PopART-IBM, a highly efficient stochastic individual-based simulation model of generalised HIV epidemics developed in the context of the HPTN 071 (PopART) trial

SEEPS: A Simulation Tool for Understanding Impacts of Contact Tracing on Epidemiological Inference from Phylogenetic Data

Motivation

Robust sampling methods are foundational to inferences using phylogenies. Yet the impact of using contact tracing, a type of non-uniform sampling used in public health applications such as infectious disease outbreak investigations, is not well understood. To understand how this non-uniform sampling method influences a recovered phylogeny, a new simulation tool is needed.

Results

We developed a new simulation tool called SEEPS (Sequence Evolution and Epidemiological Process Simulator) that allows for the simulation of contact tracing and the resulting transmission tree, pathogen phylogeny, and corresponding virus genetic sequences. Importantly, SEEPS takes within-host evolution into account when generating pathogen phylogenies and sequences from transmission histories. Using SEEPS, we demonstrate that contact tracing can significantly impact the structure of the resulting tree, as described by popular tree statistics. We also examined real data from a 2007-2008 Swedish HIV-1 outbreak and the broader 1998-2010 European HIV-1 epidemic to highlight the differences in contact tracing and expected phylogenies. Aided by SEEPS, we show that the data collection of the Swedish outbreak was strongly influenced by contact tracing even after downsampling, while the broader European Union epidemic showed little evidence of universal contact tracing, agreeing with the known epidemiological information about sampling and spread. Overall, our results highlight the importance of including possible non-uniform sampling schemes when examining phylogenetic trees. For that, SEEPS serves as a useful tool to evaluate such impacts, thereby facilitating better phylogenetic inferences of the characteristics of a disease outbreak.

Availability

SEEPS is available at github.com/MolEvolEpid/SEEPS.

Demographics of sources of HIV-1 transmission in Zambia: a molecular epidemiology analysis in the HPTN 071 PopART study

BACKGROUND

In the last decade, universally available antiretroviral therapy (ART) has led to greatly improved health and survival of people living with HIV in sub-Saharan Africa, but new infections continue to appear. The design of effective prevention strategies requires the demographic characterisation of individuals acting as sources of infection, which is the aim of this study.

METHODS

Between 2014 and 2018, the HPTN 071 PopART study was conducted to quantify the public health benefits of ART. Viral samples from 7124 study participants in Zambia were deep-sequenced as part of HPTN 071-02 PopART Phylogenetics, an ancillary study. We used these sequences to identify likely transmission pairs. After demographic weighting of the recipients in these pairs to match the overall HIV-positive population, we analysed the demographic characteristics of the sources to better understand transmission in the general population.

FINDINGS

We identified a total of 300 likely transmission pairs. 178 (59·4%) were male to female, with 130 (95% CI 110-150; 43·3%) from males aged 25-40 years. Overall, men transmitted 2·09-fold (2·06-2·29) more infections per capita than women, a ratio peaking at 5·87 (2·78-15·8) in the 35-39 years source age group. 40 (26-57; 13·2%) transmissions linked individuals from different communities in the trial. Of 288 sources with recorded information on drug resistance mutations, 52 (38-69; 18·1%) carried viruses resistant to first-line ART.

INTERPRETATION

HIV-1 transmission in the HPTN 071 study communities comes from a wide range of age and sex groups, and there is no outsized contribution to new infections from importation or drug resistance mutations. Men aged 25-39 years, underserved by current treatment and prevention services, should be prioritised for HIV testing and ART.

FUNDING

National Institute of Allergy and Infectious Diseases, US President's Emergency Plan for AIDS Relief, International Initiative for Impact Evaluation, Bill & Melinda Gates Foundation, National Institute on Drug Abuse, and National Institute of Mental Health.

Strengthening the HIV prevention cascade to maximise epidemiological impact in eastern Zimbabwe: a modelling study

BACKGROUND

HIV prevention cascades provide a systematic understanding of barriers to prevention. In this study we used mathematical modelling to understand the consequences of these barriers and how the cascade could be strengthened to maximise epidemiological impact, providing potentially important insights for programmes.

METHODS

We used an individual-based model of HIV transmission (PopART-IBM), calibrated to data from the Manicaland cohort from eastern Zimbabwe. HIV prevention cascade estimates from this cohort were used as probabilities for indicators in the model representing an individual's motivation, access, and capacity to effectively use pre-exposure prophylaxis, voluntary male medical circumcision, and condoms. We examined how current barriers affect the number and distribution of HIV infections compared with a no-barrier scenario. Using assumptions about how interventions could strengthen the HIV prevention cascade, we estimated the reduction in HIV infections over a 10-year period through addressing different elements of the cascade.

FINDINGS

21 200 new potentially avertable HIV infections will occur over the next 10 years due to existing HIV prevention cascade barriers, 74·2% of the 28 500 new infections that would occur with existing barriers in a population of approximately 1·2 million adults. Removing these barriers would reduce HIV incidence below the benchmarks for epidemic elimination. Addressing all cascade steps in one priority population is substantially more effective than addressing one step across all populations.

INTERPRETATION

Interventions exist in eastern Zimbabwe to reduce HIV towards elimination, but barriers of motivation, access, and effective use prevent their full effect being realised. Interventions need to be multilayered and address all steps along the HIV prevention cascade. Models incorporating the HIV prevention cascade can help to identify the main barriers to greater effectiveness.

FUNDING

National Institutes of Mental Health, Bill & Melinda Gates Foundation, and Medical Research Council Centre for Global Infectious Disease Analysis funding from the UK Medical Research Council and UK Foreign, Commonwealth & Development Office (FCDO).

Projected outcomes of universal testing and treatment in a generalised HIV epidemic in Zambia and South Africa (the HPTN 071 [PopART] trial): a modelling study

BACKGROUND

The long-term impact of universal home-based testing and treatment as part of universal testing and treatment (UTT) on HIV incidence is unknown. We made projections using a detailed individual-based model of the effect of the intervention delivered in the HPTN 071 (PopART) cluster-randomised trial.

METHODS

In this modelling study, we fitted an individual-based model to the HIV epidemic and HIV care cascade in 21 high prevalence communities in Zambia and South Africa that were part of the PopART cluster-randomised trial (intervention period Nov 1, 2013, to Dec 31, 2017). The model represents coverage of home-based testing and counselling by age and sex, delivered as part of the trial, antiretroviral therapy (ART) uptake, and any changes in national guidelines on ART eligibility. In PopART, communities were randomly assigned to one of three arms: arm A received the full PopART intervention for all individuals who tested positive for HIV, arm B received the intervention with ART provided in accordance with national guidelines, and arm C received standard of care. We fitted the model to trial data twice using Approximate Bayesian Computation, once before data unblinding and then again after data unblinding. We compared projections of intervention impact with observed effects, and for four different scenarios of UTT up to Jan 1, 2030 in the study communities.

FINDINGS

Compared with standard of care, a 51% (95% credible interval 40-60) reduction in HIV incidence is projected if the trial intervention (arms A and B combined) is continued from 2020 to 2030, over and above a declining trend in HIV incidence under standard of care.

INTERPRETATION

A widespread and continued commitment to UTT via home-based testing and counselling can have a substantial effect on HIV incidence in high prevalence communities.

FUNDING

National Institute of Allergy and Infectious Diseases, US President's Emergency Plan for AIDS Relief, International Initiative for Impact Evaluation, Bill & Melinda Gates Foundation, National Institute on Drug Abuse, and National Institute of Mental Health.

Are Unequal Policies in Pre-Exposure Prophylaxis Uptake Needed to Improve Equality? An Examination Among Men Who Have Sex with Men in Los Angeles County

Racial and ethnic minority men who have sex with men (MSM) are disproportionately affected by HIV/AIDS in Los Angeles County (LAC), an important epicenter in the battle to end HIV. We examine tradeoffs between effectiveness and equality of pre-exposure prophylaxis (PrEP) allocation strategies among different racial and ethnic groups of MSM in LAC and provide a framework for quantitatively evaluating disparities in HIV outcomes. To do this, we developed a microsimulation model of HIV among MSM in LAC using county epidemic surveillance and survey data to capture demographic trends and subgroup-specific partnership patterns, disease progression, patterns of PrEP use, and patterns for viral suppression. We limit analysis to MSM, who bear most of the burden of HIV/AIDS in LAC. We simulated interventions where 3000, 6000, or 9000 PrEP prescriptions are provided annually in addition to current levels, following different allocation scenarios to each racial/ethnic group (Black, Hispanic, or White). We estimated cumulative infections averted and measures of equality, after 15 years (2021-2035), relative to base case (no intervention). By comparing allocation strategies on the health equality impact plane, we find that, of the policies evaluated, targeting PrEP preferentially to Black individuals would result in the largest reductions in incidence and disparities across the equality measures we considered. This result was consistent over a range of PrEP coverage levels, demonstrating that there are "win-win" PrEP allocation strategies that do not require a tradeoff between equality and efficiency.