SimpactCyan 1.0: An Open-source Simulator for Individual-Based Models in HIV Epidemiology with R and Python Interfaces

Translating Risk Ratios, Baseline Incidence, and Proportions Diseased to Correlations and Chi-Squared Statistics: Simulation Epidemiology

Background In a population, when a disease is causing a symptom, the overall symptom incidence can be determined by proportions diseased, baseline symptom incidence, and risk ratios of developing the symptom due to the disease. There are various measures of association, including risk ratios. How risk ratios are linked to other measures of association, such as correlation coefficients and chi-squared statistics, has not been explicitly discussed. This study aims to demonstrate their connection via equations and simulations, assuming one disease causes symptoms. Methods The equations for correlation coefficients and chi-square statistics were rewritten using epidemiological measures: proportions diseased, baseline symptom incidence, and risk ratios. Simulations were conducted to test the accuracy of the equations. The baseline symptom incidence and the proportions diseased were assumed to be 0.05, 0.1, 0.2, 0.4, or 0.8. The risk ratios were assumed to be 0.5, 1, 2, 5, 10, and 25. Another disease that correlates with this disease was created (correlation = 0, 0.3, or 0.7). For each combination of symptom incidence, proportions diseased, risk ratios, and between-disease correlations, 10,000 subjects were simulated. The correlation coefficients and chi-squared statistics were approximated with epidemiologic measures and their interaction terms. R-squared was used to assess the importance of the epidemiologic measures. Results In the simulations, the overall symptom incidence, correlation coefficients, and chi-squared statistics between the disease and symptoms could be fully explained by the epidemiologic measures in the equations (R-squared = 1). When approximating correlation coefficients and chi-squared statistics with individual measures or their interaction terms, the importance of these measures depended on whether the at-risk incidence reached 1 or not. The numbers in the four cells in the contingency table predicted correlation coefficients, or chi-squared statistics, with different R-squared. Conclusion To our knowledge, this is the first study to translate the three epidemiologic measures (risk ratios, baseline symptom incidence, and proportions diseased) into correlation coefficients and chi-squared statistics. However, chi-squared statistics also depend on sample sizes. This study also provides a platform for developing teaching cases for students to investigate the causal relationship between diseases and symptoms or exposure and outcomes.

Comparison of two simulators for individual based models in HIV epidemiology in a population with HSV 2 in Yaoundé (Cameroon)

Model comparisons have been widely used to guide intervention strategies to control infectious diseases. Agreement between different models is crucial for providing robust evidence for policy-makers because differences in model properties can influence their predictions. In this study, we compared models implemented by two individual-based model simulators for HIV epidemiology in a heterosexual population with Herpes simplex virus type-2 (HSV-2). For each model simulator, we constructed four models, starting from a simplified basic model and stepwise including more model complexity. For the resulting eight models, the predictions of the impact of behavioural interventions on the HIV epidemic in Yaoundé-Cameroon were compared. The results show that differences in model assumptions and model complexity can influence the size of the predicted impact of the intervention, as well as the predicted qualitative behaviour of the HIV epidemic after the intervention. These differences in predictions of an intervention were also observed for two models that agreed in their predictions of the HIV epidemic in the absence of that intervention. Without additional data, it is impossible to determine which of these two models is the most reliable. These findings highlight the importance of making more data available for the calibration and validation of epidemiological models.

Influence of sexual risk behaviour and STI co-infection dynamics on the evolution of HIV set point viral load in MSM

HIV viral load (VL) is an important predictor of HIV progression and transmission. Anti-retroviral therapy (ART) has been reported to reduce HIV transmission by lowering VL. However, apart from this beneficial effect, increased levels of population mean set-point viral load (SPVL), an estimator for HIV virulence, have been observed in men who have sex with men (MSM) in the decade following the introduction of ART in The Netherlands. Several studies have been devoted to explain these counter-intuitive trends in SPVL. However, to our knowledge, none of these studies has investigated an explanation in which it arises as the result of a sexually transmitted infection (STI) co-factor in detail. In this study, we adapted an event-based, individual-based model to investigate how STI co-infection and sexual risk behaviour affect the evolution of HIV SPVL in MSM before and after the introduction of ART. The results suggest that sexual risk behaviour has an effect on SPVL and indicate that more data are needed to test the effect of STI co-factors on SPVL. Furthermore, the observed trends in SPVL cannot be explained by sexual risk behaviour and STI co-factors only. We recommend to develop mathematical models including also factors related to viral evolution as reported earlier in the literature. However, this requires more complex models, and the collection of more data for parameter estimation than what is currently available.

Agent-based evolving network modeling: a new simulation method for modeling low prevalence infectious diseases

Agent-based network modeling (ABNM) simulates each person at the individual-level as agents of the simulation, and uses network generation algorithms to generate the network of contacts between individuals. ABNM are suitable for simulating individual-level dynamics of infectious diseases, especially for diseases such as HIV that spread through close contacts within intricate contact networks. However, as ABNM simulates a scaled-version of the full population, consisting of all infected and susceptible persons, they are computationally infeasible for studying certain questions in low prevalence diseases such as HIV. We present a new simulation technique, agent-based evolving network modeling (ABENM), which includes a new network generation algorithm, Evolving Contact Network Algorithm (ECNA), for generating scale-free networks. ABENM simulates only infected persons and their immediate contacts at the individual-level as agents of the simulation, and uses the ECNA for generating the contact structures between these individuals. All other susceptible persons are modeled using a compartmental modeling structure. Thus, ABENM has a hybrid agent-based and compartmental modeling structure. The ECNA uses concepts from graph theory for generating scale-free networks. Multiple social networks, including sexual partnership networks and needle sharing networks among injecting drug-users, are known to follow a scale-free network structure. Numerical results comparing ABENM with ABNM estimations for disease trajectories of hypothetical diseases transmitted on scale-free contact networks are promising for application to low prevalence diseases.

Assessing the uncertainty around age-mixing patterns in HIV transmission inferred from phylogenetic trees

Understanding age-mixing patterns in Human Immunodeficiency Virus (HIV) transmission networks can enhance the design and implementation of HIV prevention strategies in sub-Saharan Africa. Due to ethical consideration, it is less likely possible to conduct a benchmark study to assess which sampling strategy, and sub-optimal sampling coverage which can yield best estimates for these patterns. We conducted a simulation study, using phylogenetic trees to infer estimates of age-mixing patterns in HIV transmission, through the computation of proportions of pairings between men and women, who were phylogenetically linked across different age groups (15-24 years, 25-39 years, and 40-49 years); and the means, and standard deviations of their age difference. We investigated also the uncertainty around these estimates as a function of the sampling coverage in four sampling strategies: when missing sequence data were missing completely at random (MCAR), and missing at random (MAR) with at most 30%-50%-70% of women in different age groups being in the sample. The results suggested that age-mixing patterns in HIV transmission can be unveiled from proportions of phylogenetic pairings between men and women across age groups; and the mean, and standard deviation of their age difference. A 55% sampling coverage was sufficient to provide the best values of estimates of age-mixing patterns in HIV transmission with MCAR scenario. But we should be cautious in interpreting proportions of men phylogenetically linked to women because they may be overestimated or underestimated, even at higher sampling coverage. The findings showed that, MCAR was the best sampling strategy. This means, it is advisable not to use sequence data collected in settings where we can find a systematic imbalance of age and gender to investigate age-mixing in HIV transmission. If not possible, ensure to take into consideration the imbalance in interpreting the results.