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 Blomstrm1, Karl Sthl1, 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. Sveriges lantbruksuniversitet www.slu.se Courtesy of Klaas Dietze, FAO Pig sector development in Africa 3. Sveriges lantbruksuniversitet www.slu.se Pig sector development Uganda FAOSTAT, 2010 4. Sveriges lantbruksuniversitet www.slu.se Why PIGS? 1. Agriculture is core sector in Ugandas 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. 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. 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. Sveriges lantbruksuniversitet www.slu.se What are the reasons for ASFV outbreaks? What can we do about it? 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. 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. Sveriges lantbruksuniversitet www.slu.se Results- Outbreaks Outbreaks reported from and confirmed in 45 villages 219 affected farmers identified and visited 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 Peresi2 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. Sveriges lantbruksuniversitet www.slu.se Results- Transmission chains Boar borrowed from A to B for breeding. Boar died in a weeks 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. Sveriges lantbruksuniversitet www.slu.se Transmission routes 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. 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. 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. Sveriges lantbruksuniversitet www.slu.se Overview of the method 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. 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. 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. Sveriges lantbruksuniversitet www.slu.se In addition to ASFV in all pools, TTV was common andthis one as well 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. Sveriges lantbruksuniversitet www.slu.se 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