Presented by Richard Bishop, Jocelyn Davies, Cynthia Onzere, Steve Kemp, Vish Nene, Guenther Keil, Marisa Arias and Edward Okoth at the ILRI BioSciences Day, Nairobi, 27 November 2013

1. African Swine Fever (ASF) control
An entry point for enhancing human welfare through pig system
improvement
Richard Bishop, Jocelyn Davies1, Cynthia Onzere, Steve Kemp, Vish Nene, Guenther
Keil2, Marisa Arias3, Edward Okoth
1
CSIRO, Australia 2Friedrich Loeffler Institute (FLI) Germany, 3CISA-INIA. Spain
ILRI BioSciences Day, Nairobi, 27 November 2013
TT

2. ASF Short Term mitigation outcomes
• Pigs are an affordable source of protein for resource poor
livestock keepers
• Pigs are primarily kept in Africa to generate income. ASF risk
reduction will facilitate increased household incomes-one pig
that farrows twice annually can pay for the education of a child
for a year ($350).
• ASF is the most important single disease constraint to pig
production in Africa
• There are two key development outcomes from short term
mitigation:
• Improved education and biosecurity implementation that directly targets
farmers from small to medium scale
• More rapid and user friendly diagnostics will assist veterinary authorities to
confirm outbreaks early and impose quarantine
• Longer term solutions will involve development of vaccines and
resistant pigs

3. PIG SYSTEMS-African livestock revolution
The pig population
in Africa increased
284% during the
20year period
1980–1999 - far
more than for any
other livestock
species during that
time period and the
trend continues.

4. Current Status of ASF and the potential for improved
control to promote system level outcomes
• Currently there is no vaccine or chemotherapeutic for ASF
– Control is implemented through test and slaughter (not affordable in endemic
areas of Africa)
– The disease is endemic in more than 30 African countries and spreading.
– It is out control in Russia threatening the borders of the EU
• In the short term, improved adoption of prophylactic biosecurity will help to
mitigate disease impact in endemic areas
• The short life cycle of pigs has already resulted in pig keeping becoming the
most dynamic livestock sector in some countries in Africa- thereby reducing
rural poverty (SLO1+ve)
• Control of the spread of ASF will be positive for global food security
(SL02=+ve)
• The proposition of improved human health and nutrition through increased
pork consumption is researchable but unproven (SLO3=?)
• Pig production in the developing world is usually not intensive and the impact
on the environment is limited (therefore SL04 is not yet applicable)

5. The problem: Global significance
• The world has approximately 1 billion pigs, 500 million
in China alone (mainly backyard)
• Pork consumption has more than doubled over the past
20 years in Asia- (Livestock Revolution Delgado et. al.
1999) and this trend is now spreading to suitable
regions of Africa
• A prime example is Uganda 100,000 to 4 million pigs in
40 years. Pork consumption in Uganda is now close to
that of beef (recent FAOSTAT data)
• The major system level outcome linkage on a global
scale is to improved food security (SLO2)

6. 1957 Angola: genotype I to
Lisbon, spreading Europe and c/s Am.
Li
s
Cuba 1971, 1980
b
Dom. Rep 1978
o
Haiti 1978
n
ASF EPIDEMIOLOGY
2007 Eastern Africa: genotype II Caucasus
Region and RF
195
7,
60
Brasil 1978
Related ASF-West Africa viruses
Georgia
June 2007

7. Methods-Short term mitigation
CSIRO-Ausaid-BecA-ILRI collaboration-Uganda-Kenya border Busia-Tororo
• Innovative combination of biophysical sampling of pigs at
household level and PCR surveillance genotyping (led by ILRIBecA) plus social science (led by CSIRO)
• Scientific approach
•
•
•
•
•
•
•
•
600 Households sampled for blood and serum (1000+ pigs)-horizontal
100 ear-tagged pigs followed up twice at 3 month intervals
Surveillance for ASF in both laboratory and field by PCR
Virus isolation
Genotyping of out break viruses and whole genome sequencing of reference isolates
Questionnaires simultaneously administered on all aspects of pig keeping ( automatically captured in MS
Access database for analysis)
Biosecurity calendar circulated -Feedback sessions (focus groups with farmers)
Social network approaches used to analyze local value chains
• Planned Phase 3 to capture development outcome
(knowledge based interventions in the trans-boundary Busia
study area )
•
•
•
Community Knowledge Worker-(smart mobile-based platform)
NGO
Busia Regional DVS
• Scale out- where appropriate to additional regions in
partnership with FAO-ECTAD

8. Results Summary AusAID CSIRO
• Database on pig husbandry compiled for 600 out of 3818 pig keeping
households (total number of households approximately 8000) in BusiaTeso-Tororo-Uganda-Kenya border study area
• Prevalence of virus in asymptomatic pigs is low in study area but
outbreaks are frequent-Why?
• Virus prevalence is much higher in slaughter slabs suggesting rapid
recognition of disease and selling by farmers
• The sylvatic cycle, involving virus from wild pigs and ticks, is rarely
associated with outbreaks either within or outside study area
• All outbreaks genotyped were the domestic pig associated genotpye IX
• The genotype IX virus appears to have recently reached the Kenya
coast - with obvious implications for future global transmission
• Farmer surveys indicate a willingness to adopt certain prophylactic
biosecurity measures
• Feed as well as disease is also a key constraint and feed availability
may drive production and market prices locally

9. Results Viral and Host Genomics
• Two major ASFV genotypes exist in East Africa
according to the gene sequence of the major surface
protein p72.
• Both are closely related to one another and distinct
from other ASFV viruses according to complete
genome sequence data
• Preliminary data exists that ‘indigenous’ African
domestic pigs exhibit a degree of resistance to
experimental infection with certain ASFV genotypes
relative to exotic breeds (e.g. landrace/large white
crosses.
-This result needs to be re-confirmed (ongoing with
Spanish funding).

10. Genome Sequencing
Un-rooted tree derived from
whole genomes showing genetic
relationships of ASFV genomes
Analysis of complete
genome sequences has
shown that p72 genotype
IX viruses in East Africa
from 2005-2013 Kenyan
ASF outbreaks in pigs
cluster with genotype X
from pigs and ticks.
These Kenyan and
Ugandan genotypes are
distinct from other
sequenced viruses

11. Where to from now? ASF Mitigation
• Testing rapid enhanced biosecurity and rapid diagnosis
and response at the Busia transboundary Kenya-Uganda
benchmark site -AusAID project Phase 3 (Edward Okoth
and Jocelyn Davies)
Key activities
• Farmer Education in Biosecurity
• Improve pig health and production practices through eextension
• Test ‘rapid diagnostics’ and develop smart systems with
mobile phone readouts so that the information is
rapidly relayed to veterinary authorities

12. Conclusions and discussion points:
Mitigation Strategies
• The mechanisms of maintenance of the virus in the
designated study area where transmission is from pig to pig
are not yet clear
• Is there a reservoir or just a constant cycle of short term infections that
burn out rapidly?
• Regional genetic variation of ASFV in Kenya and Uganda is
limited and current outbreaks in these countries are
predominantly caused by a single p72 genotype (IX)
• The challenge for short term mitigation strategies will be to
provide incentives for behavioural change by farmers
• (A) safe carcass disposal (B) Use of safe feeds-not swill (C) separate
housing of recently introduced animals (D) reporting of outbreaks
• Mitigation strategies may be hard to scale out widely due to
the inherent variation in value chains which are diverse and
determined by environmental, cultural and historical factors

13. Vaccines and Resistant Pigs-The future
Longer Term (10 years)
Vaccines:
• ILRI is PI on the first vaccine project in an endemic area
• C -Advantage –we can work at BSL2 level with cost and
biosafety implications
• Rationally attenuated live vaccines: Innovative SAVE approachwith FLI Germany
• Recombinant-empirical approach-viral vectors-identification of T
cell antigens by peptide binding to SLA (porcine class I MHC)
Resistant pigs:
• African wild pigs virus resistant; African domestic pigs partially
resistant. Research the molecular basis of resistance using
comparative and functional genomics
• Modify more productive exotic animals-based on findings: may
be able to utilise genome editing using zinc finger DNA
binding/endonuclease fusion enzymes (talens)-Novel nontransgenic approach

14. Funding Status
ASF research sources of support
• Live attenuated vaccine development in collaboration with FLI, Germany
(implementing SAVE rational attenuation approach) plus antigen identification
at ILRI (US$ 1.5 million from BMZ- currently no ILRI matching contribution)
• Further studies on indigenous pig resistance to ASFV infection, plus
development of in vivo vaccine challenge model with CISA-INIA Spain (US$
100,000+ for 2014)
• AusAID Phase 3 under negotiation (extent of funding and scope of activities for
this project currently unclear)
• Defense threat reduction agency USA (DTRA) application to determine multiple
ASFV genome sequences -white paper for genome sequencing and capacity
building submitted and under consideration
• Major 2013 USAID project for recombinant vaccines and molecular
mechanisms of ASFV resistance in wild pigs -collaboration with Borlaug
Institute-Texas A and M - successful- need to rework for other donors
• Major global consortium for vaccine development Pirbright, Jenner - Declined
by DFID in 2012-Need to seek other donors
• Limited support from CRP3.7 in 2013 (PI 20% salary mainly for proposal
development): 2014 situation currently unclear

15. Additional options for biotechnology research to
promote pig system development
improvement development
• CSIRO-Ausaid supported database provides much generic
data on smallholder pig systems. This will enable modeling
of interventions
• Bio-banked samples will allow assessment of the burdens
of other diseases that are important in the pig sector, for
example PRRS and PCV-FLI collaboration being explored
• Feed emerged as a key constraint from Busia study
-Evalution of novel feed sources to reduce input costs
linked to CKW platform is worth exploring
Possible Grameen foundation support

16. AFRICA
WORLD
Reduced
demand
Reduced employment,
business opportunities in
pork value chain
Higher pork prices
Pork unaffordable by
poor consumers
ASF endemic
Price of pork increases
Increased poverty
Reduced food security
Reduced household
income
Reduced supply of pork
Decreased
profitability of
pig industry
Introduction to
wild pigs
Increased cost of pig
production
Stamping out
Slaughter
ASFV outbreak in nonendemic countries
Reduced incentives to
invest in pig value
chains
Death of pigs kept by
smallholders
Risk of spread ASFV to
non-endemic countries
Illegal
movements
Pork
products
ASFV circulating in
domestic and wild pigs in
Africa