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JUNE: open-source individual-based epidemiology simulation

Aylett-Bullock, J.; Cuesta-Lazaro, C.; Quera-Bofarull, A.; Icaza-Lizaola, M.; Sedgewick, A.; Truong, H.; Curran, A.; Elliott, E.; Caulfield, T.; Fong, K.; Vernon, I.; Williams, J.; Bower, R.; Krauss, F.

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J. Aylett-Bullock

C. Cuesta-Lazaro

A. Quera-Bofarull

M. Icaza-Lizaola

A. Sedgewick

T. Caulfield

K. Fong

R. Bower


We introduce June, 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. June provides a suite of flexible parametrizations that describe infectious diseases, how they are transmitted and affect contaminated individuals. In this paper, we apply June 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.


Aylett-Bullock, J., Cuesta-Lazaro, C., Quera-Bofarull, A., Icaza-Lizaola, M., Sedgewick, A., Truong, H., …Krauss, F. (2021). JUNE: open-source individual-based epidemiology simulation. Royal Society Open Science, 8(7),

Journal Article Type Article
Acceptance Date Jun 22, 2021
Online Publication Date Jul 7, 2021
Publication Date 2021-07
Deposit Date Jul 22, 2021
Publicly Available Date Jul 23, 2021
Journal Royal Society Open Science
Publisher The Royal Society
Peer Reviewed Peer Reviewed
Volume 8
Issue 7
Public URL


Published Journal Article (5.9 Mb)

Publisher Licence URL

Copyright Statement
&copy; 2021 The Authors.<br /> <br /> Published by the Royal Society under the terms of the Creative Commons Attribution License, which permits unrestricted use, provided the original author and source are credited.

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