Pathogen discovery platform
George N. Michuki
ILRI BioSciences Day, Nairobi, 27 November 2013

Metagenomics and zoonotic pathogen
discovery platform
• Introduction
• Enabling livestock health and disease surveillance
• Outbreaks detection  control  preventing animal loss
• Outcomes useful to:
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Scientists and veterinarians
Health professionals
Policy makers
Farmers and livestock handlers
• Impacts of project:
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Diagnostic tools and vaccine development
Prevalent human zoonotic diseases
Appropriate control measures (human and animals)
Risks exposed to and control measures

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)
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Animal production as food source
Trade (No sanctions)
Income source (Animal sale)
Zoonotic disease control
Improved nutrition and
health (SLO3)

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

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:
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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

Results-2
• In collaboration with partners:
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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

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

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

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)

better lives through livestock
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