Cryptic circulation of chikungunya virus in Côte d'Ivoire revealed by sentinel travellers, 2023-24

Abstract

Chikungunya virus (CHIKV) is known to circulate in Africa, but there is little evidence of CHIKV transmission in Côte d’Ivoire. Using genomic data, we linked CHIKV cases imported in France from Côte d’Ivoire to a lineage from the West African genotype, likely been circulating in the country since July 2021.

Keywords: Arbovirus; chikungunya; emergence; molecular epidemiology; surveillance.

Figure 1

Evolutionary analysis of the CHIKV 2023–24 clade in Côte d'Ivoire. (A) Maximum-likelihood phylogeny including 7 CHIKV sequences from cases imported from Côte d’Ivoire into metropolitan France in 2023–24 combined with all publicly available sequences from the West African genotype and a subset of sequences representative of the phylogenetic diversity within other genotypes of CHIKV. Phylogenetic inference was performed using IQTREE2 under a GTR + F + R10 substitution model with ultrafast bootstrap approximation (1000 replicates). The tree was midpoint-rooted. Nodes with bootstrap support above 0.95 are shown with a black dot. The alignment (.fasta) and tree (.nexus) files for this analysis are available at https://github.com/rklitting/CHIKV_CIV_2023-2024. (B) Maximum clade credibility tree of CHIKV West African genotype including all publicly available sequences from CHIKV West African genotype (retrieved from BV-BRC, https://www.bv-brc.org/, on 26 August 2024) and those from the cases imported from Côte d’Ivoire into metropolitan France in 2023–24. The tree was inferred using the best-fitted model identified in BEAST v1.10.5 using marginal likelihood estimation with path sampling/stepping-stone sampling, a Shapiro-Rambaut-Drummond-2006 substitution model, with an uncorrelated lognormal clock model, and a Bayesian Skygrid coalescence model. We ran single MCMC chains of 50 million states and discarded the first 10% of steps as burn-in. The violin plot indicates the 95% highest posterior density interval for the TMRCA for the 2023–24 Ivorian lineage. Nodes with posterior support above 0.9 are shown with a black dot. The analysis (.xml), alignment (.fasta) and tree (.nexus) files for this analysis are available at https://github.com/rklitting/CHIKV_CIV_2023-2024.