Yellow Fever Outbreak in Eastern Senegal, 2020-2021

Abstract

Yellow fever virus remains a major threat in low resource countries in South America and Africa despite the existence of an effective vaccine. In Senegal and particularly in the eastern part of the country, periodic sylvatic circulation has been demonstrated with varying degrees of impact on populations in perpetual renewal. We report an outbreak that occurred from October 2020 to February 2021 in eastern Senegal, notified and managed through the synergistic effort yellow fever national surveillance implemented by the Senegalese Ministry of Health in collaboration with the World Health Organization, the countrywide 4S network set up by the Ministry of Health, the Institut Pasteur de Dakar, and the surveillance of arboviruses and hemorrhagic fever viruses in human and vector populations implemented since mid 2020 in eastern Senegal. Virological analyses highlighted the implication of sylvatic mosquito species in virus transmission. Genomic analysis showed a close relationship between the circulating strain in eastern Senegal, 2020, and another one from the West African lineage previously detected and sequenced two years ago from an unvaccinated Dutch traveler who visited the Gambia and Senegal before developing signs after returning to Europe. Moreover, genome analysis identified a 6-nucleotide deletion in the variable domain of the 3'UTR with potential impact on the biology of the viral strain that merits further investigations. Integrated surveillance of yellow fever virus but also of other arboviruses of public health interest is crucial in an ecosystem such as eastern Senegal.

Keywords: 3′UTR; Kedougou; arbovirus; eastern Senegal; genotype; lineage; next generation sequencing; sylvatic lifecycle; virus isolation; yellow fever virus.

Figure 1

Sepik virus-rooted maximum-likelihood phylogenetic tree of yellow fever virus strains from different genotypes. (Newly sequenced yellow fever viruses are shown in yellow).

Figure 2

Alignment of portion of the variable domain within the 3′UTR downstream the yellow fever virus polyprotein. (Black band surrounds the first 6 nucleotides downstream the ORF 3′ terminus; red band surrounds the deletion area of newly sequenced strains).