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Csp, Msp-1, and Msp-2. We identify regions consisting of tandem or proximally repetitive short DNA sequences, including some previously unnoticed. We conclude that the antigenic polymorphisms are consistent with the recent origin of the world populations of P. falciparum inferred from the analysis of nonantigenic genes.


The World Health Organization estimates that there are 300–500 million clinical cases of malaria per year, more than 1 million children die in sub-Saharan Africa, and more than 2 billion people are at risk throughout the world (WHO, 1995). Plasmodium falciparum is the agent of malignant malaria, the most fatal version of the disease. Malaria has been an elusive target for medical intervention. Epidemiological control efforts were first directed against the Anopheles mosquito vectors, which soon evolved resistance to massively applied insecticides. Current efforts against the mosquito vectors seek to produce transgenic mosquitoes that are unable to transmit Plasmodium, followed by massive release of the transformed vectors in endemic regions.

Greater efforts yet are invested in the development of protective vaccines or remedial drugs directed against the parasite. These exertions are handicapped, however, by the parasite's rapid evolution of drug resistance and antigens. Underlying this evolution is a wealth of genetic variation that arises rapidly by rearrangement of modular repeating elements that generate ever newly protected phenotypes.

The merozoite form of the Plasmodium parasite found in the human bloodstream is haploid. A fraction of these haploids differentiate into gametocytes, which are taken up in the mosquito's blood meal. Gametes fuse in the mosquito midgut to form transient diploids, which then undergo meiosis to yield haploid infectious forms, called sporozoites. Protective immunity against P. falciparum was demonstrated in the 1970s by immunization of human patients with irradiated sporozoites (Clyde et al., 1973). Parasite genes that code for antigenic determinants subsequently have been isolated and characterized. Notable among the genes intensively investigated and chosen for vaccine development are those encoding surface proteins of the sporozoite (Csp, coding for the circumsporozoite protein) and the merozoite (Msp-1 and Msp-2, coding for the merozoite surface proteins 1 and 2). The success of efforts to develop an effective malaria vaccine is contingent on determining the extent of diversity of these genes and on identifying the mechanisms by which this variation is generated and persists in populations of P. falciparum.

Assessment of DNA sequence variation in P. falciparum has been based almost exclusively on examination of genes coding for antigenic determi-

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