Presented by Armanda D.S. Bastos at the Closing workshop of the BecA‐ILRI‐CSIRO‐AusAID project on Understanding ASF epidemiology as a basis for control, Nairobi, Kenya, 2‐3 October 2013

1. 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 Pretoria
Armanda D S Bastos University of Pretoria
ASF in Africa: pathways to prevention & control

2. ASF IN AFRICA
PATHWAYS TO PREVENTION
& CONTROL
Armanda D.S. Bastos, University of Pretoria

3. Going 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
Past
Present
Future

4. Current understanding of ASF epidemiology
www.fao.org

5. History







Pigs (Kenya - Montgomery, 1923)  warthog-domestic pig (SA - Steyn 1928,
Pi (K
th d
ti i
1932)
Angola (1933)  indigenous/wild-domestic/exotic pig, recognised as
same d
disease agent (1943)
Ornithodoros tick (European incursion 1957, 1960) Sánchez Botija 1963
African Ornithodoros tick (Plowright et al 1969)  sylvatic cycle
al.
Large-scale surveys of ticks, warthogs & pigs in Africa  domestic
pig-tick cycle (Malawi)
West Africa
W Af i (1978) 1959, 1982, 1985, 1996  d
domestic pig cycle
i i
l
European incursion
- pig-pig (eradicated)
pig pig
- pig-tick (threat of re-emergence)  Boinas et al. 2011
Psuedo / actual sylvatic cycle (eradication unlikely)

6. The latest incursion





Genotype VIII i t d d t
G t
introduced to
Georgia in 2007 (Rowlands
et al. 2008)
Spread throughout the
S
d h
h
h
Caucasus region (2007-10)
Introduced to Russia (2011) &
poses a threat to Europe &
China (pig population
exceeds 1 billion) – Callaway
2012
Detected in Iran (Rahimi et al.
2010)
Has increased its distributional
range in Africa (Msinzo et al.
2012)
)

7. ASF distribution in Africa
Genotype I, 1959-present
Genotype II
Genotype II, 1998-2007
Genotype II, 1998
Genotype II, 2007

8. Resurgence of ASF outbreaks in Africa
Pig populations are increasing in Africa  increase in risk of ASF
Outbreaks in Cameroon in 1982
Preceded by doubling of pig population
Three-fold increase in pig numbers
1980-2010 (FAOSTAT, 2011)
True numbers likely underestimated
Local slaughter (not recorded)
Contribution of pig production to food
security & income generation is underestimated

9. Pig farming systems vary - associated ASF risks vary
g
g y
y
y
Traditional (free-range during day, confined at night)  increased ASF risk
Semi-intensive (generally confined) & intensive (pigs are confined)
with biosecurity  reduced risk of ASF and other diseases (Fasina et al. 2012)

10. Successful eradication - Mauritius





Biosecurity
Modified stamping out  soft loans
p g
Closure of abattoirs
Movement control of pigs and pig products
M
t
t l f i
d i
d t
Compliance & legislation (to confine pigs)

11. Three discrete virus cycles

12. 1. Tick-warthog-pig cycle
Tick warthog pig


Prevention: S
P
i
Separation of sylvatic (
f
(tick and
warthog) and domestic hosts  control zones
Control: Slaughter out policy
Success requires:
•Buy-in of all stakeholders
Buy in
•A structured, intensive pig industry
•Accurate demarcation of the zones
•Flexibility: continuous monitoring and adjustment of
zones
ones

13. ASF distribution in Africa
Genotype I, 1959-present
Genotype II
Genotype II, 1998-2007
Genotype II, 1998
Genotype II, 2007

14. Lessons from Nigeria





First report of disease in 1973
f
9 3
‘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
Benin.
 prolonged circulation of the virus
 uncontrolled movement of infected pigs (within
country and across borders)

16. Molecular epidemiology of ASF in Nigeria
Mozambique/60
Nigeria (Tet-36)
99/93
Nigeria (Tet-27)
Nigeria (Tet-20)
Nigeria (Tet-21)
Portugal/60 (Tet-25a)
95/97
Portugal/88 (Tet-25c)
Nigeria (Tet-27)
73/--
Nigeria (Tet-32)
Nigeria (Tet-29)
Nigeria (Tet-32)
Angola (
g
(Tet-14a)
)
77/82
Nigeria (Tet-36)
Nigeria (Tet-21)
99/99
Spain/M61 (Tet-25b)
Cameroon/82 (Tet-23b)
Dominican Republic/79 (Tet-22)
Brazil/78 (Tet-19)
Spain/Co68 (Tet-26)
Malta/78 (Tet-31)
--/60
DRC/Kat67 (Tet-23a)
Spain/M61 (Tet-25b)
Malta/78 (Tet-31)
53/55
--/50
/50
Cape Verde (Tet-17)
Spain/Co61 (Tet-28a)
(Tet 28a)
Portugal/63 (Tet-28b)
Nigeria (Tet-29)
Spain/Co68 (Tet-26)
Brazil/78 (Tet-19)
57/--
Nigeria (Tet-20)
Portugal/60 (Tet-25a)
Spain Val76 (Tet-25a)
Spain/Co61 (Tet-28a)
Portugal/88 (Tet-25c)
Dominican Republic/79 (Tet-22)
Benin97/1 (Tet-36)
58/--
Cameroon/82 (Tet-23b)
Cape Verde (Tet-17)
Angola (Tet-14a)
Belgium/85 (Tet-18)
Benin97/3 (Tet-8)
Sardinia/90 (Tet-12)
Vict/90 (Tet-14b)
Spain/Val76 (Tet-25a)
Sardinia/90 (Tet-12)
Vict/90 (Tet-14b)
Belgium/85 (Tet-18)
Dominican Republic/79 (22)
Mozambique/60
(a)
(b)
0.05
0.002
p72 gene phylogeny ( l tid d t t)
72
h l
(nucleotide dataset)
CVR phylogeny ( i acid d t t)
h l
(amino id dataset)
Benin97/1 (Tet-36)

17. CVR: Central Variable Region (Tetrameric repeat coding & alignment)
g (
p
g
g
)
Nigeria (Tet-20)
Nigeria (Tet-21)
Nigeria (Tet-27)
Nigeria (Tet 29)
(Tet-29)
Nigeria (Tet-32)
Nigeria (Tet-36)
Benin97/1(Tet-36)
DRC/67 (Tet-23a)
(Tet 23a)
Cam/82 (Tet-23b)
CapeVerde (Tet-17)
Angola/70 (Tet-14a)
Vict/90 (Tet-14b)
(Tet 14b)
Benin97/6 (Tet-8)
Malta/78 (Tet-31)
Spain/Co61 (Tet-28a)
Portugal/63 (Tet-28b)
Spain/68 (Tet-26)
Portugal/60 (Tet-25a)
Spain/M61 (Tet-25b)
Spain/Val76 (Tet-25a)
Portugal/88 (Tet-25c)
DomRep/79 (Tet-22)
Brazil/78 (Tet-19)
Belgium/85 (Tet-18)
Sardinia/90 (Tet-12)
Mozambique/60
YC---DNCCCC----GDNCCCC--GDN---------------------CKCW
YC---DNCCCC----GDNCCCCC-GDN---------------------CKCW
YC---DNCCCC----GDNCCCC--GDNCCCC----------GDN----CKCW
YC---DNCCCCC---GDNCCCC--GDNCCCCC---------GDN----CKCZ
YCCCGDNCCCCCC--GDNCCCCCCGDNCCCC----------GD?------CZ
YC---DNCCCC----GDNCCCCC-GDNCCCCCGDNCCCC--GDN----CKCZ
YC---DNCCCC----GDNCCCCC-GDNCCCCCGDNCCCC--GDN----CKCZ
Y------CCCCCCCC---------------------DNCDVMDNCCCCCCCZ
YC---DNCCCC----GDNC--------------------DVMDNCCCCCNCZ
YCC--DNC----------------------------DNCDVMDNC---CCCZ
YCC--DNC-------------------------------DVMDNC---CCCZ
Y----DNCC---------------------------KN-DVMDJ----CKKZ
YCCC-DNC-----------------------------------------DCZ
YC---DNCCCC----GDNC------DNC--DNCDNCDNCDVMDN----CKCZ
YCCC-DNCCCCCCCCGDNC--------------DNCDNCDVM-------KCZ
YC
YC---DNCCCCCCC-GDNC--------------DNCDNCDVMDN----CKCZ
DNCCCCCCC GDNC
DNCDNCDVMDN
CKCZ
YC---DNCCCCC---GDNC--------------DNCDNCDVMDN----CKCZ
YC---DNCCCC----GDNC--------------DNCDNCDVMDN----CKCZ
YC---DNCCCCCC------------D-C--DNCDNCDNCDVM-------KCZ
YC
YC---DNCCCC----GDNC--------------DNCDNCDVMDN----CKCZ
DNCCCC
GDNC
DNCDNCDVMDN
CKCZ
YC---DNCCCC----GDNC--------------DVCDNCDVMDN----CKCZ
YC---DNCCCC----GDNC-----------------DNCDNMDN----CKCZ
YC---DNCCCC----GDNC--------------------DVMDN----CKCZ
YC
YC---DNC-------------------------DNCDNCDVMDN----CKCZ
DNC
DNCDNCDVMDN
CKCZ
YC---DNCCC-------------------------------MDN----CKCZ
YC---DNCCCC----LDN------------------DNDC--DNDCD-HCLZ

18. Restrict ASF to the sylvatic cycle





Ongoing
O i surveillance: di t d at adult O ith d
ill
directed t d lt Ornithodoros
ticks (Arnot et al. 2010).
Mkuze Game Reserve, northern KZN  no evidence of
Reserve
ASF-infected Ornithodoros ticks.
Continued inclusion in the ASF control area needs to be
re-evaluated.
Currently all Ornithodoros infested areas are being
sampled in order to redefine the control zone.
l di
d t
d fi th
t l
Policies and zoning need to be as flexible and
adaptable as the virus  adjust control zones AHEAD
of adjustments in range.

19. Challenges & the Future




Different cycles  different viruses?
Monitor & predict emergence of “domestic pig
p
g
pg
adapted viral lineages”
Monitoring Tools: Molecular Biology GIS Risk
Biology, GIS,
assessment
Prevention: P li i & C
P
ti Policies Compliance
li

20. References
Based primarily on Penrith et al. 2013, Virus Research

Arnot et al. 2009, Onderstepoort J Vet Res

Boinas et al. 2011 Pl O
B i
l 2011, Plos One

Callaway, 2012, Nature

Fasina et al. 2012
al

Jori & Bastos 2009, Eco Health

Misinzo et al. 2012, Emerging Infectious Diseases

Owolodun et al. 2010, Virus Genes