Bett, Bernard K.

Christoffels, A.

Fonseca, V.

Heusden, P. van

Juma, John

Limbaso, S.

Oliveira, T. de

Oyola, Samuel O.

Roesel, Kristina

Sang, R.

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LATEX TikZposterGenomic Surveillance of the RiftValley fever: from Sequencing toLineage assignmentJohn Juma1, Vagner Fonseca2, Samson Limbaso3, Peter van Heusden4, Kristina Roesel1, Bernard Bett1,Rosemary Sang3, Alan Christoffels4, Tulio de Oliveira2, and Samuel Oyola11International Livestock Research Institute (ILRI), Nairobi, Kenya2KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of HealthSciences, University of KwaZulu-Natal, Durban, South Africa.3Kenya Medical Research Institute (KEMRI), Nairobi, Kenya4South African National Bioinformatics Institute, South African MRC Bioinformatics Unit. Cape Town, South AfricaIntroductionRift Valley fever (RVF) virus is a re-emerging zoonotic disease of arboviral origin, and belonging to the Bunyaviridae family [1]. The evolutionary history of Rift Valley fever virus (RVFV)is complex and has been greatly influenced by dramatic changes to environment throughout Africa in the past 150 years. Over this time period, RVFV gene flow has been impacted onvarious levels such as geographic dispersal and reassortment events. Overall, there are 15 lineages, designated from A to O [2]. On numerous occasions, viruses from these lineages havebeen transported outside enzootic regions through movement of infected animals and/or mosquitoes. This has led to large outbreaks in countries where the disease had not been previouslyreported. Genomic surveillance of the virus diversity is crucial in developing intervention strategies. To undertake genomic surveillance of the virus, we sought:1. To reliably classify and assign Rift Valley fever virus (RVFV) sequences to lineages.2. To genetically characterize RVFV isolates through whole genome sequencing.MethodsFigure 1: Lineage assignment process.Figure 2: The web interface offers a portal for users to perform classification and visualize the resultsResultsFigure 3: RVFV genome coverage versus cycle threshold values, Reads coverageand Maximum likelihood phylogenetic treeSuccessfully recovered 99% viral consensus sequences.Query sequence, DVS-321, clusters in lineage C clade.Query LineageaLRT UFboot Segment Length Identity(%)DVS-230 C 89 84 M 3885 99.3DVS-321 C 86 95 M 3885 99.3DVS-333 C 88 90 M 3885 99.4DVS-356 C 88 89 M 3885 99.3DVS-372 C 87 92 M 3885 99.4One Health RelevanceWe generated complete genomic sequences of 5 Rift valley fever virus isolates from out-break samples in Kenya. The isolates used were all vertebrate host (Bos taurus). Thesesequences will enrich genetic characterization of the virus by allowing phylogenetic infer-ence between known and newly sequenced strains. We developed a command line pipelineand a user-friendly Rift Valley fever virus typing tool with the aim of rapidly characterizingRVF genomic sequences. This is useful in tracing the origin of outbreaks and supportingsurveillance efforts.References1. Michel Pepin, Michèle 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. Grobbelaar A. A, Weyer J, Leman P. A., Kemp, A., Paweska, J. T., Swanepoel, R. Molecular Epidemiologyof Rift Valley Fever Virus. Emerging Infectious Diseases 17 (2011).Partners

Genomic surveillance of the Rift Valley fever: From sequencing to lineage assignment

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Genomic surveillance of the Rift Valley fever: From sequencing to lineage assignment

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