Plasmodium falciparum antigenic diversity: evidence of clonal population structure

Abstract

Plasmodium falciparum, the agent of malignant malaria, is one of mankind's most severe scourges. Efforts to develop preventive vaccines or remedial drugs are handicapped by the parasite's rapid evolution of drug resistance and protective antigens. We examine 25 DNA sequences of the gene coding for the highly polymorphic antigenic circumsporozoite protein. We observe total absence of silent nucleotide variation in the two nonrepeated regions of the gene. We propose that this absence reflects a recent origin (within several thousand years) of the world populations of P. falciparum from a single individual; the amino acid polymorphisms observed in these nonrepeat regions would result from strong natural selection. Analysis of these polymorphisms indicates that: (i) the incidence of recombination events does not increase with nucleotide distance; (ii) the strength of linkage disequilibrium between nucleotides is also independent of distance; and (iii) haplotypes in the two nonrepeat regions are correlated with one another, but not with the central repeat region they span. We propose two hypotheses: (i) variation in the highly polymorphic central repeat region arises by mitotic intragenic recombination, and (ii) the population structure of P. falciparum is clonal--a state of affairs that persists in spite of the necessary stage of physiological sexuality that the parasite must sustain in the mosquito vector to complete its life cycle.

Figure 1

Structure of the P. falciparum Csp. 5′NR and 3′NR brace the CR (hatched) made up of a variable number of tandem repeats encoding 4-aa-long motifs. The light gray boxes represent B-cell epitopes; the dark boxes represent T-cell epitopes. The gene length ranges 1,194–1,413 nucleotides because of two 5′ NR indels and a variable number of CRs.

Figure 2

Linkage disequilibrium (D) as a function of nucleotide distance. Comparisons are made within and between 5′NR and 3′NR sites. Significant D values (P < 0.05) are represented by •; nonsignificant values are represented by □.

Figure 3

Alignment of the RATs of the CR of the Csp. Letter codes for RATs are given in Table 4. The amino acid motif NVDP is shaded; NANP is unshaded. Discordant sites are shown in open boxes.

Figure 4

Maximum parsimony tree based on the nucleotide sequence of the CR, by using the alignment in Fig. 3. Displayed is the association of the CR with the 5′ and 3′NR types (see Table 3); shadings are for clarity. Bootstrap values are given for each branch. Arrows indicate a possible recombinant event.