An emerging clade of Chikungunya West African genotype discovered in real-time during 2023 outbreak in Senegal

Abstract

Chikungunya (CHIKV) is a re-emerging endemic arbovirus in West Africa. Since July 2023, Senegal and Burkina Faso have been experiencing an ongoing outbreak, with over 300 confirmed cases detected so far in the regions of Kédougou and Tambacounda in Senegal, the largest recorded outbreak yet. CHIKV is typically maintained in a sylvatic cycle in Senegal but its evolution and factors contributing to re-emergence are so far unknown in West Africa, leaving a gap in understanding and responding to recurrent epidemics. We produced, in real-time, the first locally-generated and publicly available CHIKV whole genomes in West Africa, to characterize the genetic diversity of circulating strains, along with phylodynamic analysis to estimate time of emergence and population growth dynamics. A novel strain of the West African genotype, phylogenetically distinct from strains circulating in previous outbreaks, was identified. This suggests a likely new spillover from sylvatic cycles in rural Senegal and potential of seeding larger epidemics in urban settings in Senegal and elsewhere.

Keywords: Chikungunya virus; Climate change; Genomic monitoring; Senegal; West Africa; West African genotype.

Figure 1:. Spatiotemporal distribution of Chikungunya epidemiology and ecology in Senegal.

A) Epidemiological curve of cases in Senegal and Kédougou region in 2023 and time-frame of case sampling. B) Demographic distribution of sampled cases. C) Map of CHIKV cases in Senegal in 2023, with the Kédougou region outlined in red. Sampling was performed in the Kédougou district, from Ndiormi (n=37) and Bandafassi (n=20). D) Increasing temperature trend in Senegal; the blue dashed line is the mean of the first 10 years of data (1979–1989, blue area), the red line is the annual mean, dark gray is the 50% percentile, and the light gray area are the minimum and maximum temperatures. E) Difference in mean temperature between the reference period of the first panel and the mean of the past 10 years (2013–2023). F) Vegetation cover (NDVI) in Senegal. Data is from 2018.

Figure 2.

A) Timed maximum likelihood phylogeny of all West African genotype sequences of CHIKV. B) Root-to-tip repression containing sequences from the clade highlighted in gray in the previous panel, containing public CHIKV sequences from 2005, 2009, and newly sequenced ones from 2023. C) Effective population density estimates for CHIKV in Senegal. D) Maximum Clade Credibility (MCC) phylogenetic tree of 2005, 2009 and 2023 sequences, trimmed to E1 gene, of CHIKV in Senegal, showing the posterior distributions for the root node age of the 2009 and 2023 clades, with specified 95% HPD.