Pathogen discovery platform


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Presented by George N. Michuki at the ILRI BioSciences Day, Nairobi, 27 November 2013

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  • Pathogen discovery platform

    1. 1. Pathogen discovery platform George N. Michuki ILRI BioSciences Day, Nairobi, 27 November 2013
    2. 2. Metagenomics and zoonotic pathogen discovery platform • Introduction • Enabling livestock health and disease surveillance • Outbreaks detection  control  preventing animal loss • Outcomes useful to: • • • • Scientists and veterinarians Health professionals Policy makers Farmers and livestock handlers • Impacts of project: • • • • Diagnostic tools and vaccine development Prevalent human zoonotic diseases Appropriate control measures (human and animals) Risks exposed to and control measures
    3. 3. The problem: its significance • Increase of emergence and re-emergence of zoonotic infectious diseases in Africa in the past years • Recent outbreaks of viral diseases include: • Yellow Fever, Dengue, Rift Valley Fever, Onyongnyong, Crimean Congo Hemorrhagic Fever and Chikungunya viruses • Studies revealed that livestock and wildlife are involved in the spread of these diseases and are also affected • Animal diseases control impacts on: Improved food security (SLO2) • • • • Animal production as food source Trade (No sanctions) Income source (Animal sale) Zoonotic disease control Improved nutrition and health (SLO3)
    4. 4. Methods • Analysis of samples from diverse sources • Wildlife, domestic animals, human and vectors • Analysis of diverse sample types • Tissue, blood, serum, swabs and cultures • Use of next generation sequencing and RT-PCR • Metagenomic approach • Targeted amplicon sequencing • High resolution melt analysis • Collaborating partners • Local: KWS, DVS, ICIPE, KEMRI, KARI, • International: Makerere University, OVI, CSIRO, LANL
    5. 5. Results-1 • Highly multiplexing techniques developed • Reduced cost of sequencing • Universal 16S and 18S tools developed • Enables simultaneous identification of vector and associated fungi and bacteria • Internal Local database and Genebank: o o o o o o o o Dugbe virus, Semliki Forest virus, Bunyamwera virus, Partial Rift Valley Fever virus Babanki virus West Nile Virus Ndumu viruses Developed Mosquito typing tools Impact on animal and human health
    6. 6. Results-2 • In collaboration with partners: o o o o o o ECF vaccine quality check - ILRI Equine Encephalosis Virus – (OVI – South Africa) Blue Tongue Virus (OVI – South Africa) RVF viruses (OVI – South Africa) New Castle Disease Virus – ILRI – in Genebank Pigeon Paramyxovirus Virus –KWS – in Genebank o Velogenic – fusion gene motif similar to chicken outbreak NDV o Plasmodium falciparum – Kilifi welcome trust o MHC class 1 and 2 – ILRI vaccine group o Chikungunya Viruses – in genebank and paper submitted o Identified a single mutation affecting replication rate o Ndumu virus from pigs: - in genebank • Over 250 sequences in genebank • Several publications in the pipeline
    7. 7. Conclusions and discussion points • Developed Mosquito typing tools • Useful for typing vectors involved in disease transmission • Early detection of disease by vector identification • Pigeon Paramyxovirus Virus (NDV) • Virulent determinant gene segment identified • Similar to strains causing outbreaks in chicken • Quick detection of outbreaks in chicken • Wide range of viral pathogens identified • Development of a multiplex screening diagnostic tool • What are the next challenges? • Mapping of the disease patterns • Vaccine and treatment options • NEW RESEARCH OPPORTUNITIES
    8. 8. Where to from now? • Increased surveillance coverage and larger scale of pathogen discovery • Utilization of developed tools • Decreased animal losses by early detection: • Increase income reducing poverty • Animal disease management will increase production thus improving on food security. • Control of zoonotic diseases will improve on health of farmers. • New and enforcing existing collaboration • New: LANL and DTRA • Existing: DVS, KWS, ICIPE, KEMRI
    9. 9. General discussion (facultative) • Enhancing situational awareness of emerging viral disease threats in East Africa • Proposal submitted to DTRA • At the 2nd stage (white paper submitted)
    10. 10. better lives through livestock The presentation has a Creative Commons licence. You are free to re-use or distribute this work, provided credit is given to ILRI.