Genomics reveals heterogeneous Plasmodium falciparum transmission and selection signals in Zambia

• Published in: Communications medicine 2024-04, Vol.4 (1), p.67-11, Article 67
• Main Authors: Fola, Abebe A., He, Qixin, Xie, Shaojun, Thimmapuram, Jyothi, Bhide, Ketaki P., Dorman, Jack, Ciubotariu, Ilinca I., Mwenda, Mulenga C., Mambwe, Brenda, Mulube, Conceptor, Hawela, Moonga, Norris, Douglas E., Moss, William J., Bridges, Daniel J., Carpi, Giovanna
• Format: Article
• Language: English
• Subjects: 45/23; 631/181/457/649/2219; 692/699/255/1629; Disease transmission; Drug resistance; Epidemiology; Genetic diversity; Genomes; Health surveillance; Hybridization; Intervention; Malaria; Medicine; Medicine & Public Health; Microscopy; Parasites; Provinces; Public health
• ISSN: 2730-664X; 2730-664X
• DOI: 10.1038/s43856-024-00498-8

Background Genomic surveillance is crucial for monitoring malaria transmission and understanding parasite adaptation to interventions. Zambia lacks prior nationwide efforts in malaria genomic surveillance among African countries. Methods We conducted genomic surveillance of Plasmodium falciparum parasites from the 2018 Malaria Indicator Survey in Zambia, a nationally representative household survey of children under five years of age. We whole-genome sequenced and analyzed 241  P. falciparum genomes from regions with varying levels of malaria transmission across Zambia and estimated genetic metrics that are informative about transmission intensity, genetic relatedness between parasites, and selection. Results We provide genomic evidence of widespread within-host polygenomic infections, regardless of epidemiological characteristics, underscoring the extensive and ongoing endemic malaria transmission in Zambia. Our analysis reveals country-level clustering of parasites from Zambia and neighboring regions, with distinct separation in West Africa. Within Zambia, identity by descent (IBD) relatedness analysis uncovers local spatial clustering and rare cases of long-distance sharing of closely related parasite pairs. Genomic regions with large shared IBD segments and strong positive selection signatures implicate genes involved in sulfadoxine-pyrimethamine and artemisinin combination therapies drug resistance, but no signature related to chloroquine resistance. Furthermore, differences in selection signatures, including drug resistance loci, are observed between eastern and western Zambian parasite populations, suggesting variable transmission intensity and ongoing drug pressure. Conclusions Our findings enhance our understanding of nationwide P. falciparum transmission in Zambia, establishing a baseline for analyzing parasite genetic metrics as they vary over time and space. These insights highlight the urgency of strengthening malaria control programs and surveillance of antimalarial drug resistance. Plain Language Summary Malaria is caused by a parasite that is spread to humans via mosquito bites. It is a leading cause of death in children under five years old in sub-Saharan Africa. Analysis of the malaria parasite’s complete set of DNA (its genome) can help us to understand transmission of the disease and how this changes in response to different strategies to control the disease. We analyzed the genomes of malaria parasites from children across Zambia. Our