Calmon Lucille, Colosi Elisabetta, Bassignana Giulia, Barrat Alain, Colizza Vittoria
Sorbonne Université, INSERM, Pierre-Louis Institute of Epidemiology and Public Health (IPLESP), Paris, France.
Aix Marseille Univ, Université de Toulon, CNRS, CPT, Turing Center for Living Systems, Marseille, France.
PLoS Comput Biol. 2024 Dec 9;20(12):e1012661. doi: 10.1371/journal.pcbi.1012661. eCollection 2024 Dec.
High-resolution temporal data on contacts between hosts provide crucial information on the mixing patterns underlying infectious disease transmission. Publicly available data sets of contact data are however typically recorded over short time windows with respect to the duration of an epidemic. To inform models of disease transmission, data are thus often repeated several times, yielding synthetic data covering long enough timescales. Looping over short term data to approximate contact patterns on longer timescales can lead to unrealistic transmission chains because of the deterministic repetition of all contacts, without any renewal of the contact partners of each individual between successive periods. Real contacts indeed include a combination of regularly repeated contacts (e.g., due to friendship relations) and of more casual ones. In this paper, we propose an algorithm to longitudinally extend contact data recorded in a school setting, taking into account this dual aspect of contacts and in particular the presence of repeated contacts due to friendships. To illustrate the interest of such an algorithm, we then simulate the spread of SARS-CoV-2 on our synthetic contacts using an agent-based model specific to the school setting. We compare the results with simulations performed on synthetic data extended with simpler algorithms to determine the impact of preserving friendships in the data extension method. Notably, the preservation of friendships does not strongly affect transmission routes between classes in the school but leads to different infection pathways between individual students. Our results moreover indicate that gathering contact data during two days in a population is sufficient to generate realistic synthetic contact sequences between individuals in that population on longer timescales. The proposed tool will allow modellers to leverage existing contact data, and contributes to the design of optimal future field data collection.
宿主之间接触的高分辨率时间数据为传染病传播背后的混合模式提供了关键信息。然而,就疫情持续时间而言,公开可用的接触数据通常是在短时间窗口内记录的。为了为疾病传播模型提供信息,数据因此常常被重复多次,从而产生覆盖足够长时间尺度的合成数据。由于所有接触都是确定性重复的,且在连续时间段内每个个体的接触伙伴没有任何更新,因此在短时间数据上循环以近似更长时间尺度上的接触模式可能会导致不切实际的传播链。实际接触确实包括定期重复接触(例如,由于友谊关系)和更偶然接触的组合。在本文中,我们提出了一种算法,考虑到接触的这种双重性质,特别是由于友谊而存在的重复接触,纵向扩展在学校环境中记录的接触数据。为了说明这种算法的意义,我们然后使用特定于学校环境的基于代理的模型,在我们的合成接触数据上模拟SARS-CoV-2的传播。我们将结果与使用更简单算法扩展的合成数据上进行的模拟进行比较,以确定在数据扩展方法中保留友谊的影响。值得注意的是,保留友谊对学校班级之间的传播途径影响不大,但会导致个体学生之间不同的感染途径。我们的结果还表明,在人群中两天内收集接触数据足以在更长时间尺度上生成该人群中个体之间现实的合成接触序列。所提出的工具将使建模者能够利用现有的接触数据,并有助于设计最佳的未来现场数据收集。