DIGITAL CODES FROM HYPERVARIABLE TANDEMLY REPEATED DNA-SEQUENCES IN THE PLASMODIUM-FALCIPARUM CIRCUMSPOROZOITE GENE CAN GENETICALLY BARCODEISOLATES

DNA typing systems currently used in parasitology involve either hybri dising Southern blots with repetitive sequence probes or amplifying ge nomic sequences using the polymerase chain reaction (PCR). Both such a pproaches assay allelic length variation, usually in unexpressed tande mly repeated DNA sequences. Where an appropriate target locus exists, an alternative PCR-based strategy which reveals allelic sequence varia tion in tandemly repeated DNA offers a more accurate and internally co ntrolled assay. We describe such a strategy for the rapid extraction o f information on tandem repeat sequence variation from hypervariable a lleles, and apply it to the Plasmodium falciparum CS gene. The extreme variability of such DNA 'barcodes' can be used to identify parasite s tocks and lineages. This system is also potentially useful for populat ion genetic and epidemiological studies since it offers the possibilit y of following the spread of distinctively marked parasite genotypes i n samples taken from infected individuals.