MRC Centre for Outbreak Analysis and Modelling, Department of infectious Disease Epidemiology, Imperial College London, UK.
Epidemics. 2009 Mar;1(1):21-34. doi: 10.1016/j.epidem.2008.09.001. Epub 2008 Nov 17.
This paper develops a statistical framework for a retrospective analysis for well-observed livestock epidemics during which intervention policies may conceal cases, thus potentially biasing naively derived parameter and final size estimates. We apply the methods to the 2001 foot and mouth epidemic (FMD) in Great Britain, during which a large number of farms (about 7500) were pre-emptively culled as part of the control effort without ever being diagnosed as being infected. We infer farm-level infectivity and susceptibility parameters, a distribution for the delay from infection to report, together with a time varying farm infectivity profile for farms. Hidden infections among proactively culled farms were accounted for using a data augmentation approach utilising reversible jump MCMC methods. Simulated epidemics derived using the parameter estimates obtained reproduced the 2001 epidemic well. Our analysis demonstrates that time-varying infectivity profiles fit the 2001 data better than naive assumptions of constant infectiousness. We estimate that around 210 (or 2.8%) of the farms proactively culled in the 2001 epidemic were infected. However, for the parameter estimated obtained, preliminary simulation results indicate that had contiguous culling not been applied in 2001, the epidemic might have been substantially larger.
本文提出了一种针对观察良好的家畜疫情进行回溯分析的统计框架，在这种情况下，干预政策可能会掩盖病例，从而潜在地偏向于从简单推导得出的参数和最终规模估计。我们将这些方法应用于 2001 年在英国发生的口蹄疫（FMD）疫情，在此期间，作为控制措施的一部分，大量农场（约 7500 个）被预防性扑杀，而这些农场从未被诊断出受到感染。我们推断了农场层面的感染性和易感性参数、从感染到报告的延迟分布，以及农场的时变感染性概况。通过利用可逆跳跃 MCMC 方法进行数据扩充，解决了预先扑杀农场中隐藏感染的问题。使用获得的参数估计值得出的模拟疫情很好地再现了 2001 年的疫情。我们的分析表明，时变感染性概况比简单假设的恒定传染性更符合 2001 年的数据。我们估计，在 2001 年被预防性扑杀的约 210 个（或 2.8%）农场受到了感染。然而，根据所获得的参数估计值，初步模拟结果表明，如果 2001 年没有连续扑杀，疫情可能会大得多。
