The emergence and spread of drug-resistant Plasmodium falciparum poses an immense global health threat. While we understand much about the selection of drug resistant malaria in populations, little is known about in- host evolution. Most individuals infected with falciparum malaria carry multiple genetically distinct variants ("genotypes", "strains") which continually evolve and compete for resources. This within-host competition could be as important as competition within populations. Many of the variants are present at low levels and undetectable by older genotyping technologies. In order to measure within-host competition, we propose to employ a new method uniquely capable of identifying and quantitating genotypes in a single host - Massively Parallel Pyrosequencing (MPP). With this technology, we will measure, within individual hosts, the true diversity of falciparum infections and the selective pressure of antimalarials. Specifically, we will: i) sequence and quantitate merozoite surface protein-2 (msp2) genotypes within individual subjects from two areas of different transmission intensity: Tanzania (high transmission) and Thailand (low intensity), ii) measure the rate of change in frequency (selection coefficients) for individual parasite variants from Tanzanian patients treated with Coartem and determine the effect of competing variants on frequency, and iii) measure up-selection for individual parasite variants from Thai patients treated with Artesunate-Mefloquine to define selection coefficients and better define the phenotype used to study drug resistance to artemisinins. This novel approach of quantitatively studying variant diversity within individuals will i) allow accurate measurement of within-host selection and dynamics of variants in mixed infections, ii) provide new tools for testing hypotheses about the genetic basis of low- and high-level resistance, and iii) define the factors that allow the development and spread drug resistant parasites in populations.

Public Health Relevance

Malaria remains the most important vector borne parasitic infection in the world today, causing nearly a million deaths annually. This project focuses on understanding the factors involved in the evolution of drug resistance within individual hosts and improving the methods for early detection of drug resistant parasites. A better understanding of these evolutionary processes will augment resistance management strategies, assist malaria control efforts, and help alleviate malaria's public health burden in the developing world.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Project (R01)
Project #
Application #
Study Section
Clinical Research and Field Studies of Infectious Diseases Study Section (CRFS)
Program Officer
Joy, Deirdre A
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of North Carolina Chapel Hill
Internal Medicine/Medicine
Schools of Medicine
Chapel Hill
United States
Zip Code
Parobek, Christian M; Jiang, Linda Y; Patel, Jaymin C et al. (2014) Multilocus microsatellite genotyping array for investigation of genetic epidemiology of Pneumocystis jirovecii. J Clin Microbiol 52:1391-9
Parobek, Christian M; Bailey, Jeffrey A; Hathaway, Nicholas J et al. (2014) Differing patterns of selection and geospatial genetic diversity within two leading Plasmodium vivax candidate vaccine antigens. PLoS Negl Trop Dis 8:e2796
Givens, Matthew B; Lin, Jessica T; Lon, Chanthap et al. (2014) Development of a capillary electrophoresis-based heteroduplex tracking assay to measure in-host genetic diversity of initial and recurrent Plasmodium vivax infections in Cambodia. J Clin Microbiol 52:298-301
Lin, Jessica T; Patel, Jaymin C; Kharabora, Oksana et al. (2013) Plasmodium vivax isolates from Cambodia and Thailand show high genetic complexity and distinct patterns of P. vivax multidrug resistance gene 1 (pvmdr1) polymorphisms. Am J Trop Med Hyg 88:1116-23
Bowman, Natalie M; Congdon, Seth; Mvalo, Tisungane et al. (2013) Comparative population structure of Plasmodium falciparum circumsporozoite protein NANP repeat lengths in Lilongwe, Malawi. Sci Rep 3:1990
Lin, Jessica T; Juliano, Jonathan J; Kharabora, Oksana et al. (2012) Individual Plasmodium vivax msp1 variants within polyclonal P. vivax infections display different propensities for relapse. J Clin Microbiol 50:1449-51
Bailey, Jeffrey A; Mvalo, Tisungane; Aragam, Nagesh et al. (2012) Use of massively parallel pyrosequencing to evaluate the diversity of and selection on Plasmodium falciparum csp T-cell epitopes in Lilongwe, Malawi. J Infect Dis 206:580-7
Huijben, S; Sim, D G; Nelson, W A et al. (2011) The fitness of drug-resistant malaria parasites in a rodent model: multiplicity of infection. J Evol Biol 24:2410-22
Read, Andrew F; Day, Troy; Huijben, Silvie (2011) The evolution of drug resistance and the curious orthodoxy of aggressive chemotherapy. Proc Natl Acad Sci U S A 108 Suppl 2:10871-7