Complex Agent Networks explaining the HIV epidemic among homosexual men in Amsterdam

Simulating the evolution of the Human Immunodeficiency Virus (HIV) epidemic requires a detailed description of the population network, especially for small populations in which individuals can be represented in detail and accuracy. In this paper, we introduce the concept of a Complex Agent Network(CAN) to model the HIV epidemics by combining agent-based modelling and complex networks, in which agents represent individuals that have sexual interactions. The applicability of CANs is demonstrated by constructing and executing a detailed HIV epidemic model for men who have sex with men (MSM) in Amsterdam, including a distinction between steady and casual relationships. We focus on MSM contacts because they play an important role in HIV epidemics and have been tracked in Amsterdam for a long time. Our experiments show good correspondence between the historical data of the Amsterdam cohort and the simulation results.Comment: 21 pages, 4 figures, Mathematics and Computers in Simulation, added reference

Increasing risk behaviour can outweigh the benefits of antiretroviral drug treatment on the HIV incidence among men-having-sex-with-men in Amsterdam

Background: The transmission through contacts among MSM (men who have sex with men) is one of the dominating contributors to HIV prevalence in industrialized countries. In Amsterdam, the capital of the Netherlands, the MSM risk group has been traced for decades. This has motivated studies which provide detailed information about MSM's risk behavior statistically, psychologically and sociologically. Despite the era of potent antiretroviral therapy, the incidence of HIV among MSM increases. In the long term the contradictory effects of risk behavior and effective therapy are still poorly understood.Methods: Using a previously presented Complex Agent Network model, we describe steady and casual partnerships to predict the HIV spreading among MSM. Behavior-related parameters and values, inferred from studies on Amsterdam MSM, are fed into the model; we validate the model using historical yearly incidence data. Subsequently, we study scenarios to assess the contradictory effects of risk behavior and effective therapy, by varying corresponding values of parameters. Finally, we conduct quantitative analysis based on the resulting incidence data.R

Combination interventions for Hepatitis C and Cirrhosis reduction among people who inject drugs: An agent-based, networked population simulation experiment

Hepatitis C virus (HCV) infection is endemic in people who inject drugs (PWID), with prevalence estimates above 60 percent for PWID in the United States. Previous modeling studies suggest that direct acting antiviral (DAA) treatment can lower overall prevalence in this population, but treatment is often delayed until the onset of advanced liver disease (fibrosis stage 3 or later) due to cost. Lower cost interventions featuring syringe access (SA) and medically assisted treatment (MAT) for addiction are known to be less costly, but have shown mixed results in lowering HCV rates below current levels. Little is known about the potential synergistic effects of combining DAA and MAT treatment, and large-scale tests of combined interventions are rare. While simulation experiments can reveal likely long-term effects, most prior simulations have been performed on closed populations of model agents--a scenario quite different from the open, mobile populations known to most health agencies. This paper uses data from the Centers for Disease Control's National HIV Behavioral Surveillance project, IDU round 3, collected in New York City in 2012 by the New York City Department of Health and Mental Hygiene to parameterize simulations of open populations. Our results show that, in an open population, SA/MAT by itself has only small effects on HCV prevalence, while DAA treatment by itself can significantly lower both HCV and HCV-related advanced liver disease prevalence. More importantly, the simulation experiments suggest that cost effective synergistic combinations of the two strategies can dramatically reduce HCV incidence. We conclude that adopting SA/MAT implementations alongside DAA interventions can play a critical role in reducing the long-term consequences of ongoing infection

A decade of modelling research yields considerable evidence for the importance of concurrency: a response to Sawers and Stillwaggon

In their recent article, Sawers and Stillwaggon critique the "concurrency hypothesis" on a number of grounds. In this commentary, I focus on one thread of their argument, pertaining to the evidence derived from modelling work. Their analysis focused on the foundational papers of Morris and Kretzschmar; here, I explore the research that has been conducted since then, which Sawers and Stillwaggon leave out of their review. I explain the methodological limitations that kept progress on the topic slow at first, and the various forms of methodological development that were pursued to overcome these. I then highlight recent modelling work that addresses the various limitations Sawers and Stillwaggon outline in their article. Collectively, this line of research provides considerable support for the modelling aspects of the concurrency hypothesis, and renders their critique of the literature incomplete and obsolete. It also makes clear that their call for "an end (or at least a moratorium) to research on sexual behaviour in Africa" that pertains to concurrency is unjustified

Tuning the average path length of complex networks and its influence to the emergent dynamics of the majority-rule model

We show how appropriate rewiring with the aid of Metropolis Monte Carlo computational experiments can be exploited to create network topologies possessing prescribed values of the average path length (APL) while keeping the same connectivity degree and clustering coefficient distributions. Using the proposed rewiring rules we illustrate how the emergent dynamics of the celebrated majority-rule model are shaped by the distinct impact of the APL attesting the need for developing efficient algorithms for tuning such network characteristics.Comment: 10 figure

Determining the immune response in human immunodefficiency virus infection : HIV -1 diversity as tool for epidemic monitoring

The Human Immunodeficiency Virus type 1 (HIV-1) is characterized by extensive genetic diversity at the population level but also within a single infected individual. The swift capacity of the virus to generate extensive diversity within the human host played a central role in the origin of the disease and is also key for the current global proportions of the HIV-1 pandemic. The epidemic started in Africa with multiple zoonotic transmissions of simian immunodeficiency virus (SIV) to humans. This was followed by a period of diversification and adaptation to the human population that, enhanced by the high rates of mutation and recombination of the virus, allowed the emergence of a virus capable of efficient sexual transmission among humans. The spread of the human adapted virus is estimated to have initiated from late 1950s to the early 1960s from Africa to the rest of the world. The predominance of the subtype B HIV-1 virus in Western Europe suggests that this was the first subtype to be introduced in this region. The subtype diversity pattern of HIV-1 in Portugal resembles the ones found in Central Africa being far more complex than the viral diversity patterns observed in the rest of Western Europe highlighting the relevance of in detailed studies of the Portuguese HIV-1 epidemics. In this work we have characterized the local HIV-1 epidemic of the Portuguese city of Braga in the years from 2000 to 2012. We found that the most frequent HIV-1 subtypes were G and B and by combining epidemiological and phylogenetic analysis we were able to uncover local transmission clusters of non-B and non-G subtypes among locals in association with sexual transmission networks that initiated transmission in the early 2000s. This corroborates Portugal as an early point of introduction of non-B HIV-1 subtypes in Western Europe. Having performed this characterization at the level of this local population we then focused on analyzing the duration of infection at the level of the infected patient. For this purpose we have optimized a methodology to differentiate recent from chronic infections. It was based on the study of ambiguous nucleotide calls obtained from routine HIV-1 genotyping. We found that the analysis of these ambiguities, as an expression of intra-host HIV-1 diversity, allowed the inference of the duration of infection in this study population. Subsequently, we questioned if high HIV-1 subtype diversity found in this region correlated with higher rates of transmission of drug resistance mutations. We found that the level of transmitted drug resistance in this population was similar to other European regions and independent predictors of transmitted drug resistance (TDR) could not be identified supporting the recommendation of universal viral sequencing at patient admission. This study performed in a country that is unique in Western Europe in what regards to HIV-1 diversity supported Portugal as one of the early entry-points of non-B HIV-1 subtypes in Western Europe and also reinforced the need for more efficacious local control measures targeting sexual transmission routes. We believe this study is of general importance especially in a time when several reports suggest that the prevalence of non-B subtypes in Western Europe is increasing. The knowledge herein generated also contributed for the development of method to discriminate recent from non-recent HIV-1 infections, a step of crucial importance to validate prevention strategies. Importantly, it was also shown that the higher HIV-1 subtype diversity found in this study population does not correlate with an increase in the rate of transmission of drug resistance when compared to the rest of the Western Europe.O Vírus da Imunodeficiência Humana Tipo 1 (VIH-1) é caracterizado por uma extensa diversidade genética não só a nível da população, mas também a nível individual, em cada hospedeiro. A rapidez do vírus para gerar grande diversidade dentro do hospedeiro humano desempenhou um papel central na génese da doença e é também essencial para as proporções globais atuais da pandemia do VIH-1. A epidemia começou em África, com várias transmissões zoonóticas de vírus da imunodeficiência símia (SIV) para seres humanos. Isto foi seguido por um período de diversificação e adaptação na população humana que, amplificada pelas altas taxas de mutação e de recombinação do vírus, permitiu o surgimento de uma nova espécie de vírus capaz de transmissão sexual eficiente entre os seres humanos. O início da propagação deste vírus já adaptado ao ser humano é estimada a partir do final dos anos 1950 ao início dos anos 1960, da África Central para o resto do mundo. A predominância do subtipo B do VIH-1 na Europa Ocidental sugere que este foi o primeiro subtipo a ser introduzido nesta região. O padrão de diversidade dos subtipos do VIH-1 em Portugal assemelha-se ao encontrado na África Central, sendo muito mais complexo do que os padrões de diversidade vírica observados no resto da Europa Ocidental. Este facto justifica o relevo que estudos detalhados sobre o VIH-1 em Portugal possam ter para a compreensão das epidemias de VIH-1. Neste trabalho foi caracterizada a epidemia local por VIH-1 na cidade portuguesa de Braga, entre os anos 2000 e 2012. Descobrimos que os subtipos VIH-1 mais frequentes foram G e B. Pela combinação de análise epidemiológica e filogenética pudemos demonstrar grupos de transmissão locais de subtipos não-B e não-G entre os residentes em associação com redes de transmissão sexual que iniciaram a transmissão no início da década de 2000. Isto indicia o papel de Portugal como um ponto de início da introdução de subtipos não-B do VIH-1 na Europa Ocidental. Tendo realizado esta caracterização a nível da população local, o trabalho concentrou-se na análise da duração da infeção ao nível individual. Para este efeito, aperfeiçoou-se uma metodologia para diferenciar infeção recente de infeção crónica. Baseados no estudo de posições nucleotídicas ambíguas obtidas a partir de genotipagem rotineira doVIH-1,descobrimos que a análise dessas ambiguidades, como uma expressão da diversidade intra-hospedeiro do VIH-1, permite inferir a duração da infeção nesta população em estudo. Posteriormente questionamos se a elevada diversidade do VIH-1 encontrada nesta região se poderia correlacionar com maiores taxas de transmissão de mutações de resistência aos antiretrovíricos. Descobrimos que o nível de resistência à terapêutica transmitido nesta população foi semelhante a outras regiões europeias. Não foram identificados preditores independentes de resistência transmissível aos antiretrovíricos, suportando a recomendação de sequenciamento viral universal no momento do contacto do doente com os serviços de saúde. Este estudo realizado num país que é único na Europa Ocidental no que diz respeito à diversidade do VIH-1,validoua noção de Portugal como um dos pontos de entrada iniciais de subtipos não-B do VIH-1 na Europa Ocidental e também reforçou a necessidade de medidas locais de controlo mais eficazes, que visem modos de transmissão sexual. Acreditamos que este estudo é relevante, especialmente num tempo em que vários artigos sugerem que a prevalência de subtipos não-B na Europa Ocidental está a aumentar. O conhecimento aqui gerado também contribuiu para o desenvolvimento de um método para discriminar infeções recentes pelo HIV-1 das não-recentes, um passo de importância crucial para validar as estratégias de prevenção. Relevantemente, também foi demonstrado que à maior diversidade doVIH-1 encontrada na população em estudo, não correspondeu um aumento na taxa de transmissão de resistência à terapêutica, quando comparada com o resto da Europa Ocidental

The making of people living with HIV and AIDS: Identities, illness and social organisation in Rio de Janeiro, Brazil

This dissertation examines specific issues surrounding the experience of living with HIV and AIDS in Rio de Janeiro, Brazil. It focuses on the process of identity formation in relation to local forms of social organization within the context of the AIDS epidemic since the mid-1980s. These processes are closely associated with factors, such as sexuality, gender and illness. Based on a historical and ethnographic perspective, fieldwork was mostly carried out in the metropolitan area of Rio de Janeiro. To investigate the social world of AIDS, I visited AIDS non-governmental organizations (NGOs), gay activist groups, and clinical settings involved with AIDS treatments and care. As a case-study, I conducted ethnographic research in the Grupo Pela Vidda-Rio, the leading AIDS NGO in the State of Rio de Janeiro. The thesis is composed of nine chapters. The first and second chapters give an introduction to the main research topics, aims, fieldwork, selected methodologies and a critical overview of the studies on sexuality, identity and AIDS in Brazil. Chapter three discusses the discursive practices and the cultural representations produced by the Brazilian news media, which contributed to popularize dominant cultural conceptions of the epidemic, particularly a stigmatizing identity: the "aidetico". Chapter four articulates the idea of the AIDS epidemic as a health crisis, which emerged alongside other moral and social problems. I focus on the role of Brazilian AIDS public policy and health structures in the social reproduction and incorporation of sexual and clinical identities, namely, "seropositive" and "seronegative" identities. Chapter five deals with the different forms of civil mobilization and social organization that constitute the social world of AIDS in Rio de Janeiro in relation to national and global levels. The local influence of global discourses on "solidarity" is analysed in its links to particular models of identity construction, especially discourses on the cultural meanings of "people living with HIV and AIDS". Chapter six is an ethnographic case-study of the Grupo Pela Vidda-Rio, its activities, composition, ideological aims and historical changes. As a final step to understand the broad determinacy of processes of identity formation, chapters seven and eight give an ethnographic analysis of how a range of identities (gender, sexual, and clinical ones) can be socially and culturally performed in the specific social setting of Grupo Pela Vidda. The complex logic of sociability and the power of social hierarchies in the definition and incorporation of identities are largely discussed in these two chapters. My main contribution, therefore, is to give a better understanding of the constitutive tension between broad processes and specific contexts of identity formation. This tension is fueled by different organizational and ideological models at work within the particular social world of AIDS in Rio de Janeiro