In Uganda swine is a major protein source and is kept by ca 19 per cent of the rural population. Estimations say that about two million pigs are kept in Uganda. From the governmental side pig is recommended as being ideal for poorer people, but also for bigger production, due to the large litter sizes and that they reach slaughter weight fast. Unfortunately, this also gives problems with infectious diseases of various kinds. One of the most feared diseases of pigs is African swine fever (ASF), which is caused by a virus, African Swine fever virus (ASFV). There are currently no vaccine or treatment for this disease. Occasionally there are big outbreaks and this leads to tremendous consequences for the farmer and is extremely painful for the animals. The symptoms can vary a lot from sudden death to more subtle, and therefore it can be difficult to judge if pigs have the disease or not. One reason for this is that different genetic variants circulate of the virus that have different pathogenicity. The natural reservoirs of the virus are different types of wild pigs, warthogs and bushpigs and a soft tick (Ornithodoros) and may via the latter be transferred to domestic pigs. The introduction is however often due to infected pigs or meat products. This is due both to economical reasons and knowledge gaps about the virus behind the disease. Lots of the virus epidemiology and life cycle is unknown that must be sorted out to be able to combat the viral disease in an effective way. The scope of this project, which is a part of a bigger project, is to study the virus in the tick vector using so called viral metagenomics. This is a combination of advanced molecular techniques and computer analysis (bioinformatics). This will give a more complete picture of the virus survival and spread in the vector.

1. Sveriges lantbruksuniversitet
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Metagenomic studies on virus dynamics at the
livestock/tick/wildlife interface: with special reference to
African swine fever
Mikael Berg1, Charles Masembe2, Rose Ademun Okurut3, Patrick Atimnedi6,
Anne Fischer4, Robert Skilton4, Richard P. Bishop4, Anne-Lie Blomström1, Karl
Ståhl1, 5
1) Section of Virology, Department of Biomedical Sciences and Veterinary Public Health,
Swedish University of Agricultural Sciences, Uppsala, Sweden, 2) College of Natural
Sciences, Makerere University, Kampala, Uganda, 3) Ministry of Agriculture, Animal
Industry and Fisheries, Entebbe, Uganda, 4) International Livestock Research Institute,
Nairobi, Kenya, 5) National Veterinary Institute, Uppsala, Sweden, 6) Uganda Wildlife
Authority, Kampala, Uganda
Presenter: Mikael Berg, professor in veterinary virology
(mikael.berg@slu.se)

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Courtesy of Klaas Dietze, FAO
Pig sector development in Africa

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Pig sector development
Uganda
FAOSTAT, 2010

4. Sveriges lantbruksuniversitet
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Why PIGS?
1. Agriculture is core sector in Uganda’s economy (73%
labor force, GDP)
2. Increasing local & global demand for meat and other
livestock products
3. Grow fast and give large litters
4. Pigs – walking banks
Constraints of this
1. Infectious diseases-in particular African swine fever

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• OIE listed viral disease
• Acute, highly contagious
disease of domestic pigs
• High mortality, reaching 100%
• No vaccines, no cure
• Emerging transboundary
disease
African Swine Fever

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Trends of ASF outbreaks in Africa
Year Number of
Countries
Numbers of
Outbreaks
Numbers of
Cases
Numbers of
Deaths
2007 11 101 101 823 100 188
2008 18 207 191 197 96 108
2009 19 130 10 240 7 530
2010 21 145 27 529 27 054
2011 22 471 144 950 149 116
Source AU-IBAR

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What are the reasons for ASFV outbreaks?
What can we do about it?

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1: Understanding the ASF Epidemiology
• Reservoir in soft ticks
– Survival > three years recorded
• Asymptomatic infection in warthogs
and bushpigs
• Two main mechanisms of transmission
– Sylvatic: Ticks fed on warthogs to
domestic pigs
• Current quantitative importance
unclear
• The role of the bushpig unknown
– Domestic pig to pig cycle
• The most important mode of
transmission today in most locations
• Human involvement?

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Studies on outbreaks-Gulu district
 Post conflict area in northern Uganda
 Farmers return to ancestral rural land after
25 years in IDP camps
 Small holder pig production promoted by
Government and NGOs
 Free range systems dominate
 ASF reported from 14/16 subcounties during
current outbreak

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Results- Outbreaks
 Outbreaks reported from and confirmed in 45 villages
 219 affected farmers identified and visited

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Number
Village Dead Survive
Pigs
now
Mortality
(%)
Estimated
duration
(days)
Awoo 63 11 28 85,1 15
Ocok Can 26 2 0 92,9 40
Bar Romo 34 15 14 69,4 25
Abura 17 5 2 77,3 15
Kalamomia 23 10 5 69,7 15
Boke 21 4 12 84,0 70
Boke-Bar 22 1 0 95,7 25
Arwot-Omia 68 10 41 87,2 >200*
Opok 41 7 2 85,4 30
Omoro 48 9 22 84,2 60
TeeOlam 73 4 1 94,8 25
Palenga TeOpok 20 2 2 90,9 20
Paomo 11 4 4 73,3 20
Peresi 26 15 25 63,4 25
Peresi´2 26 0 10 100 10
Labwor Omor 28 0 5 100 10
Layibi Kwite 63 12 6 84,0 30
Total 1178 288 401 80%
Results- Mortality

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Results- Transmission chains
 Boar borrowed from A to B for breeding. Boar died in a week’s time. Massive
deaths in B
 Butcher buys pig for slaughter in B and move to C
 1 kg pork bought from village C, where pigs were dying, and taken to D
 Carcass of dead pig moved from village D to E
 Massive deaths reported from E. Butcher moves pig to F
 Massive deaths in F. Sick pig taken for slaughter in G
 Kids take skin from dead pig in G for oil extraction in H
C
E
G
F
A
B
D
H

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Transmission routes

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Conclusions part I
 In spite of quarantine measures, a highly virulent strain of ASFV with
mortalities > 80% was efficiently spread throughout the study area
during the period
 Movement of sick or dead pigs, and pork from dead pigs main route of
spread between villages
 Low level of biosecurity responsible for within village spread
 All stakeholders in the pig value chain (eg farmers, traders, butchers,
consumers) involved in spread of disease…..
 …..and in causing a situation with more ASFV in circulation than ever
before…
 …jeopardizing further development of the pig sector

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Dissemination activities
Seven dissemination workshops for rural
stakeholders (farmers, butchers and
traders) organized to discuss implications
of findings and ways forward in regard to
prevention of disease outbreaks and
reduction of impact.

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Metagenomics
• Complete microbial genetic
composition of a given sample
• Initially a sequence-independent
approach
• Do not require isolation of the
pathogen
• Variety of sample types
Better understanding virus biology and epidemiology

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Overview of the method

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What can one study using metagenomics
and ”next generation of sequencing technology”
and bioinformatics?
In relation to ASFV
Genetic variation of ASFV in different host-in connection to pathogenicity
Evolution of the virus
Find novel reservoirs
Full-length genome sequencing
Etc
Other issues
Discover new viruses
Study host response
The viral community-what kind of ”virus flora” do a healthy animal contra sick animal have
Potential zoonotic viruses?
Emerging viruses?
Etc

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Reservoirs and vectors
Blastn Blastx
6 TTV 48 – 77% N/A
2 PCV 96 – 97 % N/A
10
HeV-
like
N/A 32%

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Can pigs harbor emerging infectious
diseases?
Sampling of domestic pigs in Uganda-what viruses do seamingly healthy pigs have?

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In addition to ASFV in all pools, TTV was common and…this one as well

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General Conclusions
1. ASF a main constraint to the growing and important pig industry
2. Maintenance and spread of ASF – further investigations needed
3. Metagenomics- opportunities for deeper investigations
4. Results Dissemination to grassroot farmers – disease control

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Acknowledgements
Sweden Uganda Kenya
Funding institutions
•SLU
•Sida
•Formas
•VR
•APHIS/USDA
SLU
•Dr Sofia Boqvist
•Prof Ulf Emanuelson
•Dr Mikael Berg
•MFS students
•m.fl.
MAK
•Dr Charles Masembe
•Dr Denis Muhangi
•Dr Susan Ndyanabo
•MUIENR staff
MAAIF
•Dr Tonny Aliro
•Dr Ademun Rose
•Dr Chris Rutebarika
•Dr Noelina Nantima
•Martin Esau
•Dr Lawrence Mayega
•DVOs, NADDEC staff
UWA
•Dr Patrick Atimnedi
ILRI
•Dr Richard Bishop
•Dr Edward Okoth
FAO
•Dr Klaas Dietze
APHIS
•Dale Nolte et al
Swedish Ministry of
Foreign Affairs