Sequence variation in putative functional domains of the circumsporozoite protein of Plasmodium falciparum. Implications for vaccine development.

Sequences of the circumsporozoite protein gene from five isolates of the human malaria parasite Plasmodium falciparum are compared, and the extent of sequence variability within putative functional domains is assessed in terms relating to vaccine efficacy. Nucleotide substitutions were observed outside of the immunodominant domain. Of the substitutions observed outside of the repeat domain, none were silent. The substitutions correlated with biologically functional regions, such as a helper T cell epitope (Th2R) and a region (N1) which may be important in liver invasion. Contrary to previous impressions, the small numbers of amino acid changes in these areas of the protein seem potentially very significant. The immunodominant repeat region displays several characteristics that implicate a rapid evolutionary mechanism, most probably involving recombination. The data supporting this are 1) variable numbers of repeats, 2) a shifting pattern of substitutions among the isolates, and 3) codon bias. The region thus has the potential for very rapid change should an effective anti-repeat vaccine come into use. We conclude that strain variability is significant, that the potential for large scale variation in the repeats is great, and that regions that may be critical for an effective vaccine are polymorphic. Their potential impact on malaria vaccine development must be addressed.