Bett, Bernard K.

Juma, J.

Oyola, Samuel

Sang, R.

English

Oyola, Samuel O.

CGSpace (CGIAR)

LATEX TikZposterGenomic epidemiology of Rift Valleyfever in East Africa: A data drivenintervention for effective control andprevention of the disease.John Juma1, Samuel Oyola1, Bernard Bett1, and Rosemary Sang21International Livestock Research Institute (ILRI), Nairobi, Kenya2Kenya Medical Research Institute (KEMRI), Nairobi, KenyaIntroductionRift Valley fever (RVF) virus is a re-emerging zoonotic disease of arboviral origin, and belonging to the Bunyaviridae family [1]. The disease is responsible for deaths in human and animals.It leads to major losses in livestock production, thus negatively affecting livelihoods in Sub-saharan Africa. Phylogenetic analysis on the virus have reported that it’s first emergence was inthe mid 19 th century, and was first reported in 1930s in the Rift Valley region in Kenya [3]. The RVF virus shows a simple but temporally and geographically stable genome. However,in spite of this attribute, the virus has continued to ravage new territories as exemplified by outbreaks in Egypt (1977), Western Africa (1988) and the Arabian Peninsula (2000) [1]. Therecent re-emergence of the disease in Kenya and South Africa has indeed displayed it’s real capacity to enter into new territories.RVF is one of the several diseases identified by the WorldHealth Organization, (WHO) as a likely cause of future epidemic in a new emergency plan developed after the Ebola epidemic, and classified for urgent research and development towardnew diagnostic tests, vaccines and medicines [4].PurposeTo understand the epidemiology of RVF virus in East Africa, using biobanked human and animal samples, we aim to:1. Genetically characterize the current RVF strain(s) circulating in Kenya and Uganda.2. Assess potential co-infection with Ngari virus (NRIV)3. Undertake transmission dynamics by integrating genomic and epidemiologal data to ascertain spread and persistence.WorkflowFigure 1: Process and utility of genomic epidemiology [2].Methods1. Virus culture and isolation of nucleic acid - RNA2. Confirmatory tests using serology (IgM) and Real Time quantitative polymerase chainreaction (RT-qPCR)3. Next generation sequencing: Illumina MiSeq and Oxford Nanopore (MinION)4. Genome assembly to characterize genetic diversity and viral mutations5. Multiple sequence alignment (MAFFT) and Maximum Likelihood tree inference usingRAxML under a GTR + Γ 4 nucleotide substitution model6. Reconstruction of time-scaled phylogenetic trees using the Bayesian phylogenetic infer-ence framework (BEAST).Expected resultsPreliminary data are expected to be analyzed in March, 2020. Results of the viral genomeswill be a valuable source of information for epidemic dynamics which will be used toexamine specific RVF outbreaks indepth. By combining genomic, epidemiological andspatial data, we will be able to offer insightful knowledge about the transmission of RVF.Such surveillance approach is very crucial for early detection and rapid prevention of RVFtransmission.References1. Michel Pepin, Miche`le Bouloy, Brian H. Bird, Alan Kemp, Janusz Paweska. Rift Valley fever virus (Bun-yaviridae: Phlebovirus): an update on pathogenesis, molecular epidemiology, vectors, diagnostics and pre-vention. Veterinary Research 41, 1–40 (May 2010).2. Charlene M.C. Rodrigues, Martin C.J. Maiden. A world without bacterial meningitis: how genomic epi-demiology can inform vaccination strategy. F1000Research 401, 1–13 (July 2018).3. Daubney RJ, Hudson R, Garham PG. Enzootic hepatitis of Rift Valley fever: an undescribed virus diseaseof sheep cattle and man from East Africa. The Journal of Pathology and Bacteriology 34, 545–579(1931).4. WHO. A research and development Blueprint for action to prevent epidemicsg https://www.who.int/blueprint/priority-diseases/en/. (accessed: 07.11.2019).Partners

Genomic epidemiology of Rift Valley fever in East Africa: A data driven intervention for effective control and prevention of the disease

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Genomic epidemiology of Rift Valley fever in East Africa: A data driven intervention for effective control and prevention of the disease

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