The abundant genetic 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 genetic diversity and how it changes over time will be key to devising the most efficient and effective control measures for malaria. To date, there is no data on the population genetics of P. falciparium in the southern region of Africa. The overall goal of Research Area C is to establish regional profiles of the population genetics 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-resolution 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 between 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 routinely 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 population genetic structure that will facilitate the identification 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. Multiplicity of infection (MOI) will be assessed based on the detection of polymorphisms in the msp2 gene by PCR. Special emphasis will be placed on asymptomatic and silent infections and the role that these individuals may have in transmission. The expectatoin is that the genotyping and MOI data will be used to create models for prediction of genetic diversity influence upon transmission dynamics, drug treatment efforts, and pathogenesis
P. falciparum has evolved mechanisms to generate tremendous genetic 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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