Understanding the Transmission Dynamics of the Chikungunya Virus in Africa

Abstract

The Chikungunya virus (CHIKV) poses a significant global public health concern, especially in Africa. Since its first isolation in Tanzania in 1953, CHIKV has caused recurrent outbreaks, challenging healthcare systems in low-resource settings. Recent outbreaks in Africa highlight the dynamic nature of CHIKV transmission and the challenges of underreporting and underdiagnosis. Here, we review the literature and analyse publicly available cases, outbreaks, and genomic data, providing insights into the epidemiology, genetic diversity, and transmission dynamics of CHIKV in Africa. Our analyses reveal the circulation of geographically distinct CHIKV genotypes, with certain regions experiencing a disproportionate burden of disease. Phylogenetic analysis of sporadic outbreaks in West Africa suggests repeated emergence of the virus through enzootic spillover, which is markedly different from inferred transmission dynamics in East Africa, where the virus is often introduced from Asian outbreaks, including the recent reintroduction of the Indian Ocean lineage from the Indian subcontinent to East Africa. Furthermore, there is limited evidence of viral movement between these two regions. Understanding the history and transmission dynamics of outbreaks is crucial for effective public health planning. Despite advances in surveillance and research, diagnostic and surveillance challenges persist. This review and secondary analysis highlight the importance of ongoing surveillance, research, and collaboration to mitigate the burden of CHIKV in Africa and improve public health outcomes.

Keywords: Africa; Chikungunya virus; epidemiology; genomic distribution; genomic surveillance; transmission dynamics.

Figure 1

Distribution and surveillance of genome, cases, and outbreaks of CHIKV in Africa. The colour ramp of the map illustrates the geographic distribution of CHIKV cumulative and suspected cases from 2018 to 2024 obtained from the WHO-AFRO weekly reports [27]. Overlaid markers in yellow indicate the reported year of outbreaks and reported cases in parenthesis obtained from the literature [3,6,12,13,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60], and the coloured circles show the lineages and the number of genomes generated in each country received from Bacterial and Viral Bioinformatics Resource Center (BV-BRC) [61], GISAID EpiArbo database [62], and NCBI’s GenBank databases.

Figure 2

Global distribution of CHIKV lineages. (a) World map depicting the distribution and number of genomes generated for each CHIKV lineage. Circle sizes represent the number of CHIKV genomes produced per country and colours represent the proportion of different CHIKV lineages in each country. (b) Global map coloured by the date of first genome isolation for each CHIKV lineage, ranging from 1953 to 2023. Data source: Bacterial and Viral Bioinformatics Resource Center (BV-BRC) [61].

Figure 3

Overview of genomic sequencing efforts in Africa since the 1950s. Shapes are used to illustrate the different CHIKV genotypes: the circle represents the East–Central–South African genotype, the diamond represents the Indian Ocean lineage (IOL), and the square represents the WA genotype. The shapes’ sizes show the number of genomes produced for each isolation source in each African country, represented by different colours. The figure also depicts the type of genomes produced for each host species. Data source: Bacterial and Viral Bioinformatics Resource Center (BV-BRC) [61] and NCBI GenBank.

Figure 4

Maximum likelihood time-scaled tree illustrating the evolutionary relationships among the different circulating lineages in Africa, providing insights into the temporal aspects of CHIKV evolution and dispersal. (a) ECSA genotype: This genotype is depicted as showing two geographically distinct clades. (b) The WA genotype circulates within the West African region. (c) Indian Ocean lineage, showing recent outbreaks in Africa and the initial outbreaks on Indian Ocean islands, aggregated by continent.

Figure 5

Transmission dynamics of CHIKV lineages worldwide and in Africa. World map illustrating the temporal and spatial CHIKV dissemination patterns in, out of, and within Africa. (a) The ECSA genotype and (b) IOL lineage.