The abundant geneflc diversity exhibited by P. falciparum, shaped by host and vector immunity, drug pressure, environmental change? is a key element to its success as a persistent pathogen. Understanding the nature, extent and distribution of geneflc diversity and how it changes over time will be key to devising the most efflcient and effective control measures for malaria. To date, there is no data on the population geneflcs of P. falciparium in the southern region of Africa. The overall goal of Research Area C is to establish regional proflles of the populaflon geneflcs of P. falciparium in the ICEMR study sites. This will be accomplished using array-based and PCR-based approaches that will provide both high- and low-resoluflon profiles of parasite genetic diversity. In addition to population-based issues, the proven merozoite surface protein-2 (msp2) genotyping assay will be used to assess intra-individual parasite diversity with special emphasis in asymptomatic/silent infection in areas of low transmission.
Aim 1) Obtain a high-resolution profile ofthe genotypic differences between parasite isolates within and behween ICEMR study sites in order to establish the nature and scope of parasite genetic diversity. A high-density P. falciparum tiling array on the Affymetrix platform will be used for these studies.
Aim 2) Implement and refine a PCR-based barcode approach as a simple, cost-effective tool for roufinely monitoring changes in the genetic structure of parasite populations in the ICEMR study sites. The barcode will consist of -25 SNPs defined by real time RT PCR. While the barcode will provide a lower resolution genotype than the array-based approach, its lower cost and ease of use will allow a much more comprehensive profile of regional populafion geneflc structure that will facilitate the identiflcation of changes over time due to control measures or other factors.
Aim 3) Determine the level and dynamics of parasite clonal diversity within individuals residing in low- and high-transmission areas in the ICEMR study sites. Mulflplicity of infecflon (MOI) will be assessed based on the detecflon of polymorphisms in the msp2 gene by PCR. Special emphasis will be placed on asymptomaflc and silent infecflons and the role that these individuals may have in transmission. The expectaflon is that the genotyping and MOI data will be used to create models for predicflon of geneflc diversity influence upon transmission dynamics, drug treatment efforts, and pathogenesis.
P. falciparum has evolved mechanisms to generate tremendous geneflc diversity to evade drug-based control measures and host immune responses. Understanding the nature of parasite genetic diversity and how it changes over time will be key to devising the most efficient and effective control measures for malaria.
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