Analysis of African Swine Fever epidemiology and pig value chains to underpin design of an ASF risk management strategy on the Kenya-Uganda border

Closing workshop of the BecA-ILRI-CSIRO-AusAID project (2011-13): Understanding ASF epidemiology as a basis for control

2nd-3rd October, 2013. Sarova PanAfric Hotel, Nairobi, Kenya

Invited presentation: Armanda D S Bastos University of PretoriaArmanda D.S. Bastos, University of Pretoria

ASF in Africa: pathways to prevention & control

ASF IN AFRICAASF IN AFRICAPATHWAYS TO PREVENTION & CONTROL

Armanda D.S. Bastos, University of Pretoria

Going back in order to go forwardGoing back in order to go forward

In order to effectively prevent and control ASF,we need to understand

maintenance and spread of the virus

EPIDEMIOLOGY

PastPastPresentFuture

Current understanding of ASF epidemiologyCurrent understanding of ASF epidemiology

www.fao.org

HistoryHistory

Pi (K ) th d ti i (SA Pigs (Kenya - Montgomery, 1923) warthog-domestic pig (SA - Steyn 1928, 1932)

Angola (1933) indigenous/wild-domestic/exotic pig, recognised as d ( )same disease agent (1943)

Ornithodoros tick (European incursion 1957, 1960) Sánchez Botija 1963

African Ornithodoros tick (Plowright et al 1969) sylvatic cycle African Ornithodoros tick (Plowright et al. 1969) sylvatic cycle Large-scale surveys of ticks, warthogs & pigs in Africa domestic

pig-tick cycle (Malawi)W Af i (1978) d i i l West Africa (1978) 1959, 1982, 1985, 1996 domestic pig cycle

European incursion - pig-pig (eradicated)pig pig (eradicated)- pig-tick (threat of re-emergence) Boinas et al. 2011

Psuedo / actual sylvatic cycle (eradication unlikely)

The latest incursionThe latest incursion

G t VIII i t d d t Genotype VIII introduced to Georgia in 2007 (Rowlandset al. 2008)S d h h h Spread throughout the Caucasus region (2007-10)

Introduced to Russia (2011) & poses a threat to Europe & China (pig population exceeds 1 billion) – Callaway 20122012

Detected in Iran (Rahimi et al. 2010)

Has increased its distributional range in Africa (Msinzo et al. 2012))

ASF distribution in Africa ASF distribution in Africa

Genotype I, 1959-present

Genotype II

Genotype II, 1998-2007

Genotype II, 1998

Genotype II, 2007

Resurgence of ASF outbreaks in AfricaResurgence of ASF outbreaks in Africa

Pig populations are increasing in Africa increase in risk of ASF

Outbreaks in Cameroon in 1982Outbreaks in Cameroon in 1982Preceded by doubling of pig population

Three-fold increase in pig numbers1980-2010 (FAOSTAT, 2011)

True numbers likely underestimatedLocal slaughter (not recorded)

Contribution of pig production to foodsecurity & income generation is underestimated

Pig farming systems vary - associated ASF risks varyg g y y y

Traditional (free-range during day, confined at night) increased ASF riskSemi-intensive (generally confined) & intensive (pigs are confined) with biosecurity reduced risk of ASF and other diseases (Fasina et al. 2012)

Successful eradication - MauritiusSuccessful eradication Mauritius

Biosecurity Modified stamping out soft loansp g Closure of abattoirs M t t l f i d i d t Movement control of pigs and pig products Compliance & legislation (to confine pigs)

Three discrete virus cyclesThree discrete virus cycles

1. Tick-warthog-pig cycle1. Tick warthog pig cycle

P i S f ( Prevention: Separation of sylvatic (tick and warthog) and domestic hosts control zones

Control: Slaughter out policy

Success requires:•Buy-in of all stakeholdersBuy in of all stakeholders•A structured, intensive pig industryAccurate demarcation of the zones•Accurate demarcation of the zones

•Flexibility: continuous monitoring and adjustment of ones zones

ASF distribution in Africa ASF distribution in Africa

Genotype I, 1959-present

Genotype II

Genotype II, 1998-2007

Genotype II, 1998

Genotype II, 2007

Lessons from NigeriaLessons from Nigeria

f 9 3 First report of disease in 1973 ‘Re-introduction’ in the mid 1990s Molecular characterisation of viruses collected

between 1998 and 2006 recover a monophyletic lineage (single introduction) and six CVR variants, of which one is identical to a virus isolated in 1997 in BBenin.

prolonged circulation of the virus uncontrolled movement of infected pigs (within

country and across borders)

Molecular epidemiology of ASF in NigeriaMolecular epidemiology of ASF in Nigeria

Nigeria (Tet-36)

Nigeria (Tet-27)

Portugal/60 (Tet-25a)

Portugal/88 (Tet-25c)

Nigeria (Tet-32)

Angola (Tet-14a)

Mozambique/60

Nigeria (Tet-20)Nigeria (Tet-21)

Nigeria (Tet-27)Nigeria (Tet-29)

Nigeria (Tet-32)

99/93

73/--

77/82

95/97

g ( )

Nigeria (Tet-21)

Spain/M61 (Tet-25b)

Dominican Republic/79 (Tet-22)

Spain/Co68 (Tet-26)

DRC/Kat67 (Tet-23a)

Malta/78 (Tet-31)

Nigeria (Tet-36)Benin97/1 (Tet-36)

Cameroon/82 (Tet-23b)

Brazil/78 (Tet-19)

Malta/78 (Tet-31)

Spain/M61 (Tet-25b)

Spain/Co61 (Tet-28a)

99/99

77/82

53/55

--/60

/50Cape Verde (Tet-17)

Nigeria (Tet-29)

Brazil/78 (Tet-19)

Nigeria (Tet-20)

Spain/Co61 (Tet-28a)

Benin97/1 (Tet-36)

Spain/Co61 (Tet 28a)

Portugal/63 (Tet-28b)

Spain/Co68 (Tet-26)

Portugal/60 (Tet-25a)

Spain Val76 (Tet-25a)

Portugal/88 (Tet-25c)

Dominican Republic/79 (Tet-22)

57/--

53/55--/50

Cameroon/82 (Tet-23b)

Belgium/85 (Tet-18)

Sardinia/90 (Tet-12)

Spain/Val76 (Tet-25a)

Vict/90 (Tet-14b)

Cape Verde (Tet-17)

Angola (Tet-14a)

Benin97/3 (Tet-8)

Vict/90 (Tet-14b)

Sardinia/90 (Tet-12)

Belgium/85 (Tet-18)

Dominican Republic/79 (22)

58/--

Mozambique/60

0.002(a)

Dominican Republic/79 (22)

0.05(b)

72 h l ( l tid d t t) CVR h l ( i id d t t) p72 gene phylogeny (nucleotide dataset) CVR phylogeny (amino acid dataset)

CVR: Central Variable Region (Tetrameric repeat coding & alignment)g ( p g g )Nigeria (Tet-20) YC---DNCCCC----GDNCCCC--GDN---------------------CKCWNigeria (Tet-21) YC---DNCCCC----GDNCCCCC-GDN---------------------CKCWNigeria (Tet-27) YC---DNCCCC----GDNCCCC--GDNCCCC----------GDN----CKCWNigeria (Tet 29) YC---DNCCCCC---GDNCCCC--GDNCCCCC---------GDN----CKCZNigeria (Tet-29) YC---DNCCCCC---GDNCCCC--GDNCCCCC---------GDN----CKCZNigeria (Tet-32) YCCCGDNCCCCCC--GDNCCCCCCGDNCCCC----------GD?------CZ Nigeria (Tet-36) YC---DNCCCC----GDNCCCCC-GDNCCCCCGDNCCCC--GDN----CKCZBenin97/1(Tet-36) YC---DNCCCC----GDNCCCCC-GDNCCCCCGDNCCCC--GDN----CKCZDRC/67 (Tet 23a) Y------CCCCCCCC---------------------DNCDVMDNCCCCCCCZDRC/67 (Tet-23a) Y------CCCCCCCC---------------------DNCDVMDNCCCCCCCZCam/82 (Tet-23b) YC---DNCCCC----GDNC--------------------DVMDNCCCCCNCZCapeVerde (Tet-17) YCC--DNC----------------------------DNCDVMDNC---CCCZAngola/70 (Tet-14a) YCC--DNC-------------------------------DVMDNC---CCCZVict/90 (Tet 14b) Y----DNCC---------------------------KN-DVMDJ----CKKZVict/90 (Tet-14b) Y----DNCC---------------------------KN-DVMDJ----CKKZBenin97/6 (Tet-8) YCCC-DNC-----------------------------------------DCZMalta/78 (Tet-31) YC---DNCCCC----GDNC------DNC--DNCDNCDNCDVMDN----CKCZSpain/Co61 (Tet-28a) YCCC-DNCCCCCCCCGDNC--------------DNCDNCDVM-------KCZPortugal/63 (Tet-28b) YC---DNCCCCCCC-GDNC--------------DNCDNCDVMDN----CKCZPortugal/63 (Tet-28b) YC DNCCCCCCC GDNC DNCDNCDVMDN CKCZSpain/68 (Tet-26) YC---DNCCCCC---GDNC--------------DNCDNCDVMDN----CKCZPortugal/60 (Tet-25a) YC---DNCCCC----GDNC--------------DNCDNCDVMDN----CKCZSpain/M61 (Tet-25b) YC---DNCCCCCC------------D-C--DNCDNCDNCDVM-------KCZSpain/Val76 (Tet-25a) YC---DNCCCC----GDNC--------------DNCDNCDVMDN----CKCZSpain/Val76 (Tet-25a) YC DNCCCC GDNC DNCDNCDVMDN CKCZPortugal/88 (Tet-25c) YC---DNCCCC----GDNC--------------DVCDNCDVMDN----CKCZDomRep/79 (Tet-22) YC---DNCCCC----GDNC-----------------DNCDNMDN----CKCZBrazil/78 (Tet-19) YC---DNCCCC----GDNC--------------------DVMDN----CKCZBelgium/85 (Tet-18) YC---DNC-------------------------DNCDNCDVMDN----CKCZBelgium/85 (Tet-18) YC DNC DNCDNCDVMDN CKCZSardinia/90 (Tet-12) YC---DNCCC-------------------------------MDN----CKCZMozambique/60 YC---DNCCCC----LDN------------------DNDC--DNDCD-HCLZ

Restrict ASF to the sylvatic cycleRestrict ASF to the sylvatic cycle

O i ill di t d t d lt O ith d Ongoing surveillance: directed at adult Ornithodorosticks (Arnot et al. 2010).

Mkuze Game Reserve northern KZN no evidence of Mkuze Game Reserve, northern KZN no evidence of ASF-infected Ornithodoros ticks.

Continued inclusion in the ASF control area needs to be re-evaluated.

Currently all Ornithodoros infested areas are being l d i d t d fi th t l sampled in order to redefine the control zone.

Policies and zoning need to be as flexible and adaptable as the virus adjust control zones AHEAD adaptable as the virus adjust control zones AHEAD of adjustments in range.

Challenges & the FutureChallenges & the Future

Different cycles different viruses? Monitor & predict emergence of “domestic pig p g p g

adapted viral lineages” Monitoring Tools: Molecular Biology GIS Risk Monitoring Tools: Molecular Biology, GIS, Risk

assessmentP ti P li i & C li Prevention: Policies & Compliance

ReferencesReferences

Based primarily on Penrith et al. 2013, Virus Research Arnot et al. 2009, Onderstepoort J Vet Res

B i l 2011 Pl O Boinas et al. 2011, Plos One

Callaway, 2012, Nature

Fasina et al 2012 Fasina et al. 2012

Jori & Bastos 2009, Eco Health

Misinzo et al. 2012, Emerging Infectious Diseases

Owolodun et al. 2010, Virus Genes