Modeling the Ebola Outbreak in West Africa, 2014

Sept 16th Update

Bryan Lewis PhD, MPH (blewis@vbi.vt.edu)Caitlin Rivers MPH, Eric Lofgren PhD, James Schlitt, Katie Dunphy,

Henning Mortveit PhD, Dawen Xie MS, Samarth Swarup PhD, Hannah Chungbaek, Keith Bisset PhD, Maleq Khan PhD, Chris Kuhlman PhD,

Stephen Eubank PhD, Madhav Marathe PhD, and Chris Barrett PhD

2

Currently Used Data

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

● Sierra Leone case counts censored up to 4/30/14.

● Time series was filled in with missing dates, and case counts were interpolated.

Cases DeathsGuinea 861

557Liberia 24071137Nigeria 22

8Sierra Leone 1603524Total 48932226

3

Liberia- Case Locations

4

Liberia – Health Care Workers

5

Liberia – Contact Tracing

6

Liberia – Community based cases

7

Sierra Leone – Case Locations

8

Sierra Leone – Case Finding

9

Sierra Leone – Case FindingAssuming all cases are followed to the same degree, this what the “observed” Re would be based on cases found from contacts (using time lagged 7,10,12 day reported cases as denominator)

10

Line Listing

• Gathered 50 case descriptions from media reports• Tried to piece together all info we’d like access to

from “comprehensive source”case_id,exposure_date,onset_date,hospital_date,death_date,recovery_date,age,sex,country,sub_location,sub_sub_location,legrand,exposure,hcw,source_id,identifying_notes,source

case_id exposure_date onset_date hospital_date death_date recovery_date age sex countrysub_location sub_sub_location legrand exposure hcw source_id identifying_notes ource

1 2013-12-02 2013-12-06 child GuineaGueckedou Meliandou c zoonotic N http://www.nejm.org/doi/full/10.1056/NEJMoa1404505

2 2013-12-13 adult F GuineaGueckedou Meliandou c family N 1 mother http://www.nejm.org/doi/full/10.1056/NEJMoa1404506

3 2013-12-25 2013-12-27 child F GuineaGueckedou Meliandou c family N 1 sister http://www.nejm.org/doi/full/10.1056/NEJMoa1404507

4 2014-01-01 elderly F GuineaGueckedou c family Y 1 grandmother http://www.nejm.org/doi/full/10.1056/NEJMoa1404508

5 2014-01-29 2014-01-31 adult F GuineaGueckedou h hcw Y 1 nurse http://www.nejm.org/doi/full/10.1056/NEJMoa1404509

6 2014-01-25 2014-02-02 adult F GuineaGueckedou h hcw Y 1 midwife http://www.nejm.org/doi/full/10.1056/NEJMoa1404510

11

Line Listing - Epidemiology

12

Line Listing – Exposure Type

13

Line Listing – Transmission Trees

14

Twitter TrackingMost common images:

Information about bushmeat, info about case locations, joke about soap cost, and dealing with Ebola patients,

15

Liberia Forecasts

8/13 – 8/19

8/20 – 8/26

8/27 – 9/02

9/3 – 9/9

9/10 – 9/16

9/17-9/23

9/24 – 9/30

Actual 175 353 321 468 544 --Forecast 176 229 304 404 533 801 1064

Forecast performance Reproductive NumberCommunity 1.34Hospital 0.35Funeral 0.53Overall 2.22

52% of Infected arehospitalized

16

Liberia Forecasts – Role of Prior Immunity

17

Sierra Leone Forecasts

Reproductive NumberCommunity 1.22Hospital 0.23Funeral 0.24Overall 1.69

Forecast performance

59% of cases are hospitalized

18

Prevalence of Cases

19

All Countries Forecasts

rI:0.85rH:0.74rF:0.31Overal:1.90

Model Parameters'alpha':1/10'beta_I':0.200121'beta_H':0.029890'beta_F':0.1'gamma_h':0.330062'gamma_d':0.043827gamma_I':0.05'gamma_f':0.25'delta_1':.55'delta_2':.55'dx':0.6

20

Combined Forecasts

8/10 – 8/16

8/17 – 8/23

8/24 – 8/30

8/31– 9/6

9/8 – 9/13

9/14-9/20

9/21 – 9/27

9/28 – 10/4

Actual 231 442 559 783 681 -- -- --Forecast 329 393 469 560 693 830 994 1191

21

Synthetic Sierra Leone

Now integrated into the ISIS interface

22

ISIS - based Calibration

23

Next Steps - Compartmental

• Interventions under way– More hospital beds in urban areas– More “home-care” kits in rural areas– Arrival of therapeutics

• Inform the agent-based model– Geographic disaggregation– Parameter estimation– Intervention comparison

24

Next Steps – Agent-based

• Implement new disease mapping– Has been

• Add regional mobility• ABM stochastic space larger than

compartmental, how to accommodate?• Integrating data to assist in logistical questions– Locations of ETCs, lab facilities from OCHA– Road network– Capacities of existing support operations

25

APPENDIXSupporting material describing model structure, and additional results

26

Further evidence of endemic Ebola• 1985 manuscript finds ~13% sero-prevalence of Ebola in remote Liberia

– Paired control study: Half from epilepsy patients and half from healthy volunteers– Geographic and social group sub-analysis shows all affected ~equally

27

Legrand et al. Model Description

Legrand, J, R F Grais, P Y Boelle, A J Valleron, and A Flahault. “Understanding the Dynamics of Ebola Epidemics” Epidemiology and Infection 135 (4). 2007. Cambridge University Press: 610–21. doi:10.1017/S0950268806007217.

28

Compartmental Model

• Extension of model proposed by Legrand et al.Legrand, J, R F Grais, P Y Boelle, A J Valleron, and A Flahault. “Understanding the Dynamics of Ebola Epidemics” Epidemiology and Infection 135 (4). 2007. Cambridge University Press: 610–21. doi:10.1017/S0950268806007217.

29

Legrand et al. Approach

• Behavioral changes to reduce transmissibilities at specified days

• Stochastic implementation fit to two historical outbreaks – Kikwit, DRC, 1995 – Gulu, Uganda, 2000

• Finds two different “types” of outbreaks– Community vs. Funeral driven

outbreaks

30

Parameters of two historical outbreaks

31

NDSSL Extensions to Legrand Model

• Multiple stages of behavioral change possible during this prolonged outbreak

• Optimization of fit through automated method

• Experiment:– Explore “degree” of fit using the two different

outbreak types for each country in current outbreak

32

Optimized Fit Process• Parameters to explored selected– Diag_rate, beta_I, beta_H, beta_F, gamma_I, gamma_D,

gamma_F, gamma_H– Initial values based on two historical outbreak

• Optimization routine– Runs model with various

permutations of parameters– Output compared to observed case

count– Algorithm chooses combinations that

minimize the difference between observed case counts and model outputs, selects “best” one

33

Fitted Model Caveats

• Assumptions:– Behavioral changes effect each transmission route

similarly– Mixing occurs differently for each of the three

compartments but uniformly within• These models are likely “overfitted”– Many combos of parameters will fit the same curve– Guided by knowledge of the outbreak and additional

data sources to keep parameters plausible– Structure of the model is supported

34

Liberia model params

35

Sierra Leone model params

36

All Countries model params

37

Long-term Operational Estimates

• Based on forced bend through extreme reduction in transmission coefficients, no evidence to support bends at these points– Long term projections are unstable

Turn from 8-26

End from 8-26

Total Case Estimate

1 month 3 months 13,400

1 month 6 months 15,800

1 month 18 months 31,300

3 months 6 months 64,300

3 months 12 months 91,000

3 months 18 months 120,000

6 months 12 months 682,100

6 months 18 months 857,000