Estimation of the Basic Reproductive Number and Mean Serial Interval of a Novel Pathogen in a Small, Well-Observed Discrete Population.
Estimation of the Basic Reproductive Number and Mean Serial Interval of a Novel Pathogen in a Small, Well-Observed Discrete Population.
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DOI：
10.1371/journal.pone.0148061
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Riley S
中科院分区：
文献类型：
--
作者：
Wu KM;Riley S
准确评估一种新型人类病原体的传播性和连续间隔是公共卫生的优先事项，以便确定干预措施的时机和所需的力度。最近的理论工作集中在最大限度地利用大量人口中发病率增长的初始指数阶段的数据。我们用基本繁殖数R0和序列间隔平均值Tg来衡量代传性。首先，我们构建了一个模拟算法，用于从已知规模的小群体中产生的病例数据，其中R0和Tg也已知。然后，我们开发了一个推断模型，将这些病例数据的可能性作为R0和Tg的函数。该模型旨在捕获a)初始随机阶段序列区间分布的任何信号b)指数阶段的增长率c) R0和Tg的独特组合，该组合在小种群的易感部分被耗尽时产生特定形状的峰值发生率。广泛的重复模拟和参数估计显示，R0和Tg的单变量估计没有偏倚。我们还能同时估计R0和Tg。然而，准确的最终估计只能在疫情爆发后很久才能获得。特别是，在发病率高峰过去之前，双变量情况下的Tg估计相当不准确。在新发病原体爆发期间，可以实时同时估计基本繁殖数和平均序列间隔。在流行病开始时将这些方法反复应用于小规模疫情，将能够准确估计关键参数。
Accurately assessing the transmissibility and serial interval of a novel human pathogen is public health priority so that the timing and required strength of interventions may be determined. Recent theoretical work has focused on making best use of data from the initial exponential phase of growth of incidence in large populations. We measured generational transmissibility by the basic reproductive number R0 and the serial interval by its mean Tg. First, we constructed a simulation algorithm for case data arising from a small population of known size with R0 and Tg also known. We then developed an inferential model for the likelihood of these case data as a function of R0 and Tg. The model was designed to capture a) any signal of the serial interval distribution in the initial stochastic phase b) the growth rate of the exponential phase and c) the unique combination of R0 and Tg that generates a specific shape of peak incidence when the susceptible portion of a small population is depleted. Extensive repeat simulation and parameter estimation revealed no bias in univariate estimates of either R0 and Tg. We were also able to simultaneously estimate both R0 and Tg. However, accurate final estimates could be obtained only much later in the outbreak. In particular, estimates of Tg were considerably less accurate in the bivariate case until the peak of incidence had passed. The basic reproductive number and mean serial interval can be estimated simultaneously in real time during an outbreak of an emerging pathogen. Repeated application of these methods to small scale outbreaks at the start of an epidemic would permit accurate estimates of key parameters.