Modeling the Ebola Outbreak in West Africa January 6th 2015 update

DRAFT – Not for a.ribu2on or distribu2on

Modeling the Ebola Outbreak in West Africa, 2014

January 6th Update

Bryan Lewis PhD, MPH ([email protected]) presen2ng on behalf of the Ebola Response Team of

Network Dynamics and Simula2on Science Lab from the Virginia Bioinforma2cs Ins2tute at Virginia Tech

Technical Report #15-‐001


NDSSL Ebola Response Team Staff: Abhijin Adiga, Kathy Alexander, Chris Barre., Richard Beckman, Keith Bisset, Jiangzhuo Chen, Youngyoun Chungbaek, Stephen Eubank, Sandeep Gupta, Maleq Khan, Chris Kuhlman, Eric Lofgren, Bryan Lewis, Achla Marathe, Madhav Marathe, Henning Mortveit, Eric Nordberg, Paula Stretz, Samarth Swarup, Meredith Wilson,Mandy Wilson, and Dawen Xie, with support from Ginger Stewart, Maureen Lawrence-‐Kuether, Kayla Tyler, Kathy Laskowski, Bill Marmagas Students: S.M. Arifuzzaman, Aditya Agashe, Vivek Akupatni, Caitlin Rivers, Pyrros Telionis, Jessie Gunter, Elisabeth Musser, James Schli., Youssef Jemia, Margaret Carolan, Bryan Kaperick, Warner Rose, Kara Harrison

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Currently Used Data (as of Dec 22nd, 2014)

●  Data from WHO, MoH Liberia, and MoH Sierra Leone, available at h.ps://github.com/cmrivers/ebola

●  MoH and WHO have reasonable agreement ●  Sierra Leone case counts censored up

to 4/30/14. ●  Time series was filled in with missing

dates, and case counts were interpolated.

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Cases Deaths Guinea 2,730 1,739 Liberia 8,115 3,423 Sierra Leone 9,633 2,827 Total 20,478 7,989


Liberia – Case Loca2ons

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Liberia infec2on rate

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Liberia Forecast

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11/24 to

11/30

12/1 to

12/8

12/9 to

12/16

12/15 to

12/21

12/22 to

12/28

12/29 to

1/04

1/05 to

1/11

1/12 to

1/18

1/19-‐1/25

1/26-‐2/01

Reported 246 362 99 35 101

Newer model 303 285 270 255 240 226 214 201 190 180

Reproduc2ve Number Community 0.23 Hospital 0.3 Funeral 0.2 Overall 0.8


Liberia long term forecasts

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Date Weekly forecast

12/08 270

12/15 255

12/22 240

12/29 227

1/05 213

1/12 202

1/19 190

1/26 179

2/2 169

2/9 160

2/16 150

2/23 142

3/02 134

3/09 126


Liberia-‐ Prevalence

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Date People in H + I

12/08 652

12/15 616

12/22 580

12/29 548

1/05 517

1/12 488

1/19 460

1/26 434

2/2 410

2/9 386

2/16 365

2/23 344

3/02 325

3/09 306


Sierra Leone – County Data

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Sierra Leone infec2on rate

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Sierra Leone Forecast

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35% of cases are hospitalized

ReproducRve Number Community 0.8 Hospital 0.3 Funeral 0.1 Overall 1.1

11/24 to

11/30

12/1 to

12/8

12/9 to

12/16

12/15 to

12/21

12/22 to

12/28

12/29 to

1/04

1/05 to

1/11

1/12 to

1/18

1/19-‐1/25

1/26-‐2/01

Reported 641 598 702 531 651 467

Newer model 612 635 660 686 713 740 769 799 830 862


SL longer term forecast

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Sierra Leone – Newer Model fit – Weekly Incidence Date Weekly forecast

12/08 660

12/15 686

12/22 713

12/29 740

1/05 769

1/12 799

1/19 830

1/26 862

2/2 895

2/9 929

2/16 965

2/23 1002

3/02 1040

3/09 1080


Sierra Leone -‐ Prevalence

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Date People in H + I

12/08 898

12/15 932

12/22 968

12/29 1006

1/05 1045

1/12 1085

1/19 1128

1/26 1171

2/2 1216

2/9 1263

2/16 1319

2/23 1370

3/02 1423

3/09 1477


Guinea Forecasts

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40% of cases are hospitalized

ReproducRve Number Community 0.7 Hospital 0.1 Funeral 0.1 Overall 0.9

11/24 to

11/30

12/1 to

12/8

12/9 to

12/16

12/15 to

12/21

12/22 to

12/28

12/29 to

1/04

1/05 to

1/11

1/12 to

1/18

1/19-‐1/25

1/26-‐2/01

Reported 129 44 127 132 166 106

Newer model 89 85 81 78 75 72 68 66 60 58


Guinea – longer term forecast

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Date Weekly forecast

12/08 81

12/15 78

12/22 75

12/29 72

1/05 69

1/12 66

1/19 63

1/26 60

2/2 58

2/9 55

2/16 53

2/23 51

3/02 48


Guinea Prevalence

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Date People in H+I

12/08 98

12/15 94

12/22 90

12/29 86

1/05 82

1/12 79

1/19 76

1/26 72

2/2 69

2/9 66

2/16 64

2/23 61

3/02 58


Agent-‐based model progress

•  Sierra Leone calibra2on – Behavioral Shil of 17% in Mid-‐Oct – Debugging of HPC environment – 2nd round of calibra2on is be.er, s2ll not sa2sfied

•  Fundamental science of calibra2on – Methods for iden2fying epidemic instances being developed

– Extensions to simula2on engine to generate an “enriched” set of instances underway

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Sierra Leone Calibra2on

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App Development •  EpiViewer enhancements – Added more filters –  Improving visualiza2on before broader release

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App Development •  Eyes-‐on-‐the-‐Ground –  Sierra Leone road network analysis underway

–  Support for older browser being inves2gated •  Older version of std didn’t support current implementa2on

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Modeling the Ebola Outbreak in West Africa January 6th 2015 update

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