Common host variation drives malaria parasite fitness in healthy human red cells

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Abstract

The replication of Plasmodium falciparum parasites within red blood cells (RBCs) causes severe disease in humans, especially in Africa. Deleterious alleles like hemoglobin S are well-known to confer strong resistance to malaria, but the effects of common RBC variation are largely undetermined. Here we collected fresh blood samples from 121 healthy donors, most with African ancestry, and performed exome sequencing, detailed RBC phenotyping, and parasite fitness assays. Over one third of healthy donors unknowingly carried alleles for G6PD deficiency or hemoglobinopathies, which were associated with characteristic RBC phenotypes. Among non-carriers alone, variation in RBC hydration, membrane deformability, and volume was strongly associated with P. falciparum growth rate. Common genetic variants in PIEZO1, SPTA1/SPTB, and several P. falciparum invasion receptors were also associated with parasite growth rate. Interestingly, we observed little or negative evidence for divergent selection on non-pathogenic RBC variation between Africans and Europeans. These findings suggest a model in which globally widespread variation in a moderate number of genes and phenotypes modulates P. falciparum fitness in RBCs.

Data availability

All data generated or analyzed during this study are included in the manuscript and supporting files. Source data files have been provided for Figures 1, 4, and 5 and other raw data and normalization scripts are available at https://github.com/emily-ebel/RBC

The following data sets were generated

1. Ebel ER
2. Kuypers FA
3. Lin C
4. Petrov DA
5. and Egan ES
(2020) Exome Sequencing from Participants in RBC/Malaria Study
Sequence Read Archive PRJNA683732.

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA683732/

Article and author information

Author details

Emily R Ebel

Biology, Stanford University, Stanford, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-3244-4250
Frans A Kuypers

Children's Hospital Oakland Research Institute, Oakland, United States

Competing interests
The authors declare that no competing interests exist.
Carrie Lin

Stanford University School of Medicine, Stanford, United States

Competing interests
The authors declare that no competing interests exist.
Dmitri A Petrov

Department of Biology, Stanford University, Stanford, United States

For correspondence
dpetrov@stanford.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-3664-9130
Elizabeth S Egan

Stanford University School of Medicine, Stanford, United States

For correspondence
eegan@stanford.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-2112-7700

Funding

Stanford Maternal and Child Health Research Institute (N/A)

Elizabeth S Egan

Stanford University School of Medicine Office of Faculty Development and Diversity (N/A)

Elizabeth S Egan

Stanford Center for Computational, Evolutionary, and Human Genomics (N/A)

Emily R Ebel

National Institute of General Medical Sciences (5R35GM118165-05)

Dmitri A Petrov

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Human subjects: Written informed consent and consent to publish was obtained from each subject and/or their parent as part of a protocol approved by the Stanford University Institutional Review Board (#40479).

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.