Post on 03-Aug-2015
DRAFT – Not for a.ribu2on or distribu2on
Modeling the Ebola Outbreak in West Africa, 2014
January 13th Update
Bryan Lewis PhD, MPH (blewis@vbi.vt.edu) 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
DRAFT – Not for a.ribu2on or distribu2on
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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DRAFT – Not for a.ribu2on or distribu2on
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.
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Cases Deaths Guinea 2,776 1,786 Liberia 8,256 3,496 Sierra Leone 9,930 2,977 Total 20,962 8,259
DRAFT – Not for a.ribu2on or distribu2on
Liberia Forecast
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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
DRAFT – Not for a.ribu2on or distribu2on
Liberia long term forecasts
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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
DRAFT – Not for a.ribu2on or distribu2on
Liberia-‐ Prevalence
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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
DRAFT – Not for a.ribu2on or distribu2on
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
12/1 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
DRAFT – Not for a.ribu2on or distribu2on
SL longer term forecast
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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
DRAFT – Not for a.ribu2on or distribu2on
Sierra Leone -‐ Prevalence
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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
DRAFT – Not for a.ribu2on or distribu2on
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
12/1 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
DRAFT – Not for a.ribu2on or distribu2on
Guinea – longer term forecast
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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
DRAFT – Not for a.ribu2on or distribu2on
Guinea Prevalence
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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
DRAFT – Not for a.ribu2on or distribu2on
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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DRAFT – Not for a.ribu2on or distribu2on
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
DRAFT – Not for a.ribu2on or distribu2on
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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DRAFT – Not for a.ribu2on or distribu2on
Prelim Vax Campaign
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Several Replicates provide a good match to observed
DRAFT – Not for a.ribu2on or distribu2on
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
DRAFT – Not for a.ribu2on or distribu2on
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
efficacy 50 -‐ compliance high
efficacy 80 -‐ compliance low
efficacy 80 -‐ compliance high
Cases 60 days aXer vax campaign started
DRAFT – Not for a.ribu2on or distribu2on
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%
efficacy 30 -‐ compliance low
efficacy 30 -‐ compliance high
efficacy 50 -‐ compliance low
efficacy 50 -‐ compliance high
efficacy 80 -‐ compliance low
efficacy 80 -‐ compliance high
ReducQon in cases from baseline aXer 60 days
DRAFT – Not for a.ribu2on or distribu2on
App Development
• EpiViewer – Aggregator of • Eyes-‐on-‐the-‐Ground – Liberian version – Sierra Leone version
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DRAFT – Not for a.ribu2on or distribu2on
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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