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Microbial Metagenomic Approach Uncovers the First Rabbit Haemorrhagic Disease Virus genome in Sub-Saharan Africa

By Anise Nkenjop Happi, Olusola A. Ogunsanya, Judith Oguzie, Paul E. Oluniyi, Alhaji S Olono, Jonathan Luke Heeney, Christian Happi

Posted 19 Nov 2020
bioRxiv DOI: 10.1101/2020.11.19.390559

Rabbit Haemorrhagic Disease (RHD) causes high morbidity and mortality in rabbits and hares. Here, we report the first genomic characterization of Rabbit Hemorrhagic Disease Virus (RHDV) from sub-Saharan Africa. While suspected, only a single PCR finding without sequence confirmation or characterization has been reported. Here, we used a microbial metagenomic approach to confirm and characterize pathogens causing the suspected outbreak of RHD in Ibadan, Nigeria. The liver, spleen, and lung samples of five rabbits from an outbreak in 2 farms in Ibadan, Nigeria were analyzed for the vp60 gene of RHDV by RT-PCR. Subsequently, Next Generation Sequencing revealed one full and two partial RHDV2 genomes on both farms. Phylogenetic analysis showed close clustering with RHDV2 lineages from Europe, in particular, 98.6% similarity with RHDV2 in the Netherlands, and 99.1 to 100% identity with RHDV2 in Germany, suggesting potential importation from Europe. The detection of twelve unique mutations in RHDV2 sequences from the Ibadan outbreak compared to other RHDV2 sequences in the same clade suggests significant genetic diversity of the GI.2 strains in Nigeria. This highlights the need to further understand the genetic diversity of Lagoviruses to, inform vaccine development, and for accurate tracking, monitoring, and control of outbreaks in Africa.

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