J une : open-source individual-based epidemiology simulation | Zendy

Joseph Aylett-Bullock | Zendy; Carolina Cuesta-Lazaro | Zendy; Arnau Quera-Bofarull | Zendy; Miguel Icaza-Lizaola | Zendy; Aidan Sedgewick | Zendy; Henry Truong | Zendy; Aoife Curran | Zendy; Edward J Elliott | Zendy; Tristan Caulfield | Zendy; Kevin Fong | Zendy; Ian Ver | Zendy; Julian Williams | Zendy; R. G. Bower | Zendy; Frank Krauss | Zendy

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J une : open-source individual-based epidemiology simulation

Author(s) -

Joseph Aylett-Bullock,

Carolina Cuesta-Lazaro,

Arnau Quera-Bofarull,

Miguel Icaza-Lizaola,

Aidan Sedgewick,

Henry Truong,

Aoife Curran,

Edward J Elliott,

Tristan Caulfield,

Kevin Fong,

Ian Ver,

Julian Williams,

R. G. Bower,

Frank Krauss

Publication year - 2021

Publication title -

royal society open science

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.84

H-Index - 51

ISSN - 2054-5703

DOI - 10.1098/rsos.210506

Subject(s) - suite , census , open source , computer science , geography , population , covid-19 , econometrics , demography , sociology , economics , medicine , infectious disease (medical specialty) , disease , archaeology , software , pathology , programming language

We introduce J une , an open-source framework for the detailed simulation of epidemics on the basis of social interactions in a virtual population constructed from geographically granular census data, reflecting age, sex, ethnicity and socio-economic indicators. Interactions between individuals are modelled in groups of various sizes and properties, such as households, schools and workplaces, and other social activities using social mixing matrices. J une provides a suite of flexible parametrizations that describe infectious diseases, how they are transmitted and affect contaminated individuals. In this paper, we apply J une to the specific case of modelling the spread of COVID-19 in England. We discuss the quality of initial model outputs which reproduce reported hospital admission and mortality statistics at national and regional levels as well as by age strata.

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