Publication: Plasmodium falciparum population dynamics in East Africa and genomic surveillance along the Kenya‑Uganda border
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2024-08-05
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Scientific Reports
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Abstract
East African countries accounted for ~ 10% of all malaria prevalence worldwide in 2022, with an
estimated 23.8 million cases and > 53,000 deaths. Despite recent increases in malaria incidence, high‑
resolution genome‑wide analyses of Plasmodium parasite populations are sparse in Kenya, Tanzania,
and Uganda. The Kenyan‑Ugandan border region is a particular concern, with Uganda confirming
the emergence and spread of artemisinin resistant P. falciparum parasites. To establish genomic
surveillance along the Kenyan‑Ugandan border and analyse P. falciparum population dynamics within
East Africa, we generated whole‑genome sequencing (WGS) data for 38 parasites from Bungoma,
Western Kenya. These sequences were integrated into a genomic analysis of available East African
isolate data (n = 599) and revealed parasite subpopulations with distinct genetic structure and diverse
ancestral origins. Ancestral admixture analysis of these subpopulations alongside isolates from across
Africa (n = 365) suggested potential independent ancestral populations from other major African
populations. Within isolates from Western Kenya, the prevalence of biomarkers associated with
chloroquine resistance (e.g. Pfcrt K76T) were significantly reduced compared to wider East African
populations and a single isolate contained the PfK13 V568I variant, potentially linked to reduced
susceptibility to artemisinin. Overall, our work provides baseline WGS data and analysis for future
malaria genomic surveillance in the region