High-resolution micro-epidemiology of parasite spatial and temporal dynamics in a high malaria transmission setting in Kenya

Cody S. Nelson (), Kelsey M. Sumner, Elizabeth Freedman, Joseph W. Saelens, Andrew A. Obala, Judith N. Mangeni, Steve M. Taylor and Wendy P. O’Meara
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Cody S. Nelson: Duke University
Kelsey M. Sumner: University of North Carolina
Elizabeth Freedman: Duke University School of Medicine
Joseph W. Saelens: Duke University School of Medicine
Andrew A. Obala: Moi University College of Health Sciences
Judith N. Mangeni: Moi University College of Health Sciences
Steve M. Taylor: Duke University
Wendy P. O’Meara: Duke University

Nature Communications, 2019, vol. 10, issue 1, 1-13

Abstract: Abstract Novel interventions that leverage the heterogeneity of parasite transmission are needed to achieve malaria elimination. To better understand spatial and temporal dynamics of transmission, we applied amplicon next-generation sequencing of two polymorphic gene regions (csp and ama1) to a cohort identified via reactive case detection in a high-transmission setting in western Kenya. From April 2013 to July 2014, we enrolled 442 symptomatic children with malaria, 442 matched controls, and all household members of both groups. Here, we evaluate genetic similarity between infected individuals using three indices: sharing of parasite haplotypes on binary and proportional scales and the L1 norm. Symptomatic children more commonly share haplotypes with their own household members. Furthermore, we observe robust temporal structuring of parasite genetic similarity and identify the unique molecular signature of an outbreak. These findings of both micro- and macro-scale organization of parasite populations might be harnessed to inform next-generation malaria control measures.

Date: 2019
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DOI: 10.1038/s41467-019-13578-4

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