Sveriges lantbruksuniversitet
www.slu.se
Metagenomic studies on virus dynamics at the
livestock/tick/wildlife interface: w...
Sveriges lantbruksuniversitet
www.slu.se
Courtesy of Klaas Dietze, FAO
Pig sector development in Africa
Sveriges lantbruksuniversitet
www.slu.se
Pig sector development
Uganda
FAOSTAT, 2010
Sveriges lantbruksuniversitet
www.slu.se
Why PIGS?
1. Agriculture is core sector in Uganda’s economy (73%
labor force, GDP...
Sveriges lantbruksuniversitet
www.slu.se
• OIE listed viral disease
• Acute, highly contagious
disease of domestic pigs
• ...
Sveriges lantbruksuniversitet
www.slu.se
Trends of ASF outbreaks in Africa
Year Number of
Countries
Numbers of
Outbreaks
N...
Sveriges lantbruksuniversitet
www.slu.se
What are the reasons for ASFV outbreaks?
What can we do about it?
Sveriges lantbruksuniversitet
www.slu.se
1: Understanding the ASF Epidemiology
• Reservoir in soft ticks
– Survival > thre...
Sveriges lantbruksuniversitet
www.slu.se
Studies on outbreaks-Gulu district
 Post conflict area in northern Uganda
 Farm...
Sveriges lantbruksuniversitet
www.slu.se
Results- Outbreaks
 Outbreaks reported from and confirmed in 45 villages
 219 a...
Sveriges lantbruksuniversitet
www.slu.se
Number
Village Dead Survive
Pigs
now
Mortality
(%)
Estimated
duration
(days)
Awoo...
Sveriges lantbruksuniversitet
www.slu.se
Results- Transmission chains
 Boar borrowed from A to B for breeding. Boar died ...
Sveriges lantbruksuniversitet
www.slu.se
Transmission routes
Sveriges lantbruksuniversitet
www.slu.se
Conclusions part I
 In spite of quarantine measures, a highly virulent strain of...
Sveriges lantbruksuniversitet
www.slu.se
Dissemination activities
Seven dissemination workshops for rural
stakeholders (fa...
Sveriges lantbruksuniversitet
www.slu.se
Metagenomics
• Complete microbial genetic
composition of a given sample
• Initial...
Sveriges lantbruksuniversitet
www.slu.se
Overview of the method
Sveriges lantbruksuniversitet
www.slu.se
What can one study using metagenomics
and ”next generation of sequencing technolo...
Sveriges lantbruksuniversitet
www.slu.se
Reservoirs and vectors
Blastn Blastx
6 TTV 48 – 77% N/A
2 PCV 96 – 97 % N/A
10
He...
Sveriges lantbruksuniversitet
www.slu.se
Can pigs harbor emerging infectious
diseases?
Sampling of domestic pigs in Uganda...
Sveriges lantbruksuniversitet
www.slu.se
In addition to ASFV in all pools, TTV was common and…this one as well
Sveriges lantbruksuniversitet
www.slu.se
General Conclusions
1. ASF a main constraint to the growing and important pig ind...
Sveriges lantbruksuniversitet
www.slu.se
Sveriges lantbruksuniversitet
www.slu.se
Acknowledgements
Sweden Uganda Kenya
Funding institutions
•SLU
•Sida
•Formas
•VR
...
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Metagenomic studies on virus dynamics at the livestock/tick/wildlife interface: with special reference to African swine fever

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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.

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Metagenomic studies on virus dynamics at the livestock/tick/wildlife interface: with special reference to African swine fever

  1. 1. Sveriges lantbruksuniversitet www.slu.se 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)
  2. 2. Sveriges lantbruksuniversitet www.slu.se Courtesy of Klaas Dietze, FAO Pig sector development in Africa
  3. 3. Sveriges lantbruksuniversitet www.slu.se Pig sector development Uganda FAOSTAT, 2010
  4. 4. Sveriges lantbruksuniversitet www.slu.se 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
  5. 5. Sveriges lantbruksuniversitet www.slu.se • 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
  6. 6. Sveriges lantbruksuniversitet www.slu.se 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
  7. 7. Sveriges lantbruksuniversitet www.slu.se What are the reasons for ASFV outbreaks? What can we do about it?
  8. 8. Sveriges lantbruksuniversitet www.slu.se 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?
  9. 9. Sveriges lantbruksuniversitet www.slu.se 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
  10. 10. Sveriges lantbruksuniversitet www.slu.se Results- Outbreaks  Outbreaks reported from and confirmed in 45 villages  219 affected farmers identified and visited
  11. 11. Sveriges lantbruksuniversitet www.slu.se 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
  12. 12. Sveriges lantbruksuniversitet www.slu.se 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
  13. 13. Sveriges lantbruksuniversitet www.slu.se Transmission routes
  14. 14. Sveriges lantbruksuniversitet www.slu.se 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
  15. 15. Sveriges lantbruksuniversitet www.slu.se 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.
  16. 16. Sveriges lantbruksuniversitet www.slu.se 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
  17. 17. Sveriges lantbruksuniversitet www.slu.se Overview of the method
  18. 18. Sveriges lantbruksuniversitet www.slu.se 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
  19. 19. Sveriges lantbruksuniversitet www.slu.se Reservoirs and vectors Blastn Blastx 6 TTV 48 – 77% N/A 2 PCV 96 – 97 % N/A 10 HeV- like N/A 32%
  20. 20. Sveriges lantbruksuniversitet www.slu.se Can pigs harbor emerging infectious diseases? Sampling of domestic pigs in Uganda-what viruses do seamingly healthy pigs have?
  21. 21. Sveriges lantbruksuniversitet www.slu.se In addition to ASFV in all pools, TTV was common and…this one as well
  22. 22. Sveriges lantbruksuniversitet www.slu.se 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
  23. 23. Sveriges lantbruksuniversitet www.slu.se
  24. 24. Sveriges lantbruksuniversitet www.slu.se 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

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