SRA

Seven years after the declaration of the first Ebola virus disease (EVD) epidemic in Guinea, the country is facing a new Ebola outbreak in a town located only 200 km from the epicenter of the previous epidemic. In order to discriminate whether this new outbreak was caused by a new zoonotic transmission event or by resurgence of the viral strain that circulated in the previous West African outbreak (2013-2016) whole genome sequencing was attempted at CERFIG in Conakry, Guinea, on viral extracts from samples that were positive for Zaire ebolavirus (EBOV). After enrichment of filoviral sequences by hybridization capture and sequencing on an Illumina iSeq platform, we were able to construct four high quality EBOV genomes. In a maximum likelihood phylogenetic tree, the new Guinean EBOV genomes nest within the clade of sequences from the 2013-2016 EBOV epidemic. Within this clade they also form a well-supported sub-clade with certain genomes from Guinea, Liberia and Sierra Leone from the 2013-2016 EBOV epidemic. This pattern shows clearly that the new outbreak is not the result of a new zoonotic spill-over, but rather the resurgence of a strain that circulated in the West African outbreak from 2013-2016. The unexpectedly short branch leading to the 2021 Guinean EBOV genomes suggests a marked substitution rate slowdown, which might be associated to latency in a survivor. The human origin of the current EVD outbreak and the associated shift in our perception of EBOV emergence, call for careful attention to survivors. The possibility of resurgence of Ebola, up to 5 years or more after EVD, opens new challenges for survivors, their families and their communities but also for the health system that has to create ways to work with communities, known and unknown survivors, without creating further stigmatization.