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

• 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

ASF Short Term mitigation outcomes

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.

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)

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)

Related ASF-West Africa viruses

Lisbon

1957, 60

Cuba 1971, 1980

Dom. Rep 1978

Haiti 1978

Brasil 1978

GeorgiaJune 2007

ASF EPIDEMIOLOGY 1957 Angola: genotype I to Lisbon, spreading Europe and c/s Am.

2007 Eastern Africa: genotype II Caucasus Region and RF

Methods-Short term mitigationCSIRO-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 ILRI-BecA) 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

Results Summary AusAID CSIRO

• Database on pig husbandry compiled for 600 out of 3818 pig keeping households (total number of households approximately 8000) in Busia-Teso-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

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).

Genome Sequencing

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

Un-rooted tree derived from whole genomes showing genetic relationships of ASFV genomes

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 e-

extension• Test ‘rapid diagnostics’ and develop smart systems with

mobile phone readouts so that the information is rapidly relayed to veterinary authorities

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

Vaccines and Resistant Pigs-The futureLonger 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 approach-

with 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 non-transgenic approach

Funding StatusASF 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

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

ASFV circulating in domestic and wild pigs in

Africa

Pork products

Illegal movements

Risk of spread ASFV to non-endemic countries

Death of pigs kept by smallholders

Reduced incentives to invest in pig value

chains

Reduced supply of pork

Reduced household income

Increased povertyReduced food security

Price of pork increases

Pork unaffordable by poor consumers

ASFV outbreak in non-endemic countries

Stamping outSlaughter

Increased cost of pig production

Higher pork prices

Decreased profitability of

pig industry

Reduced demand

Introduction to wild pigs

ASF endemic

AFRICA WORLD

Reduced employment, business opportunities in

pork value chain