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

Abstract

Background The Ebola virus is one of the deadliest known viral pathogens. It was first discovered in 1976 during two consecutive outbreaks in the Democratic Republic of Congo (DRC) and Sudan. Since then six known strains have been documented to cause outbreaks in Africa. Uganda experienced a new outbreak in Bundibugyo from 1st August 2007 to February 2008, a town approximately 400km from DRC. This outbreak affected 116 individuals with 39 laboratory confirmed deaths. After 5 years, the DRC faced a new outbreak of the same strain. This was declared by the WHO on the 17th August 2012. In this outbreak, 36 human cases with 13 laboratory confirmed deaths were registered. Despite several research studies conducted in the past, there is still limited information available on the Genetic diversity of Bundibugyo ebolavirus. Materials and Methods The approaches used were; Quality Control, Reference Mapping, Variant Calling, Annotation, Multiple Sequence Alignment and Phylogenetic Analysis to determine the genetic relationship of Bundibugyo ebolavirus between the two epidemics. Overall, we used 41 whole genome sequences that were retrieved from the National Center for Biotechnology Information (NCBI). The Quality of all the raw sequence data was assessed prior to any downstream analysis. Downstream analysis was performed using the different tools available. Results Our analysis identified 14,362 unique genomic variants from the two epidemics. The Uganda sequences had 5,740 unique variants, 75 of which were considered to be high impacts. This was a predetermined effect by the tool used. 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. This region is of significance as a mutated RNA polymerase gene affects primer design. For the DRC genomes, 8,622 variant sites were identified. Examples are C577T, T5928C and T6587C. Phylogenetic reconstruction identified two separate and unique clusters from the two epidemics. Conclusion Our analysis provided further insights into the genetic diversity of Bundibugyo ebolavirus from the two epidemics. The Bundibugyo ebolavirus strain was genetically diverse with multiple variations. Phylogenetic reconstruction identified two unique variants. This suggests an independent spillover event from nature and not a contact with a past Ebola virus survivor that initiated the resurgence in DRC in 2012. Therefore, the two epidemics are not genetically linked.