Preserving friendships in school contacts: An algorithm to construct synthetic temporal networks for epidemic modelling

被引:2
作者
Calmon, Lucille [1 ]
Colosi, Elisabetta [1 ,4 ]
Bassignana, Giulia [1 ]
Barrat, Alain [2 ]
Colizza, Vittoria [1 ,3 ]
机构
[1] Sorbonne Univ, Pierre Louis Inst Epidemiol & Publ Hlth IPLESP, INSERM, Paris, France
[2] Aix Marseille Univ, Univ Toulon, Turing Ctr Living Syst, CPT,CNRS, Marseille, France
[3] Georgetown Univ, Dept Biol, Washington, DC 20057 USA
[4] Bocconi Univ, Dondena Ctr Res Social Dynam & Publ Policy, Milan, Italy
基金
欧盟地平线“2020”;
关键词
SPREAD;
D O I
10.1371/journal.pcbi.1012661
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页数:20
相关论文
共 56 条
[1]  
[Anonymous], 2024, nx.transitivity-NetworkX v3.3 Manual
[2]  
[Anonymous], 2024, scipy.spatial.distance.jensenshannon-SciPy v1.12.0 Manual
[3]   Molecular detection of SARS-CoV-2 and other respiratory viruses in saliva and classroom air: a two winters tale [J].
Banholzer, Nicolas ;
Bittel, Pascal ;
Jent, Philipp ;
Furrer, Lavinia ;
Zuercher, Kathrin ;
Egger, Matthias ;
Hascher, Tina ;
Fenner, Lukas .
CLINICAL MICROBIOLOGY AND INFECTION, 2024, 30 (06) :e1-e4
[4]   Effect of manual and digital contact tracing on COVID-19 outbreaks: a study on empirical contact data [J].
Barrat, A. ;
Cattuto, C. ;
Kivela, M. ;
Lehmann, S. ;
Saramaeki, J. .
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 2021, 18 (178)
[5]   Measuring contact patterns with wearable sensors: methods, data characteristics and applications to data-driven simulations of infectious diseases [J].
Barrat, A. ;
Cattuto, C. ;
Tozzi, A. E. ;
Vanhems, P. ;
Voirin, N. .
CLINICAL MICROBIOLOGY AND INFECTION, 2014, 20 (01) :10-16
[6]  
Bastian M., 2009, INT AAAI C WEBLOGS S, DOI DOI 10.1609/ICWSM.V3I1.13937
[7]   The French Connection: The First Large Population-Based Contact Survey in France Relevant for the Spread of Infectious Diseases [J].
Beraud, Guillaume ;
Kazmercziak, Sabine ;
Beutels, Philippe ;
Levy-Bruhl, Daniel ;
Lenne, Xavier ;
Mielcarek, Nathalie ;
Yazdanpanah, Yazdan ;
Boelle, Pierre-Yves ;
Hens, Niel ;
Dervaux, Benoit .
PLOS ONE, 2015, 10 (07)
[8]   Dynamics of Person-to-Person Interactions from Distributed RFID Sensor Networks [J].
Cattuto, Ciro ;
Van den Broeck, Wouter ;
Barrat, Alain ;
Colizza, Vittoria ;
Pinton, Jean-Francois ;
Vespignani, Alessandro .
PLOS ONE, 2010, 5 (07)
[9]   Minimising school disruption under high incidence conditions due to the Omicron variant in France, Switzerland, Italy, in January 2022 [J].
Colosi, Elisabetta ;
Bassignana, Giulia ;
Barratt, Alain ;
Lina, Bruno ;
Vanhems, Philippe ;
Bielicki, Julia ;
Colizza, Vittoria .
EUROSURVEILLANCE, 2023, 28 (05)
[10]   Screening and vaccination against COVID-19 to minimise school closure: a modelling study [J].
Colosi, Elisabetta ;
Bassignana, Giulia ;
Contreras, Diego Andres ;
Poirier, Canelle ;
Boelle, Pierre-Yves ;
Cauchemez, Simon ;
Yazdanpanah, Yazdan ;
Lina, Bruno ;
Fontanet, Arnaud ;
Barrat, Alain ;
Colizza, Vittoria .
LANCET INFECTIOUS DISEASES, 2022, 22 (07) :977-989