylogenies.

RESULTS

In total, 68 index cases and 210 contacts (71 HIV infected) were reported. The contact tracing network involved 58 components with low overall density (1.2% statewide); 33% of first-degree contacts could not be located. Among 38 (56%) of 68 index cases and 34 (48%) of 71 contacts with sequences, 13 phylogenetic clusters were identified (size 2-4 members). Four clusters connected network components that were not linked in contact tracing. The largest component (n = 28 cases) included 2 distinct phylogenetic clusters and spanned 2 regions.

CONCLUSIONS

We identified the concurrent expansion of multiple small transmission clusters rather than a single outbreak in a largely disconnected contact tracing network. Integration of phylogenetic analyses provided timely information on transmission networks during the investigation. Our findings highlight the potential of combined methods to better identify high-risk networks for intervention.

Assessing the role of transmission chains in the spread of HIV-1 among men who have sex with men in Quebec, Canada

BACKGROUND

Phylogenetics has been used to investigate HIV transmission among men who have sex with men. This study compares several methodologies to elucidate the role of transmission chains in the dynamics of HIV spread in Quebec, Canada.

METHODS

The Quebec Human Immunodeficiency Virus (HIV) genotyping program database now includes viral sequences from close to 4,000 HIV-positive individuals classified as Men who have Sex with Men (MSMs), collected between 1996 and early 2016. Assessment of chain expansion may depend on the partitioning scheme used, and so, we produce estimates from several methods: the conventional Bayesian and maximum likelihood-bootstrap methods, in combination with a variety of schemes for applying a maximum distance criterion, and two other algorithms, DM-PhyClus, a Bayesian algorithm that produces a measure of uncertainty for proposed partitions, and the Gap Procedure, a fast non-phylogenetic approach. Sequences obtained from individuals in the Primary HIV Infection (PHI) stage serve to identify incident cases. We focus on the period ranging from January 1st 2012 to February 1st 2016.

RESULTS AND CONCLUSION

The analyses reveal considerable overlap between chain estimates obtained from conventional methods, thus leading to similar estimates of recent temporal expansion. The Gap Procedure and DM-PhyClus suggest however moderately different chains. Nevertheless, all estimates stress that longer older chains are responsible for a sizeable proportion of the sampled incident cases among MSMs. Curbing the HIV epidemic will require strategies aimed specifically at preventing such growth.

Exploring Evolutionary and Transmission Dynamics of HIV Epidemic in Serbia: Bridging Socio-Demographic With Phylogenetic Approach

Previous molecular studies of Serbian HIV epidemic identified the dominance of subtype B and presence of clusters related HIV-1 transmission, in particular among men who have sex with men (MSM). In order to get a deeper understanding of the complexities of HIV sub-epidemics in Serbia, epidemic trends, temporal origin and phylodynamic characteristics in general population and subpopulations were analyzed by means of mathematical modeling, phylogenetic analysis and latent class analysis (LCA). Fitting of the logistic curve of trends for a cumulative annual number of new HIV cases in 1984–2016, in general population and MSM transmission group, was performed. Both datasets fitted the logistic growth model, showing the early exponential phase of the growth curve. According to the suggested model, in the year 2030, the number of newly diagnosed HIV cases in Serbia will continue to grow, in particular in the MSM transmission group. Further, a detailed phylogenetic analysis was performed on 385 sequences from the period 1997–2015. Identification of transmission clusters, estimation of population growth (Ne), of the effective reproductive number (Re) and time of the most recent common ancestor (tMRCA) were estimated employing Bayesian and maximum likelihood methods. A substantial proportion of 53% of subtype B sequences was found within transmission clusters/network. Phylodynamic analysis revealed Re over one during the whole period investigated, with the steepest slopes and a recent tMRCA for MSM transmission group subtype B clades, in line with a growing trend in the number of transmissions in years approaching the end of the study period. Contrary, heterosexual clades in both studied subtypes – B and C – showed modest growth and stagnation. LCA analysis identified five latent classes, with transmission clusters dominantly present in 2/5 classes, linked to MSM transmission living in the capital city and with the high prevalence of co-infection with HBV and/or other STIs.Presented findings imply that HIV epidemic in Serbia is still in the exponential growth phase, in particular, related to the MSM transmission, with estimated steep growth curve until 2030. The obtained results imply that an average new HIV patient in Serbia is a young man with concomitant sexually transmitted infection.

Insights on transmission of HIV from phylogenetic analysis to locally optimize HIV prevention strategies

PURPOSE OF REVIEW

Phylogenetic analysis can identify transmission networks by clustering genetically related HIV genotypes that are routinely collected. In this study, we will review phylogenetic insights gained on transmission of HIV and phylogenetically optimized HIV prevention strategies.

RECENT FINDINGS

Phylogenetic analysis reports that HIV transmission varies by geographical region and by route of transmission. In high-income countries, HIV is predominantly transmitted between recently infected MSM who live in the same country. In rural Uganda, transmission of HIV is frequently between different communities. Age-discrepant transmission has been reported across the world. Four studies have used phylogenetic optimization of HIV prevention. Three studies predict that immediate treatment after diagnosis would have prevented 19-42% of infections, and that preexposure prophylaxis would have prevented 66% of infections. One phylogenetic study guided a public health response to an actively ongoing HIV outbreak. Phylogenetic clustering requires a dense sample of patients and small time-gaps between infection and diagnosis.

SUMMARY

Phylogenetic analysis can be an important tool to identify a local strategy that prevents most infections. Future studies that use phylogenetic analysis for optimizing HIV prevention strategies should also include cost-effectiveness so that the most cost-effective prevention method is identified.

Social Networks of Substance-Using Populations: Key Issues and Promising New Approaches for HIV

PURPOSE OF REVIEW

This paper presents recent literature on substance using networks and HIV, highlighting renewed and emerging themes in the field. The goal is to draw attention to research that holds considerable promise for advancing our understanding of the role of networks in shaping behaviors, while also providing critical information for the development of interventions, programs, and policies to reduce HIV and other drug-related harms.

RECENT FINDINGS

Recent research advances our understanding of networks and HIV, including among understudied populations, and provides new insight into how risk environments shape the networks and health of substance-using populations. In particular, the integration of network approaches with molecular epidemiology, research on space and place, and intervention methods provides exciting new avenues of investigation. Continued advances in network research are critical to supporting the health and rights of substance-using populations and ensuring the development of high-impact HIV programs and policies.

Experts' Perspectives on Key Ethical Issues Associated With HIV Phylogenetics as Applied in HIV Transmission Dynamics Research

The use of phylogenetics in HIV molecular epidemiology has considerably increased our ability to understand the origin, spread, and characteristics of HIV epidemics. Despite its potential to advance knowledge on HIV transmission dynamics, the ethical issues associated with HIV molecular epidemiology have received minimal attention. In-depth interviews were conducted with scientists from diverse backgrounds to explore their perspectives on ethical issues associated with phylogenetic analysis of HIV genetic data as applied to HIV transmission dynamics studies. The Emanuel framework was used as the analytical framework. Favorable risk-benefit ratio and informed consent were the most invoked ethical principles and fair participant selection the least. Fear of loss of privacy and disclosure of HIV transmission were invariably cited as key ethical concerns. As HIV sequence data become increasingly available, comprehensive guidelines should be developed to guide its access, sharing and use, cognizant of the potential harms that may result.

Transmission dynamics among participants initiating antiretroviral therapy upon diagnosis of early acute HIV-1 infection in Thailand

OBJECTIVE

To assess transmission characteristics in a predominantly MSM cohort initiating antiretroviral therapy (ART) immediately following diagnosis of acute HIV-1infection (AHI).

METHODS

A longitudinal study (2009-2017) was performed in participants with AHI (n = 439) attending a single clinic in Bangkok. Plasma samples obtained prior to ART were used to obtain HIV-1 pol sequences and combined with clinical and epidemiologic data to assess transmission dynamics (cluster formation and size) using phylogenetic analysis. Clusters were estimated using maximum likelihood, genetic distance of 1.5% and visual inspection. The potential transmitter(s) in a cluster was determined using time to viral suppression and interview data.

RESULTS

The cohort was predominantly MSM (93%) and infected with HIV-1 CRF01_AE (87%). Medians (ranges) for age and viral load prior to ART were 26 (18-70) years and 5.9 (2.5-8.2) log10 HIV-1 RNA copies/ml. Median time from history of HIV-1 exposure to diagnosis was 19 (3-61) days. Viral suppression was observed in 388 of 412 (94%) participants at a median time of 12 weeks following ART. Twenty-six clusters with median cluster size of 2 (2-5) representing 62 of 439 (14%) participants were observed. Younger age was associated with cluster formation: median 28 versus 30 years for unique infections (P = 0.01). A potential transmitter was identified in 11 of 26 (42%) clusters.

CONCLUSION

Despite high rates of viral suppression following diagnosis and treatment of AHI within a cohort of young Thai MSM, HIV-1 transmission continued, reflecting the need to expand awareness and treatment access to the entire MSM population.

New Challenges in HIV Research: Combining Phylogenetic Cluster Size and Epidemiological Data

An exciting new direction in HIV research is centered on using molecular phylogenetics to understand the social and behavioral drivers of HIV transmission. SPOT was an intervention designed to offer HIV point of care testing to men who have sex with men at a community-based site in Montreal, Canada; at the time of testing, a research questionnaire was also deployed to collect data on socio-demographic and behavioral characteristics of participating men. The men taking part in SPOT could be viewed, from the research perspective, as having been recruited via a convenience sample. Among men who were found to be HIV positive, phylogenetic cluster size was measured using a large cohort of HIV-positive individuals in the province of Quebec. The cluster size is likely subject to under-estimation. In this paper, we use SPOT data to evaluate the association between HIV transmission cluster size and the number of sex partners for MSM, after adjusting for the SPOT sampling scheme and correcting for measurement error in cluster size by leveraging external data sources. The sampling weights for SPOT participants were calculated from another study of men who have sex with men in Montreal by fitting a weight-adjusted model, whereas measurement error was corrected using the simulation-extrapolation conditional on covariates approach.

DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference

Background

Conventional phylogenetic clustering approaches rely on arbitrary cutpoints applied a posteriori to phylogenetic estimates. Although in practice, Bayesian and bootstrap-based clustering tend to lead to similar estimates, they often produce conflicting measures of confidence in clusters. The current study proposes a new Bayesian phylogenetic clustering algorithm, which we refer to as DM-PhyClus (Dirichlet-Multinomial Phylogenetic Clustering), that identifies sets of sequences resulting from quick transmission chains, thus yielding easily-interpretable clusters, without using any ad hoc distance or confidence requirement.

Results

Simulations reveal that DM-PhyClus can outperform conventional clustering methods, as well as the Gap procedure, a pure distance-based algorithm, in terms of mean cluster recovery. We apply DM-PhyClus to a sample of real HIV-1 sequences, producing a set of clusters whose inference is in line with the conclusions of a previous thorough analysis.

Conclusions

DM-PhyClus, by eliminating the need for cutpoints and producing sensible inference for cluster configurations, can facilitate transmission cluster detection. Future efforts to reduce incidence of infectious diseases, like HIV-1, will need reliable estimates of transmission clusters. It follows that algorithms like DM-PhyClus could serve to better inform public health strategies.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2347-3) contains supplementary material, which is available to authorized users.

Tracing HIV-1 strains that imprint broadly neutralizing antibody responses

Understanding the determinants of broadly neutralizing antibody (bNAb) evolution is crucial for the development of bNAb-based HIV vaccines¹. Despite emerging information on cofactors that promote bNAb evolution in natural HIV-1 infections, in which the induction of bNAbs is genuinely rare², information on the impact of the infecting virus strain on determining the breadth and specificity of the antibody responses to HIV-1 is lacking. Here we analyse the influence of viral antigens in shaping antibody responses in humans. We call the ability of a virus strain to induce similar antibody responses across different hosts its antibody-imprinting capacity, which from an evolutionary biology perspective corresponds to the viral heritability of the antibody responses. Analysis of 53 measured parameters of HIV-1-binding and neutralizing antibody responses in a cohort of 303 HIV-1 transmission pairs (individuals who harboured highly related HIV-1 strains and were putative direct transmission partners or members of an HIV-1 transmission chain) revealed that the effect of the infecting virus on the outcome of the bNAb response is moderate in magnitude but highly significant. We introduce the concept of bNAb-imprinting viruses and provide evidence for the existence of such viruses in a systematic screening of our cohort. The bNAb-imprinting capacity can be substantial, as indicated by a transmission pair with highly similar HIV-1 antibody responses and strong bNAb activity. Identification of viruses that have bNAb-imprinting capacities and their characterization may thus provide the potential to develop lead immunogens.

Evolution of HIV-1 transmitted drug resistance in Italy in the 2007-2014 period: A weighted analysis

BACKGROUND

Recent studies suggest that transmitted drug resistance (TDR) may be decreasing in latest years, likely because of the reduced frequency of acquired resistance. However, specific risk factors, geographical areas and special HIV-infected populations may be disproportionally affected by TDR.

OBJECTIVES

Correlates of TDR and time trends were evaluated from 2007 to 2014.

STUDY DESIGN

We evaluated the genotypic results of 2155 naïve patients enrolled in the I.Co.N.A cohort at 23 clinical Centers in Italy between 2007 and 2014. A weighted analysis was performed to account for the patients enrolled in the cohort in each clinical Centre at each biennium (total number of patients: 3737).

RESULTS

Overall prevalence of TDR was 10.7%. Independent predictors of TDR were sexual risk factor (OR 2.315, p = 0.020) and non-Italian geographical origin (OR 1.57, p = 0.038). The weighted prevalence of TDR was 10.5% with a stable proportion over calendar years. Generally, TDR prevalence was numerically higher, although not significantly, in clinical Centers of metropolitan areas with more than 3 millions of residents as compared to others (11.3% vs. 9.2%). The difference in TDR prevalence between these Centers decreased in more recent years.

CONCLUSIONS

A stable frequency of TDR was observed during the most recent years in Italy, with opposite and converging trends in large metropolitan areas as compared to the rest of the country, suggesting a more homogeneous spread of TDR across the country in latest years. Concerns remain for sexual route of infection and non-Italian origin, reinforcing the need for specific prevention strategies prioritizing specific populations.

HIV-1 infection among crack cocaine users in a region far from the epicenter of the HIV epidemic in Brazil: Prevalence and molecular characteristics

Brazil has the largest cocaine market in South America, and crack cocaine use is closely associated with HIV-1 infection. This study investigated the prevalence, risk factors, and HIV-1 subtypes, including recombinant forms and mutations associated with drug resistance, among crack cocaine users in Central-West Brazil. We recruited 600 crack cocaine users admitted to a referral hospital in Goiânia for psychiatric disorders. The participants were interviewed; blood samples were collected for anti-HIV-1/2 serological screening. HIV-1 pol gene sequences (entire protease [PR] and partial reverse transcriptase [RT]) were obtained from plasma RNA. HIV-1 subtypes, recombinant viruses, transmitted drug resistance (TDR), and secondary drug resistance mutations were investigated. The median participant age was 30 years (range, 18-68 years); most were male, single, unemployed, and of mixed races. Among them, 2.8% (17/600) were HIV-1 positive: 2.2% of men (11/507) and 6.5% of women (6/93). The main predictors of HIV-1 seropositivity were a sexual partner with HIV infection, irregular condom use, and previous homelessness. HIV-1 pol sequences (12/17) indicated the predominance of subtype B (n = 7), followed by recombinant forms FPR/BRT (n = 1) and BPR/FRT (n = 2) and subtypes F1 (n = 1) and C (n = 1). TDR prevalence was 58.3% (7/12). Isolates from two participants showed mutations associated with resistance to nucleoside reverse transcriptase inhibitors (NRTI) only (M41L, T125C, T125F, M184V), while an isolate from one patient who had received antiretroviral therapy (ART) since 2008 had a mutation associated with resistance to non-NRTI (G190S). Five isolates had secondary mutations to protease inhibitors (K20M, L10V, L33I, A71T, A71V). In conclusion, the findings of HIV-1 circulation, TDR to NRTI, and secondary mutations to protease inhibitors in ART-naïve crack cocaine users support the importance of monitoring this population in regions far from the epicenter of the HIV epidemic.

An Adaptive Approach to Locating Mobile HIV Testing Services

BACKGROUND

Public health agencies suggest targeting "hotspots" to identify individuals with undetected HIV infection. However, definitions of hotspots vary. Little is known about how best to target mobile HIV testing resources.

METHODS

We conducted a computer-based tournament to compare the yield of 4 algorithms for mobile HIV testing. Over 180 rounds of play, the algorithms selected 1 of 3 hypothetical zones, each with unknown prevalence of undiagnosed HIV, in which to conduct a fixed number of HIV tests. The algorithms were: 1) Thompson Sampling, an adaptive Bayesian search strategy; 2) Explore-then-Exploit, a strategy that initially draws comparable samples from all zones and then devotes all remaining rounds of play to HIV testing in whichever zone produced the highest observed yield; 3) Retrospection, a strategy using only base prevalence information; and; 4) Clairvoyance, a benchmarking strategy that employs perfect information about HIV prevalence in each zone.

RESULTS

Over 250 tournament runs, Thompson Sampling outperformed Explore-then-Exploit 66% of the time, identifying 15% more cases. Thompson Sampling's superiority persisted in a variety of circumstances examined in the sensitivity analysis. Case detection rates using Thompson Sampling were, on average, within 90% of the benchmark established by Clairvoyance. Retrospection was consistently the poorest performer.

LIMITATIONS

We did not consider either selection bias (i.e., the correlation between infection status and the decision to obtain an HIV test) or the costs of relocation to another zone from one round of play to the next.

CONCLUSIONS

Adaptive methods like Thompson Sampling for mobile HIV testing are practical and effective, and may have advantages over other commonly used strategies.

HIV-1 strains belonging to large phylogenetic clusters show accelerated escape from integrase inhibitors in cell culture compared with viral isolates from singleton/small clusters

Objectives: Viral phylogenetics revealed two patterns of HIV-1 spread among MSM in Quebec. While most HIV-1 strains (n = 2011) were associated with singleton/small clusters (cluster size 1–4), 30 viral lineages formed large networks (cluster size 20–140), contributing to 42% of diagnoses between 2011 and 2015. Herein, tissue culture selections ascertained if large cluster lineages possessed higher replicative fitness than singleton/small cluster isolates, allowing for viral escape from integrase inhibitors.

Methods: Primary HIV-1 isolates from large 20+ cluster (n = 11) or singleton/small cluster (n = 6) networks were passagedin vitro in escalating concentrations of dolutegravir, elvitegravir and lamivudine for 24–36 weeks. Sanger and deep sequencing assessed genotypic changes under selective drug pressure.

Results: Large cluster HIV-1 isolates selected for resistance to dolutegravir, elvitegravir and lamivudine faster than HIV-1 strains forming small clusters. With dolutegravir, large cluster HIV-1 variants acquired solitary R263K (n = 7), S153Y (n = 1) or H51Y (n = 1) mutations as the dominant quasi-species within 8–12 weeks as compared with small cluster lineages where R263K (n = 1/6), S153Y (1/6) or WT species (4/6) were observed after 24 weeks. Interestingly, dolutegravir-associated mutations compromised viral replicative fitness, precluding escalations in concentrations beyond 5–10 nM. With elvitegravir, large cluster variants more rapidly acquired first mutations (T66I, A92G, N155H or S147G) by week 8 followed by sequential accumulation of multiple mutations leading to viral escape (>10 μM) by week 24.

Conclusions: Further studies are needed to understand virological features of large cluster viruses that may favour their transmissibility, replicative competence and potential to escape selective antiretroviral drug pressure.

Genotypic and Phylogenetic Insights on Prevention of the Spread of HIV-1 and Drug Resistance in "Real-World" Settings

HIV continues to spread among vulnerable heterosexual (HET), Men-having-Sex with Men (MSM) and intravenous drug user (IDU) populations, influenced by a complex array of biological, behavioral and societal factors. Phylogenetics analyses of large sequence datasets from national drug resistance testing programs reveal the evolutionary interrelationships of viral strains implicated in the dynamic spread of HIV in different regional settings. Viral phylogenetics can be combined with demographic and behavioral information to gain insights on epidemiological processes shaping transmission networks at the population-level. Drug resistance testing programs also reveal emergent mutational pathways leading to resistance to the 23 antiretroviral drugs used in HIV-1 management in low-, middle- and high-income settings. This article describes how genotypic and phylogenetic information from Quebec and elsewhere provide critical information on HIV transmission and resistance, Cumulative findings can be used to optimize public health strategies to tackle the challenges of HIV in “real-world” settings.

Factors Driving the HIV Epidemic in Southern Africa

The HIV pandemic has disproportionately impacted sub-Saharan Africa and Southern Africa in particular. The concurrent presence of overlapping epidemic drivers likely underpins how and why the HIV epidemic is so explosive in this region, with implications for understanding approaches to reduce transmission. In this review, we discuss the relative contribution and interaction between epidemic drivers in the Southern African context, including factors both distally and proximally associated with the likelihood and degree of exposure to HIV and factors that increase the probability of transmission when exposure occurs. In particular, we focus on young women as a key population in need of HIV prevention and highlight factors that increase their risk on several levels.

HIV-1 transmission networks in high risk fishing communities on the shores of Lake Victoria in Uganda: A phylogenetic and epidemiological approach

BACKGROUND

Fishing communities around Lake Victoria in sub-Saharan Africa have been characterised as a population at high risk of HIV-infection.

METHODS

Using data from a cohort of HIV-positive individuals aged 13-49 years, enrolled from 5 fishing communities on Lake Victoria between 2009-2011, we sought to identify factors contributing to the epidemic and to understand the underlying structure of HIV transmission networks. Clinical and socio-demographic data were combined with HIV-1 phylogenetic analyses. HIV-1 gag-p24 and env-gp-41 sub-genomic fragments were amplified and sequenced from 283 HIV-1-infected participants. Phylogenetic clusters with ≥2 highly related sequences were defined as transmission clusters. Logistic regression models were used to determine factors associated with clustering.

RESULTS

Altogether, 24% (n = 67/283) of HIV positive individuals with sequences fell within 34 phylogenetically distinct clusters in at least one gene region (either gag or env). Of these, 83% occurred either within households or within community; 8/34 (24%) occurred within household partnerships, and 20/34 (59%) within community. 7/12 couples (58%) within households clustered together. Individuals in clusters with potential recent transmission (11/34) were more likely to be younger 71% (15/21) versus 46% (21/46) in un-clustered individuals and had recently become resident in the community 67% (14/21) vs 48% (22/46). Four of 11 (36%) potential transmission clusters included incident-incident transmissions. Independently, clustering was less likely in HIV subtype D (adjusted Odds Ratio, aOR = 0.51 [95% CI 0.26-1.00]) than A and more likely in those living with an HIV-infected individual in the household (aOR = 6.30 [95% CI 3.40-11.68]).

CONCLUSIONS

A large proportion of HIV sexual transmissions occur within house-holds and within communities even in this key mobile population. The findings suggest localized HIV transmissions and hence a potential benefit for the test and treat approach even at a community level, coupled with intensified HIV counselling to identify early infections.

Implications for a policy of initiating antiretroviral therapy in people diagnosed with human immunodeficiency virus: the CAPRA research programme

Background

More than 100,000 people in the UK are living with a human immunodeficiency virus (HIV) infection. There are currently estimated to be around 4000 people newly infected in the UK per year, mostly men who have sex with men (MSM). It has become increasingly clear that antiretroviral therapy (ART) used to treat people infected with HIV also has a profound effect on infectivity. At the initiation of the programme, it was the policy in the UK to initiate ART in people when their cluster of differentiation 4 (CD4) count was approaching 350/µl.

Objectives

To assess what would be the effectiveness and cost-effectiveness of a policy of immediate initiation of ART at diagnosis among MSM, taking into account the potential reductions in new infections.

Design

We calibrated an individual-based model of HIV transmission, progression and the effect of ART in MSM, informed by a series of studies on sexual behaviour in relation to ART use and the transmission risk in people with viral suppression on ART, and by surveillance data collected by Public Health England.

Setting, participants and interventions

The series of studies used to inform the model included (1) the Antiretrovirals, Sexual Transmission Risk and Attitudes (ASTRA) study, a cross-sectional self-administered questionnaire study of people diagnosed with HIV attending eight HIV outpatient clinics in the UK (2011–12); (2) the Cognitive Impairment in People with HIV in the European Region (CIPHER) study, a study of levels of neurocognitive impairment in HIV-positive ASTRA participants and people from HIV clinics in Rome, Copenhagen and Minsk; (3) the Attitudes to, and Understanding of, Risk of Acquisition of HIV (AURAH) study, a cross-sectional self-administered questionnaire study of individuals who have not been diagnosed as HIV-positive attending 20 genitourinary medicine clinics across the UK (2013–14); (4) a substudy of sexual behaviour among individuals enrolled in an open-label multicentre international randomised trial (from 2013) of immediate versus deferred ART (to CD4 cell counts of 350/µl) in people with CD4 cell counts of > 500/µl [the Strategic Timing of Antiretroviral Therapy (START) trial]; and (5) Partners of People on ART: a new Evaluation of the Risks (PARTNER), an observational multicentre longitudinal study of HIV serodifferent heterosexual and MSM couples, in which the HIV-positive partner is on ART (2010–14).

Main outcome measures

The main outcome measures were the clinical effectiveness and cost-effectiveness of a policy of immediate initiation of ART at diagnosis.

Results

Based on data from studies (i)–(v), we estimated from our modelling work that increases in condomless sex (CLS) among MSM as a whole may explain the increase in HIV infection incidence in MSM epidemics over a time when ART coverage and viral suppression increased, demonstrating the limiting effects of non-condom use on the HIV epidemic among MSM. Accordingly, an increase in the overall proportion of MSM living with HIV who are virally suppressed on ART from the current level of < 60% to 90% without increases in CLS was required to achieve a reduction in the incidence of HIV among MSM to < 1 per 1000 person-years. The incremental cost-effectiveness ratio associated with the fourfold increase in levels of HIV testing and ART at diagnosis required to provide this increase from < 60% to 90% was £20,000 if we assumed continuation of current ART prices. However, this value falls to £3500 if we assume that ART prices will fall to 20% of their current cost as a result of the introduction of generic drugs. Therefore, our evaluation suggests that ART initiation at diagnosis is likely to be highly cost-effective in MSM at a population level, particularly accounting for future lower ART costs as generic drugs are used. The impact will be much greater if levels of HIV testing can be enhanced.

Limitations

It was necessary to make some assumptions beyond the available data in order to extrapolate cost-effectiveness through modelling.

Conclusions

Our findings suggest that ART initiation at diagnosis is likely to be cost-effective in MSM. Of note, after this programme of work was completed, results from the main START trial demonstrated benefit in ART initiation even in people with CD4 cell counts of > 500/µl, supporting ART initiation in people diagnosed with a HIV infection.

Future work

There is a need for future research into the means of increasing the frequency with which MSM test for HIV.

Funding

The National Institute for Health Research Programme Grants for Applied Research programme.

Genetic characterization of human immunodeficiency virus type 1 transmission in the Middle East and North Africa

BACKGROUND

The HIV-1 spread in the Middle East and North Africa (MENA) has not been previously characterised using the phylogenetic approach. The aim of the current study was to investigate the genetic diversity and domestic transmission of HIV-1 in the MENA.

METHODS

A total of 2036 HIV-1 sequences available in Genbank and collected in the MENA during 1988-2016 were used together with 715 HIV-1 reference sequences that were retrieved from Genbank based on genetic similarity with the MENA sequences. The REGA and COMET tools were used to determine HIV-1 subtypes and circulating recombinant forms. Maximum Likelihood and Bayesian phylogenetic analyses were used to identify and date HIV-1 transmission clusters.

RESULTS

At least 21 HIV-1 subtypes and recombinant forms were prevalent in the MENA. Subtype B was the most common variant (39%), followed by CRF35_AD (19%) and CRF02_AG (14%). The most common genetic region was pol, and 675 partial pol sequences (average of 1005 bp) were eligible for detailed phylogenetic analysis. Fifty-four percent of the MENA sequences formed HIV-1 transmission clusters. Whereas numerous clusters were country-specific, some clusters indicated transmission links between countries for subtypes B, C and CRF02_AG. This was more common in North Africa compared with the Middle East (p < 0.001). Recombinant forms had a larger proportion of clustering compared to pure subtypes (p < 0.001). The largest MENA clusters dated back to 1991 (an Algerian CRF06_cpx cluster of 43 sequences) and 2002 (a Tunisian CRF02_AG cluster of 48 sequences).

CONCLUSIONS

We found an extensive HIV-1 diversity in the MENA and a high proportion of sequences in transmission clusters. This study highlights the need for preventive measures in the MENA to limit HIV-1 spread in this region.

Treatment as Prevention: Characterization of Partner Infections in the HIV Prevention Trials Network 052 Trial

HIV Prevention Trials Network 052 demonstrated that antiretroviral therapy (ART) prevents HIV transmission in serodiscordant couples. HIV from index-partner pairs was analyzed to determine the genetic linkage status of partner infections. Forty-six infections were classified as linked, indicating that the index was the likely source of the partner's infection. Lack of viral suppression and higher index viral load were associated with linked infection. Eight linked infections were diagnosed after the index started ART: 4 near the time of ART initiation and 4 after ART failure. Linked infections were not observed when the index participant was stably suppressed on ART.

Defining HIV-1 transmission clusters based on sequence data

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

Transmitted drug resistance in patients with acute/recent HIV infection in Brazil

Introduction

The widespread use of antiretroviral therapy increased the transmission of antiretroviral resistant HIV strains. Antiretroviral therapy initiation during acute/recent HIV infection limits HIV reservoirs and improves immune response in HIV infected individuals. Transmitted drug resistance may jeopardize the early goals of early antiretroviral treatment among acute/recent HIV infected patients.

Methods

Patients with acute/recent HIV infection who underwent resistance test before antiretroviral treatment initiation were included in this analysis. HIV-1 sequences were obtained using an in house protease/reverse transcriptase genotyping assay. Transmitted drug resistance was identified according to the Stanford HIV Database for Transmitted Drug Resistance Mutations, based on WHO 2009 surveillance list, and HIV-1 subtyping according to Rega HIV-1 subtyping tool. Comparison between patients with and without transmitted drug resistance was made using Kruskal–Wallis and Chi-square tests.

Results

Forty-three patients were included, 13 with acute HIV infection and 30 with recent HIV infection. The overall transmitted drug resistance prevalence was 16.3% (95% confidence interval [CI]: 8.1–30.0%). The highest prevalence of resistance (11.6%, 95% CI: 8.1–24.5) was against non-nucleoside reverse transcriptase inhibitors, and K103N was the most frequently identified mutation.

Conclusions

The high prevalence of nonnucleoside reverse transcriptase inhibitors resistance indicates that efavirenz-based regimen without prior resistance testing is not ideal for acutely/recently HIV-infected individuals in our setting. In this context, the recent proposal of including integrase inhibitors as a first line regimen in Brazil could be an advantage for the treatment of newly HIV infected individuals. However, it also poses a new challenge, since integrase resistance test is not routinely performed for antiretroviral naive individuals. Further studies on transmitted drug resistance among acutely/recently HIV-infected are needed to inform the predictors of transmitted resistance and the antiretroviral therapy outcomes among these population.

A national study of the molecular epidemiology of HIV-1 in Australia 2005-2012

Introduction

Rates of new HIV-1 diagnoses are increasing in Australia, with evidence of an increasing proportion of non-B HIV-1 subtypes reflecting a growing impact of migration and travel. The present study aims to define HIV-1 subtype diversity patterns and investigate possible HIV-1 transmission networks within Australia.

Methods

The Australian Molecular Epidemiology Network (AMEN) HIV collaborating sites in Western Australia, South Australia, Victoria, Queensland and western Sydney (New South Wales), provided baseline HIV-1 partial pol sequence, age and gender information for 4,873 patients who had genotypes performed during 2005–2012. HIV-1 phylogenetic analyses utilised MEGA V6, with a stringent classification of transmission pairs or clusters (bootstrap ≥98%, genetic distance ≤1.5% from at least one other sequence in the cluster).

Results

HIV-1 subtype B represented 74.5% of the 4,873 sequences (WA 59%, SA 68.4%, w-Syd 73.8%, Vic 75.6%, Qld 82.1%), with similar proportion of transmission pairs and clusters found in the B and non-B cohorts (23% vs 24.5% of sequences, p = 0.3). Significantly more subtype B clusters were comprised of ≥3 sequences compared with non-B clusters (45.0% vs 24.0%, p = 0.021) and significantly more subtype B pairs and clusters were male-only (88% compared to 53% CRF01_AE and 17% subtype C clusters). Factors associated with being in a cluster of any size included; being sequenced in a more recent time period (p<0.001), being younger (p<0.001), being male (p = 0.023) and having a B subtype (p = 0.02). Being in a larger cluster (>3) was associated with being sequenced in a more recent time period (p = 0.05) and being male (p = 0.008).

Conclusion

This nationwide HIV-1 study of 4,873 patient sequences highlights the increased diversity of HIV-1 subtypes within the Australian epidemic, as well as differences in transmission networks associated with these HIV-1 subtypes. These findings provide epidemiological insights not readily available using standard surveillance methods and can inform the development of effective public health strategies in the current paradigm of HIV prevention in Australia.

Transmission fitness of drug-resistant HIV revealed in a surveillance system transmission network

Test-and-treat programs are central to the global control of HIV, but transmitted drug resistance threatens the effectiveness of these programs. HIV mutations conferring resistance to antiretroviral drugs reduce replicative fitness in vitro, but their effect on propagation in vivo is less understood. Here, we estimate transmission fitness of these mutations in antiretroviral-naïve populations in the U.S. National HIV Surveillance System by comparing their frequency of clustering in a genetic transmission network relative with wild-type viruses. The large dataset (66,221 persons), comprising 30,196 antiretroviral-naïve persons, permitted the evaluation of sixty-nine resistance mutations. Decreased transmission fitness was demonstrated for twenty-three mutations, including M184V. In contrast, many high prevalence mutations (e.g. K103N, Y181C, and L90M) had transmission fitness that was indistinguishable from or exceeded wild-type fitness, permitting the establishment of large, self-sustaining drug resistance reservoirs. We highlight implications of these findings on strategies to preserve global treatment effectiveness.

The multi-faceted dynamics of HIV-1 transmission in Northern Alberta: A combined analysis of virus genetic and public health data

Molecular epidemiology has become a key tool for tracking infectious disease epidemics. Here, the spread of the most prevalent HIV-1 subtypes in Northern Alberta, Canada, was characterized with a Bayesian phylogenetic approach using 1146 HIV-1 pol sequences collected between 2007 and 2013 for routine clinical management purposes. Available patient metadata were qualitatively interpreted and correlated with onwards transmission using Fisher exact tests and logistic regression. Most infections were from subtypes A (n=36), B (n=815) and C (n=211). Africa is the dominant origin location for subtypes A and C while the subtype B epidemic was seeded from the USA and Middle America and, from the early 1990s onwards, mostly by interprovincial spread. Subtypes A (77.8%) and C (74.0%) were usually heterosexually transmitted and circulate predominantly among Blacks (61.1% and 85% respectively). Subtype B was mostly found among Caucasians (48.6%) and First Nations (36.8%), and its modes of transmission were stratified by ethnic origin. Compared to subtypes A (5.6%) and C (3.8-10.0%), a larger portion of subtype B patients were found within putative provincial transmission networks (20.3-29.5%), and this almost doubled when focusing on nationwide transmission clusters (37.9-57.5%). No clear association between cluster membership and particular patient characteristics was found. This study reveals complex and multi-faceted transmission dynamics of the HIV-1 epidemic in this otherwise low HIV prevalence population in Northern Alberta, Canada. These findings can aid public health planning.

Correcting covariate-dependent measurement error with non-zero mean

There are many settings in which the distribution of error in a mismeasured covariate varies with the value of another covariate. Take, for example, the case of HIV phylogenetic cluster size, large values of which are an indication of rapid HIV transmission. Researchers wish to find behavioral correlates of HIV phylogenetic cluster size; however, the distribution of its measurement error depends on the correctly measured variable, HIV status, and does not have a mean of zero. Further, it is not feasible to obtain validation data or repeated measurements. We propose an extension of simulation-extrapolation, an estimation technique for bias reduction in the presence of measurement error that does not require validation data and can accommodate errors whose distribution depends on other, error-free covariates. The proposed extension performs well in simulation, typically exhibiting less bias and variability than either regression calibration or multiple imputation for measurement error. We apply the proposed method to data from the province of Quebec in Canada to examine the association between HIV phylogenetic cluster size and the number of reported sex partners. Copyright © 2017 John Wiley & Sons, Ltd.

Large cluster outbreaks sustain the HIV epidemic among MSM in Quebec

OBJECTIVE

HIV-1 epidemics among MSM remain unchecked despite advances in treatment and prevention paradigms. This study combined viral phylogenetic and behavioural risk data to better understand underlying factors governing the temporal growth of the HIV epidemic among MSM in Quebec (2002-2015).

METHODS

Phylogenetic analysis of pol sequences was used to deduce HIV-1 transmission dynamics (cluster size, size distribution and growth rate) in first genotypes of treatment-naïve MSM (2002-2015, n = 3901). Low sequence diversity of first genotypes (0-0.44% mixed base calls) was used as an indication of early-stage infection. Behavioural risk data were obtained from the Montreal rapid testing site and primary HIV-1-infection cohorts.

RESULTS

Phylogenetic analyses uncovered high proportion of clustering of new MSM infections. Overall, 27, 45, 48, 53 and 57% of first genotypes within one (singleton, n = 1359), 2-4 (n = 692), 5-9 (n = 367), 10-19 (n = 405) and 20+ (n = 1277) cluster size groups were early infections (<0.44% diversity). Thirty viruses within large 20+ clusters disproportionately fuelled the epidemic, representing 13, 25 and 42% of infections, first genotyped in 2004-2007 (n = 1314), 2008-2011 (n = 1356) and 2012-2015 (n = 1033), respectively. Of note, 35, 21 and 14% of MSM belonging to 20+, 2-19 and one (singleton) cluster groups were under 30 years of age, respectively. Half of persons seen at the rapid testing site (2009-2011, n = 1781) were untested in the prior year. Poor testing propensity was associated with fewer reported partnerships.

CONCLUSION

Addressing the heterogeneity in transmission dynamics among HIV-1-infected MSM populations may help guide testing, treatment and prevention strategies.

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSION

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

Longitudinal Trends in Western Australian HIV-1 Sequence Diversity and Viral Transmission Networks and Their Influence on Clinical Parameters: 2000-2014

We examined baseline HIV-1 protease and reverse transcriptase sequences and HIV clinical parameters from 1,021 consecutive patients (814 male, 207 female) through the Royal Perth Hospital HIV service to investigate HIV-1 subtype diversity and local phylogenetic networks from 2000 to 2014. HIV-1 subtype B virus sequences were demonstrated in 619 (61%) of cases, with increasing non-B HIV-1 subtypes from 23.2% (2000-2003) to 48% (2008-2011) and 43% (2012-2014) (p < 0.001), including the CRF01_AE subtype [6.6% (2000-2003) to 21.5% (2008-2011)] and HIV-1 C subtype [9.5% (2000-2003) to 20.2% (2008-2011)]. More HIV-1 B subtypes were assigned to phylogenetic clusters compared to non-B subtypes (34% vs. 18%; p < 0.001), with larger clusters identified (cluster size >2: 135/211; 64% vs. 13/69; 19%; p = 0.001), including one cluster of 53 HIV-1 B subtype sequences that evolved from 2008 to 2014. Non-B subtype HIV-1 was associated with lower baseline CD4 T cell count (p = 0.005) but not plasma HIV-1 RNA levels (p = 0.31), suggesting relatively delayed diagnosis. Baseline viral load was strongly associated with calendar time [mean 18,620 copies/ml in 2000-2003; 75,858 copies/ml in 2012-2014 (p < 0.001)], and was also associated with larger phylogenetic clusters (size >2) in adjusted analyses (p = 0.03). This study identifies a number of temporal trends over the past 15 years, including an increasing prevalence of non-B subtype HIV-1 that highlights the growing influence of migration and travel on the Australian HIV-1 epidemic and the associated increased role of heterosexual HIV-1 transmission in this context. At the same time, these data indicate that local transmission within predominantly male networks remains a challenging issue for HIV-1 prevention.

Phylogenetic Investigation of a Statewide HIV-1 Epidemic Reveals Ongoing and Active Transmission Networks Among Men Who Have Sex With Men

BACKGROUND

Molecular epidemiological evaluation of HIV-1 transmission networks can elucidate behavioral components of transmission that can be targets for intervention.

METHODS

We combined phylogenetic and statistical approaches using pol sequences from patients diagnosed between 2004 and 2011 at a large HIV center in Rhode Island, following 75% of the state's HIV population. Phylogenetic trees were constructed using maximum likelihood, and putative transmission clusters were evaluated using latent class analyses to determine association of cluster size with underlying demographic/behavioral characteristics. A logistic growth model was used to assess intracluster dynamics over time and predict "active" clusters that were more likely to harbor undiagnosed infections.

RESULTS

Of the 1166 HIV-1 subtype B sequences, 31% were distributed among 114 statistically supported, monophyletic clusters (range: 2-15 sequences/cluster). Sequences from men who have sex with men (MSM) formed 52% of clusters. Latent class analyses demonstrated that sequences from recently diagnosed (2008-2011) MSM with primary HIV infection (PHI) and other sexually transmitted infections (STIs) were more likely to form larger clusters (odds ratio: 1.62-11.25, P < 0.01). MSM in clusters were more likely to have anonymous partners and meet partners at sex clubs and pornographic stores. Four large clusters with 38 sequences (100% male, 89% MSM) had a high probability of harboring undiagnosed infections and included younger MSM with PHI and STIs.

CONCLUSIONS

In this first large-scale molecular epidemiological investigation of HIV-1 transmission in New England, sexual networks among recently diagnosed MSM with PHI and concomitant STIs contributed to the ongoing transmission. Characterization of transmission dynamics revealed actively growing clusters, which may be targets for intervention.

A Polyglot Approach to Bioinformatics Data Integration: A Phylogenetic Analysis of HIV-1

As sequencing technologies continue to drop in price and increase in throughput, new challenges emerge for the management and accessibility of genomic sequence data. We have developed a pipeline for facilitating the storage, retrieval, and subsequent analysis of molecular data, integrating both sequence and metadata. Taking a polyglot approach involving multiple languages, libraries, and persistence mechanisms, sequence data can be aggregated from publicly available and local repositories. Data are exposed in the form of a RESTful web service, formatted for easy querying, and retrieved for downstream analyses. As a proof of concept, we have developed a resource for annotated HIV-1 sequences. Phylogenetic analyses were conducted for >6,000 HIV-1 sequences revealing spatial and temporal factors influence the evolution of the individual genes uniquely. Nevertheless, signatures of origin can be extrapolated even despite increased globalization. The approach developed here can easily be customized for any species of interest.