Enhancing Bayesian risk prediction for epidemics using contact tracing

Contact tracing data collected from disease outbreaks has received relatively little attention in the epidemic modelling literature because it is thought to be unreliable: infection sources might be wrongly attributed, or data might be missing due to resource contraints in the questionnaire exercise. Nevertheless, these data might provide a rich source of information on disease transmission rate. This paper presents novel methodology for combining contact tracing data with rate-based contact network data to improve posterior precision, and therefore predictive accuracy. We present an advancement in Bayesian inference for epidemics that assimilates these data, and is robust to partial contact tracing. Using a simulation study based on the British poultry industry, we show how the presence of contact tracing data improves posterior predictive accuracy, and can directly inform a more effective control strategy.Comment: 40 pages, 9 figures. Submitted to Biostatistic

Value of Information: Sensitivity Analysis and Research Design in Bayesian Evidence Synthesis.

Suppose we have a Bayesian model that combines evidence from several different sources. We want to know which model parameters most affect the estimate or decision from the model, or which of the parameter uncertainties drive the decision uncertainty. Furthermore, we want to prioritize what further data should be collected. These questions can be addressed by Value of Information (VoI) analysis, in which we estimate expected reductions in loss from learning specific parameters or collecting data of a given design. We describe the theory and practice of VoI for Bayesian evidence synthesis, using and extending ideas from health economics, computer modeling and Bayesian design. The methods are general to a range of decision problems including point estimation and choices between discrete actions. We apply them to a model for estimating prevalence of HIV infection, combining indirect information from surveys, registers, and expert beliefs. This analysis shows which parameters contribute most of the uncertainty about each prevalence estimate, and the expected improvements in precision from specific amounts of additional data. These benefits can be traded with the costs of sampling to determine an optimal sample size. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement

Estimation of HIV burden through Bayesian evidence synthesis

Planning, implementation and evaluation of public health policies to control the human immunodeficiency virus (HIV) epidemic require regular monitoring of disease burden. This includes the proportion living with HIV, whether diagnosed or not, and the rate of new infections in the general population and in specific risk groups and regions. Estimation of these quantities is not straightforward: data informing them directly are not typically available, but a wealth of indirect information from surveillance systems and ad hoc studies can inform functions of these quantities. In this paper we show how the estimation problem can be successfully solved through a Bayesian evidence synthesis approach, relaxing the focus on "best available" data to which classical methods are typically restricted. This more comprehensive and flexible use of evidence has led to the adoption of our proposed approach as the official method to estimate HIV prevalence in the United Kingdom since 2005

Modeling of the HIV infection epidemic in the Netherlands: A multi-parameter evidence synthesis approach

Multi-parameter evidence synthesis (MPES) is receiving growing attention from the epidemiological community as a coherent and flexible analytical framework to accommodate a disparate body of evidence available to inform disease incidence and prevalence estimation. MPES is the statistical methodology adopted by the Health Protection Agency in the UK for its annual national assessment of the HIV epidemic, and is acknowledged by the World Health Organization and UNAIDS as a valuable technique for the estimation of adult HIV prevalence from surveillance data. This paper describes the results of utilizing a Bayesian MPES approach to model HIV prevalence in the Netherlands at the end of 2007, using an array of field data from different study designs on various population risk subgroups and with a varying degree of regional coverage. Auxiliary data and expert opinion were additionally incorporated to resolve issues arising from biased, insufficient or inconsistent evidence. This case study offers a demonstration of the ability of MPES to naturally integrate and critically reconcile disparate and heterogeneous sources of evidence, while producing reliable estimates of HIV prevalence used to support public health decision-making.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS488 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Bayesian evidence synthesis to estimate HIV prevalence in men who have sex with men in Poland at the end of 2009.

HIV spread in men who have sex with men (MSM) is an increasing problem in Poland. Despite the existence of a surveillance system, there is no direct evidence to allow estimation of HIV prevalence and the proportion undiagnosed in MSM. We extracted data on HIV and the MSM population in Poland, including case-based surveillance data, diagnostic testing prevalence data and behavioural data relating to self-reported prior diagnosis, stratified by age (⩽35, >35 years) and region (Mazowieckie including the capital city of Warsaw; other regions). They were integrated into one model based on a Bayesian evidence synthesis approach. The posterior distributions for HIV prevalence and the undiagnosed fraction were estimated by Markov Chain Monte Carlo methods. To improve the model fit we repeated the analysis, introducing bias parameters to account for potential lack of representativeness in data. By placing additional constraints on bias parameters we obtained precisely identified estimates. This family of models indicates a high undiagnosed fraction [68·3%, 95% credibility interval (CrI) 53·9-76·1] and overall low prevalence (2·3%, 95% CrI 1·4-4·1) of HIV in MSM. Additional data are necessary in order to produce more robust epidemiological estimates. More effort is urgently needed to ensure timely diagnosis of HIV in Poland