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Recovery simulations for infectious diseases in African Great Apes
NCEAS 12164: Walsh: Efficient wildlife disease control: From social network self-organization to optimal vaccination
National Center for Ecological Analysis and Synthesis
Sadie
Ryan
SUNY College of Environmental Science and Forestry
Syracuse
New York
USA
sjryan@esf.edu
Xueying
Han
Sadie
Ryan
associatedParty
Peter
Walsh
Co-owner
2012-01-23
Supplemental material for Ryan SJ, Walsh PD (2011) Consequences of Non-Intervention for Infectious Disease in African Great Apes. PLoS ONE 6(12): e29030. doi:10.1371/journal.pone.0029030
Ebola
Model simulations
African Great Apes
Simian immunodeficiency virus
Gorilla
Infectious diseases
Outbreaks
Recovery time
Vaccination
None
no restrictions
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0029030
digital
1966
2011
Virunga Mountains of Rwanda
29.5481
29.5481
-1.4292
-1.4292
Species
Gorilla beringei beringei
Sadie
Ryan
SUNY College of Environmental Science and Forestry
Syracuse
New York
USA
sjryan@esf.edu
Methods
Mortality rates typical of disease outbreaks in
wild apes were characterized from data compiled from sixteen previously published outbreaks, wherein community size, number infected and the mortality rate were explicitly reported. We used a demographic modeling exercise to demonstrate the resilience of populations to disease outbreaks. To describe population growth in gorillas we used a discrete,
logistic model:
N(t+1)=N(t)+R*N(t)*(K-N(t)/K)
We parameterized the model using an estimated demographic rate (R) for gorillas in the Virunga Mountains of Rwanda. To be conservative, we used highly optimistic estimates which tended to overestimate gorilla reproductive potential. They yielded a Leslie matrix estimate for the annual rate of increase of R= 3.7% (Walsh and Caillaud, unpublished). The estimated population size was 320
gorillas, and the carrying capacity estimate (K) was 300 to 500, so we used a midpoint of K = 400.
We considered a series of five scenarios in which proportional mortality rate, a, corresponded to the mortality rate observed in a real outbreak. In each scenario, we seeded the logistic growth model with an initial, post-outbreak population size of
N(0)=N-a*N
then iterated the logistic model in annual times steps until gorilla population size reached the initial population size, N, as a measure
of recovery time. To examine the resilience of gorillas to disease we considered five disease mortality scenarios and the outputs of these simulations are reported here.
We examined human vaccination rates and reported cases (where available) for five exemplar great ape range countries using the UNICEF/WHO 2009 global immunization summary and the WHO 2009 WHS (World Health Statistics), for seven diseases known to be communicable to great apes. We also included data from the United Kingdom, a leading source country for ape tourists. We conducted a literature review of human vaccines for pathogens that were either already known to infect wild apes or presented a high risk of infection (e.g. respiratory pathogens likely to be carried by tourists). For each pathogen we scored whether at least one vaccine was licensed (L) or under development; in the advanced stage of development (A) if the most advanced vaccine was in human clinical trials; or in the early stage of development (E), if the most advanced vaccine was not yet in human clinical trials but had protected captive non-human primates from pathogen challenge. We also identified mode of transmission, the identity of the reservoir host, and the likely duration of vaccineinduced immunity.
Bwindi gorilla population simulation.csv
Bwindi gorilla population simulation.csv
31158
1
#x0A
column
,
ecogrid://knb/han.19.1
Time
Time (in years) of the simulation.
nominalYear
natural
Respiratory (Gombe 2000)
Population size after suffering from the Gombe 2000 respiratory disease outbreak
dimensionless
natural
Flu-like (Mahale 1993)
Population size after suffering from the Mahale 1993 flu-like outbreak
dimensionless
natural
Flu-like (Bossou 2003)
Population size after suffering from the Bossou 2003 flu-like outbreak
dimensionless
natural
STLV or Strep (Tai 1999)
Population size after suffering from the Tai 1999 STLV (or Strep) outbreak
dimensionless
natural
Ebola (Lossi 2003-2004)
Population size after suffering from the Lossi 2003-2004 ebola disease outbreak
dimensionless
natural
Initial population
Initial population size
dimensionless
natural
455
Disease outbreak.csv
Disease outbreak.csv
418
1
#x0A
column
,
ecogrid://knb/han.21.1
Disease outbreak
List of 16 previously published outbreaks for which the mortality impact, the percentage mortality in the group is given or was possible to estimate
Gombe 2000 Respiratory
Gombe 2000 respiratory outbreak
Gombe 1997 Mange
Gombe 1997 mange outbreak
Gombe 1968 Respiratory
Gombe 1968 respiratory outbreak
Gombe 1966 Polio
Gombe 1966 polio outbreak
Mahale flu-like 1993
Mahale flu like 1993 outbreak
Tai Mystery 1993
Tai mystery 1993 outbreak
Tai Ebola Cote d'Ivoire
Tai ebola cote d'Ivoire outbreak
Gombe 1987 Respiratory
Gombe 1987 respiratory outbreak
Mahale flu-like 2006
Mahale flu like 2006 outbreak
Bossou 2003 Flu-like
Bossou 2003 flu like outbreak
Tai 1999 STLV or Strep
Tai 1999 STLV or strep outbreak
Ebola Chimpanzees
Ebola chimpanzee outbreak
Lossi 2002-2003 Ebola
Lossi 2002-2003 ebola outbreak
Lossi 2003-2004 Ebola
Lossi 2003-2004 ebola outbreak
Mortality impact
The percentage mortality of the population that was recorded for each disease outbreak
dimensionless
natural
15
Vaccinations for wile ape populations.csv
Vaccinations for wile ape populations.csv
827
1
#x0A
column
,
ecogrid://knb/han.22.2
Pathogen
Type of pathogen
Measles virus
Measles virus
Mumps virus
Mumps virus
Rubella virus
Rubella virus
Influenza virus
Influenza virus
Varicella virus (chickenpox)
Varicella virus (chickenpox)
Respiratory syncitial virus (RSV)
Respiratory syncitial virus (RSV)
Human metapneumo virus
Human metapneumo virus
Diptheria virus
Diptheria virus
Pertussis virus (whooping cough)
Pertussis virus (whooping cough)
Streptoccocus pneumoniae
Streptoccocus pneumoniae
Hepatitis A virus
Hepatitis A virus
Hepatitis B virus
Hepatitis B virus
Tuberculosis
Tuberculosis
Polio virus
Polio virus
Rabies virus
Rabies virus
Ebola virus
Ebola virus
Anthrax
Anthrax
Malaria
Malaria
Tetanus
Tetanus
Simian immunodificiency virus (SIV)
Simian immunodificiency virus (SIV)
Dengue fever virus
Dengue fever virus
Yellow fever virus
Yellow fever virus
Transmission mode
Transmission mode of pathogen
R
Respiratory
F
Fecal
S
Sexual
B
Bite
?
Unknown
V
Vectorborne
W
Wound
Wild Apes
Whether or not the pathogen has been explicity identified in wild apes
Yes
Yes, it has been explicity identified in wild apes
Reservoir
The disease reservoir
Human
Humans are the reservoir
Ape
Apes are the reservoir
Domestic dog
Domestic dogs are the reservoir
Bat?
Possibly bats are the reservoir
?
Unknown
Primate
Primates are the reservoir
Immunity Duration
Immunity duration of the vaccination
L
Longterm
S
Shortterm
U
Unknown
Licensing Status
Licensing status of the vaccination
L
Licensed
E
Early experimental
A
Advanced experimental
A*
Advanced experimental but for human strain only
E*
Early experimental but for human strain only
22
Vaccination coverage.csv
Vaccination coverage.csv
1286
1
#x0A
column
,
ecogrid://knb/han.23.1
Country
Exemplar great ape range countries
Congo
Congo
Cote d'Ivoire
Cote d'Ivore
DRC
Democratic Republic of Congo
CAR
Central African Republic
Gabon
Gabon
Uganda
Uganda
UK
United Kingdom (a tourist country)
Disease
Disease
Measles
Measles
Mumps
Mumps
Rubella
Rubella
Pertussis
Pertussis
Polio
Polio
Tetanus
Tetanus
TB
Tuberculosis
Vaccine
Vaccines for the disease
MCV
Measles containing vaccine including MMR (mumps measles rubella)
DPT1/DPT3
First and third Diptheria, pertusis and tetanus vaccinations given so that the rate at which the third is given is likely best representation of coverage
Pol3
Pol3 is the third in a series given
TT2
Second of five in a series and confers up to 5 years of expected protection and is usually given to pregnant mothers to prevent neonatal tetanus
BCG
Bacillus Calmette-Guerin attenuated bovine tuberculosis strain is though to be around 80% effective for 15 years
Vaccination coverage
Vaccination coverage (%) in exemplar great ape range countries. For Pertusis, the value listed is (value1/value2) which corresponds to percent coverage for (DPT1/DPT3) respectively. "nr" indicates not reported.
dimensionless
natural
Cases reported
Number of cases reported for a particular disease. "nr" denotes not reported.
dimensionless
natural
49