Modeling the Ebola Outbreak in West Africa, January 13th 2015 update

DRAFT – Not for a.ribu2on or distribu2on

Modeling the Ebola Outbreak in West Africa, 2014

January 13th 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-‐003


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

2


Currently Used Data (as of Jan 9th, 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.

3

Cases Deaths Guinea 2,776 1,786 Liberia 8,256 3,496 Sierra Leone 9,930 2,977 Total 20,962 8,259


Liberia – Case Loca2ons

4


Liberia infec2on rate

5


Liberia Forecast

6

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

1/27-‐2/01

Reported 362 99 35 101 131 116

Newer model

285 270 255 240 191 178 166 155 144 135

Reproduc2ve Number Community 0.3 Hospital 0.3 Funeral 0.2 Overall 0.8


Liberia long term forecasts

7

Date Weekly forecast

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

8

Date People in H + I

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 infec2on rate

9


Sierra Leone Forecast

10

35% of cases are hospitalized

ReproducQve Number Community 0.7 Hospital 0.2 Funeral 0.1 Overall 1.0

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 598 702 531 651 467 344

Newer model 635 660 686 713 740 607 620 632 645


SL longer term forecast

11

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

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

12

Date People in H + I

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

13

40% of cases are hospitalized

ReproducQve Number Community 0.7 Hospital 0.1 Funeral 0.1 Overall 0.9

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 44 127 132 166 106 62

Newer model 85 81 78 75 72 68 86 84 82


Guinea – longer term forecast

14

Date Weekly forecast

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

15

Date People in H+I

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 •  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

16


Sierra Leone – Long Distance Travel

•  Iden2fied mismatch with Flowminder data

17

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

18


Sierra Leone – Household Dynamics

19



20



21


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

22


Prelim Vax Campaign

23

Baseline Case


Prelim Vax Campaign

24

Several Replicates provide a good match to observed


Prelim Vax Campaign

25

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

26

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

27

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

28


EpiViewer •  Ready for use, preloaded with forecasts

29


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:

30


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

31