Download pdf - Modeling the Ebola Outbreak in West Africa, January 20th 2015 update

DRAFT – Not for a.ribu2on or distribu2on

Modeling the Ebola Outbreak in West Africa, 2014

January 20th 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-‐008


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 Jan 14th, 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 2,806 1,814 Liberia 8,331 3,538 Sierra Leone 10,124 3,062 Total 21,261 8,414


Liberia – Case Loca2ons

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Liberia infec2on rate

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Liberia Forecast

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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

1/27-‐2/01

2/02 -‐

2/08

2/09 -‐

2/15

Reported 35 101 131 116

Newer model

241 224 180 168 156 145 135 125 116 108

Reproduc2ve Number Community 0.3 Hospital 0.3 Funeral 0.2 Overall 0.8


Liberia long term forecasts

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Date Weekly forecast

1/26 135

2/2 126

2/9 117

2/16 108

2/23 101

3/02 94

3/09 87

3/16 81

3/23 75


Liberia-‐ Prevalence

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Date People in H + I

1/19 369

1/26 397

2/2 319

2/9 297

2/16 276

2/23 256

3/02 238

3/09 222


Sierra Leone infec2on rate

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Sierra Leone Forecast

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35% of cases are hospitalized

ReproducQve Number Community 0.7 Hospital 0.2 Funeral 0.1 Overall 1.0

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

2/02 -‐

2/08

2/09 -‐

2/15

Reported 531 651 467 344

Newer model 571 583 595 607 620 632 645 658 671


SL longer term forecast

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

1/19 632

1/26 645

2/2 558

2/9 671

2/16 685

2/23 699

3/02 713

3/09 727

3/16 741

3/23 756


Sierra Leone -‐ Prevalence

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Date People in H + I

1/12 847

1/19 864

1/26 882

2/2 900

2/9 918

2/16 937

2/23 995

3/02 1015

3/09 1034


Guinea Forecasts

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40% of cases are hospitalized

ReproducQve Number Community 0.7 Hospital 0.1 Funeral 0.1 Overall 0.9

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

2/02 -‐

2/08

2/09 -‐

2/15

Reported 132 166 106 62

Newer model 78 75 72 68 86 84 82 80 78


Guinea – longer term forecast

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Date Weekly forecast

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

1/19 76

1/26 72

2/2 69

2/9 66

2/16 64

2/23 61

3/02 58


Agent Based Model •  Long distance travel for Sierra Leone •  Explora2on of Dynamics of infec2on – Age distribu2on – Household

•  Preliminary Vaccine campaign results •  Ongoing studies: – Ex2nc2on study – how likely is Ebola to go ex2nct by chance under different condi2ons

– Loca2on based targe2ng of vaccine campaign

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Sierra Leone – Long Distance Travel

•  Iden2fied mismatch with Flowminder data

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County Flowmider PopulaQon

NDSSL PopulaQon

NDSSL FracQon

2010 EsQmate Wikipedia

NDSSL FracQon

Kailahun 472,521 427,574 0.90 409,520 1.04 Kenema 690,511 538,120 0.78 545,327 0.99 Kono 538,271 383,369 0.71 352,328 1.09 Bombali 550,437 469,677 0.85 434,319 1.08 Kambia 362,084 271,352 0.75 313,765 0.86 Koinadugu 358,522 279,423 0.78 251,091 1.11 Port Loko 612,547 539,616 0.88 500,992 1.08 Tonkolili 472,176 428,895 0.91 385,322 1.11 Bo 641,236 547,713 0.85 561,524 0.98 Bonthe 191,754 164,805 0.86 140,845 1.17 Moyamba 352,832 283,422 0.80 252,390 1.12 Pujehun 316,360 288,496 0.91 252,390 1.14 Western_Urban 540,326 946,629 1.75 1,473,873 0.64 Western_Rural 775,376 110,278 0.14 205,400 0.54 Uncatogorized 64,356 Total 6,874,954 5,743,725 0.84 6,079,086 0.94

Western Combined 1,315,702 1,056,907 0.80 1,679,273 0.63


Sierra Leone – Age Distribu2on

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Sierra Leone – Household Dynamics

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Sierra Leone – Prelim Vax Campaign

•  Study Design: – Calibrated spread to current Sierra Leone outbreak

– 300k vaccines available, early February – Applied with high and low compliance to contacts of cases and others in community

– Efficacy levels of 30, 50, 80

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Prelim Vax Campaign

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Baseline Case


Prelim Vax Campaign

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Several Replicates provide a good match to observed


Prelim Vax Campaign

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With Vaccine In early Feb (Day 305) Several Replicates provide a good match to observed

Low compliance 30% efficacy

High compliance 50% efficacy


Prelim Vax Campaign

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0

5000

10000

15000

20000

25000

baseline efficacy 30 -‐ compliance low

efficacy 30 -‐ compliance high

efficacy 50 -‐ compliance low




Cases 60 days aXer vax campaign started


Prelim Vax Campaign

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0.0%

5.0%

10.0%

15.0%

20.0%

25.0%

30.0%

35.0%

40.0%

45.0%

50.0%







ReducQon in cases from baseline aXer 60 days


App Development

•  EpiViewer – Aggregator of •  Eyes-‐on-‐the-‐Ground – Liberian version – Sierra Leone version

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EpiViewer •  Ready for use, preloaded with forecasts

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Eyes-‐on-‐the-‐Ground •  Fixed many issues for older browsers and firewall restric2ons

•  Liberia version ready for widespread use: – h.p://socialeyes.vbi.vt.edu/eyesontheground/surveypage.jsp

•  Includes detailed report page:

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Eyes-‐on-‐the-‐Ground

•  Road Network available and analyzed for Sierra Leone – Es2mates between towns available

•  Support for mul2ple countries etc. requires more development on App server backend

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