Natural selection and population genetic structure of domain-I of Plasmodium falciparum apical membrane antigen-1 in India

- Genetic diversity of domain-I of Pfama-1 in Kolkata clinical isolates was studied.
- An abundance of low frequency alleles suggested parasite population expansion.
- High Rm and dN/dS highlighted the roles of recombination and selection.
- Amino acid changes on PfAMA-1 favored its interaction with PfRON2 in RBC invasion.
- Strong genetic differentiation between Kolkata & other Indian samples was observed.

Development of a vaccine against Plasmodium falciparum infection is an urgent priority particularly because of widespread resistance to most traditionally used drugs. Multiple evidences point to apical membrane antigen-1(AMA-1) as a prime vaccine candidate directed against P. falciparum asexual blood-stages. To gain understanding of the genetic and demographic forces shaping the parasite sequence diversity in Kolkata, a part of Pfama-1 gene covering domain-I was sequenced from 100 blood samples of malaria patients. Statistical and phylogenetic analyses of the sequences were performed using DnaSP and MEGA. Very high haplotype diversity was detected both at nucleotide (0.998 ± 0.002) and amino-acid (0.996 ± 0.001) levels. An abundance of low frequency polymorphisms (Tajima's D = −1.190, Fu & Li's D∗ and F∗ = −3.068 and −2.722), unimodal mismatch distribution and a star-like median-joining network of ama-1 haplotypes indicated a recent population expansion among Kolkata parasites. The high minimum number of recombination events (Rm = 26) and a significantly high dN/dS of 3.705 (P < 0.0001) in Kolkata suggested recombination and positive selection as major forces in the generation and maintenance of ama-1 allelic diversity. To evaluate the impact of observed non-synonymous substitutions in the context of AMA-1 functionality, PatchDock and FireDock protein-protein interaction solutions were mapped between PfAMA-1-PfRON2 and PfAMA-1-host IgNAR. Alterations in the desolvation and global energies of PfAMA-1-PfRON2 interaction complexes at the hotspot contact residues were observed together with redistribution of surface electrostatic potentials at the variant alleles with respect to referent Pf3D7 sequence. Finally, a comparison of P. falciparum subpopulations in five Indian regional isolates retrieved from GenBank revealed a significant level of genetic differentiation (FST = 0.084-0.129) with respect to Kolkata sequences. Collectively, our results indicated a very high allelic and haplotype diversity, a high recombination rate and a signature of natural selection favoring accumulation of non-synonymous substitutions that facilitated PfAMA-1-PfRON2 interaction and hence parasite growth in Kolkata clinical isolates.