Population structure of the genes encoding the polymorphic Plasmodium falciparum apical membrane antigen 1: Implications for vaccine design

Abstract

Immunization with the highly polymorphic Plasmodium falciparum apical membrane antigen 1 (PfAMA1) induces protection in animals but primarily against parasites that express the same or similar alleles. One strategy to overcome the obstacle of polymorphism is to combine PfAMA1 proteins representing major haplotypes into one vaccine. To determine the minimum number of haplotypes that would confer broad protection, we sequenced the coding region of PfAMA1 from 97 clones from around the world and 61 isolates from Mali, identifying 150 haplotypes for domains 1 to 3 that included previous sequences. A clustering algorithm grouped the 150 haplotypes into six populations that were independent of geographic location. Each of the six populations contained haplotypes predominantly of that population (predominant haplotypes) and haplotypes that were a mixture of haplotypes represented in other populations (admixed haplotypes). To determine the biological relevance of the populations identified through the clustering algorithm, antibodies induced against one predominant haplotype of population 1 (3D7) and one admixed haplotype of population 5 (FVO) were tested for their ability to block parasite invasion of erythrocytes. Parasites expressing PfAMA1s belonging to population 1 were efficiently inhibited by 3D7-specific antibodies, whereas parasites expressing PfAMA1s belonging to other populations were not. For FVO-specific antibodies, we observed growth inhibition against itself as well as isolates belonging to populations 3 and 6. Our data suggests that the inclusion of PfAMA1 sequences from each of the six populations may result in a vaccine that induces protective immunity against a broad range of malaria parasites.

Simulation of B Cell Affinity Maturation Explains Enhanced Antibody Cross-Reactivity Induced by the Polyvalent Malaria Vaccine AMA1

“…A recent phase 2b AMA1 vaccine trial in 1-6-y-old children in Mali found 64% efficacy against malaria caused by vaccine-like strains, underscoring its potential as a malaria vaccine (41). Unfortunately, AMA1 displays immense antigenic variation: .10% of its residues are polymorphic, and .200 unique haplotypes have been identified (42,43). A crystal structure of AMA1 reveals that the protein consists of three domains that present two immunologically distinct regions: a conserved face, consisting of a cluster of largely conserved epitopes along domain I and III, and a polymorphic face, consisting of a cluster of highly polymorphic epitopes along domain II (44,45).…”

“…A crystal structure of AMA1 reveals that the protein consists of three domains that present two immunologically distinct regions: a conserved face, consisting of a cluster of largely conserved epitopes along domain I and III, and a polymorphic face, consisting of a cluster of highly polymorphic epitopes along domain II (44,45). Previous studies suggested that no fewer than 6-10 strains of AMA1, and possibly many more, must be included in a polyvalent vaccine to provide sufficient allelic coverage for broad protection (42,43,46). However, several studies developed polyvalent formulations of AMA1, using two to six strains, and demonstrated significant cross-reactivity and protection relative to the monovalent vaccine of any single strain (47)(48)(49)(50).…”

Using Population Genetics to Guide Malaria Vaccine Design

“…The potential of AMA1 as a malaria vaccine candidate has been demonstrated in rodent models of malaria with both strain-specific [87][88][89] and cross-protective [90] protection observed. High levels of polymorphism in AMA1 [8,91,92] due to strong balancing selection [93] has resulted in hundreds of distinct AMA1 haplotypes; this might indicate that the development of a broadly effective AMA1-based malaria vaccine will be difficult. However, little is known about the antigenic diversity of AMA1 and recent studies suggest that immunization with a small number of different alleles might give broad reactivity [94,95].…”

“…This analysis has also been adapted to understand relationships among haplotypes of several malaria vaccine candidates [8,91,92,226]. A study of 150 AMA1 sequences by Xin Zhuan Su and colleagues demonstrated that they clustered into six distinct subgroups.…”

Molecular vaccines for malaria

“…The LMIV at NIH in collaboration with MRTC in Mali has applied a clustering algorithm to AMA1 sequence data from isolates around the world and identified six distinct populations based primarily on geographic area that in limited testing have induced non-cross-protective antibodies, thus constituting a minimum requirement for the number variants needed for a vaccine. 29 The Biomedical Primate Research Center (BPRC) in The Netherlands has synthesized three "diversity covering" versions of AMA1 encompassing 97% of the amino acid variability observed in nature and conducted preliminary studies in rabbits showing the induction of crossinhibitory antibodies. 30 Similar studies are underway at the La Trobe University and at the Walter and Eliza Hall Institute of Medical Research in Australia.…”