Genetic Diversity of Bundibugyo Ebolavirus from Uganda and the Democratic Republic of Congo

Omara, I. E.; Muyingo, S. K.; Balinandi, S.; Nyakarahuka, L.; Kiconco, J.; Kayiwa, J. T.; Mboowa, G.; Jjingo, D.; Lutwama, J. J.

doi:10.1101/2021.10.18.464898

bioRxiv · 10.1101/2021.10.18.464898

Genetic Diversity of Bundibugyo Ebolavirus from Uganda and the Democratic Republic of Congo

Omara, I. E.·Muyingo, S. K.·Balinandi, S.·Nyakarahuka, L.·Kiconco, J.·Kayiwa, J. T.·Mboowa, G.·Jjingo, D.·Lutwama, J. J.

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Abstract

BackgroundThe Ebolavirus is one of the deadliest viral pathogens which was first discovered in the year 1976 during two consecutive outbreaks in the Democratic Republic of Congo and Sudan. Six known strains have been documented. The Bundibugyo Ebolavirus in particular first emerged in the year 2007 in Uganda. This outbreak was constituted with 116 human cases and 39 laboratory confirmed deaths. After 5 years, it re-emerged and caused an epidemic for the first time in the Democratic Republic of Congo in the year 2012 as reported by the WHO. Here, 36 human cases with 13 laboratory confirmed deaths were registered. Despite several research studies conducted in the past, there is still scarcity of knowledge available on the genetic diversity of Bundibugyo Ebolavirus. We undertook a research project to provide insights into the unique variants of Bundibugyo Ebolavirus that circulated in the two epidemics that occurred in Uganda and the Democratic Republic of Congo Materials and MethodsThe Bioinformatics approaches used were; Quality Control, Reference Mapping, Variant Calling, Annotation, Multiple Sequence Alignment and Phylogenetic analysis to identify genomic variants as well determine the genetic relatedness between the two epidemics. Overall, we used 41 viral sequences that were retrieved from the publicly available sequence database, which is the National Center for Biotechnology and Information Gen-bank database. ResultsOur analysis identified 14,362 unique genomic variants from the two epidemics. The Uganda isolates had 5,740 unique variants, 75 of which had high impacts on the genomes. These were 51 frameshift, 15 stop gained, 5 stop lost, 2 missense, 1 synonymous and 1 stop lost and splice region. Their effects mainly occurred within the L-gene region at reference positions 17705, 11952, 11930 and 11027. For the DRC genomes, 8,622 variant sites were identified. The variants had a modifier effect on the genome occurring at reference positions, 213, 266 and 439. Examples are C213T, A266G and C439T. Phylogenetic reconstruction identified two separate and unique clusters from the two epidemics. ConclusionOur analysis provided further insights into the genetic diversity of Bundibugyo Ebolavirus from the two epidemics. The Bundibugyo Ebolavirus strain was genetically diverse with multiple variants. Phylogenetic reconstruction identified two unique variants. This signified an independent spillover event from a natural reservoir, rather a continuation from the ancestral outbreak that initiated the resurgence in DRC in the year 2012. Therefore, the two epidemics were not genetically related.

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Omara, I. E., Muyingo, S. K., Balinandi, S., Nyakarahuka, L., Kiconco, J., Kayiwa, J. T., Mboowa, G., Jjingo, D., Lutwama, J. J.. 2021-10-18. Genetic Diversity of Bundibugyo Ebolavirus from Uganda and the Democratic Republic of Congo. https://doi.org/10.1101/2021.10.18.464898

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