Modelling the spread of COVID-19 in England

June Dalziel Almeida

JUNE

Arnau Quera-Bofarull

Durham University CDT PhD student

Who are we?

Arnau Quera-Bofarull

Aidan Sedgewick

Miguel De Icaza Lizaola

Carolina Cuesta-Lazaro

Henry Truong

Astronomy / Particle Physics CDT students

Amazon

Joseph Aylett-Bullock

United Nations

Procter & Gamble

HEP Inspire

Boeing

Ibex

Kevin Fong

the (actual) doctor

Ian Vernon

 the statistician

Tristan Caulfield

the hacker

Bryan Lawrence

the climate scientist

Julian Williams

the business man

Frank Krauss

the particle physicist

Who are we?

Other Researchers

What is JUNE?

England Digital Twin

Epidemiological model

Agent-based simulation

England Digital twin

Geography

England Digital twin

Demography

  • age  (27)
  • sex (f)
  • ethnic group (Caribbean)
  • deprivation index 2 (1-10)
  • work sector / subsector (healthcare/doctor)
  • mode of transport (public)
  • area of residence
  • super area of work

Main data source: census data (NOMIS)

male

female

granular Demography

male

female

England Digital twin

dynamics (where can people go?)

  • Residence
    • Care Home
    • Household
  • Primary activity
    • Company
    • Hospital
    • School
    • Care Home
    • University
  • Travel
    • Commute
    • National travel
  • Leisure
    • Shopping
    • Pubs / restaurants
    • Cinema
    • Household visits

City of London workers' usual residence

Matching workplace and residence

places are geolocalized

DURHAM STUDENT POPULATION

43 yo

38 yo

10 yo

How do people transmit the infection?

j

j

i

Intensity of contacts (per group)

Infectiousness profile

Contact

Matrix

Disease Trajectory

Odds calibrated to data

POlicies

MODEl fitting

We have

Model (18 free parameters)

+

Data (quite messy)

It takes ~400 CPU hours to run one simulation....

How do we fit it?

bayesian emulator + history matching

bayesian emulator + history matching

Train Bayesian emulator

Run emulator

O(500k) times

Run full simulation O(100) times

Narrow parameter space search

IT WORKS!

checkout the code at

github.com/IDAS-Durham/JUNE

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