Analysis of polymorphisms and selective pressures on ama1 gene in Plasmodium knowlesi isolates from Sabah, Malaysia

Abstract

The apical membrane antigen-1 (AMA-1) of Plasmodium spp. is a merozoite surface antigen that is essential for the recognition and invasion of erythrocytes. Polymorphisms occurring in this surface antigen will cause major obstacles in developing effective malaria vaccines based on AMA-1. The objective of this study was to characterize ama1 gene in Plasmodium knowlesi isolates from Sabah. DNA was extracted from blood samples collected from Keningau, Kota Kinabalu and Kudat. The Pkama1 gene was amplified using nested PCR and subjected to bidirectional sequencing. Analysis of DNA sequence revealed that most of the nucleotide polymorphisms were synonymous and concentrated in domain I of PkAMA-1. Forteen haplotypes were identified based on amino acid variations and haplotype K5 was the most common haplotype. d/d ratios implied that purifying selection was prevalent in Pkama1 gene. Fu and Li's D and F values further provided evidence of negative selection acting on domain II of Pkama1. Lownucleotide diversitywas also detected for the Pkama1 sequences,which is similar to reports on Pkama1 from Peninsular Malaysia and Sarawak. The presence of purifying selection and low nucleotide diversity indicated that domain II of Pkama1 can be used as a target for vaccine development.

Genetic diversity of the full length apical membrane antigen-1 of Plasmodium knowlesi clinical isolates from Peninsular Malaysia

“…In the present study, the nucleotide diversity and haplotype diversity of Domain I (π: 0.007, Hd: 0.974) are close to the diversity of Domain I (π: 0.008, Hd: 0.941) reported previously for Peninsular Malaysia P. knowlesi isolates (Fong et al, 2015c). The nucleotide diversity of PkAMA-1 from Peninsular Malaysia (π: 0.006) was just slightly higher than that of Sarawak (π: 0.005) (Faber et al, 2015) and Sabah (π: 0.004) (Chua et al, 2017). Thus, it can be generally concluded that genetic polymorphism of PkAMA-1 is low.…”

“…Although AMA-1 is found in all Plasmodium species, but different species show different level of polymorphism of this protein. Studies showed high level of polymorphism in AMA-1 of P. falciparum and P. vivax (Escalante et al, 2001;Rajesh et al, 2007), whereas low level of polymorphism was found in P. knowlesi (Faber et al, 2015;Fong et al, 2015c;Chua et al, 2017).…”

<em>Plasmodium knowlesi</em> malaria: current research perspectives

“…At the same time, the mutations are deleterious to the parasite and the P. knowlesi population is screening for best-adapted variants. 75 Long-term population expansion of P. knowlesi in Malaysia has been suggested to be the cause of this selection. 73 , 79 , 83 There are, however, some differences in natural selection of these proteins in different geographical regions and different parts of the protein.…”

“… 79 These polymorphisms are probably results of recombination and reproduction cycle of P. knowlesi in multiple hosts. 75 Indeed, the Anopheles vector may exert strong evolutionary pressure on vector-related genes of the parasite, which is an evidence of adaptation of the parasite to the vector distribution or vectorial capacity. 86 …”

Plasmodium knowlesi: the game changer for malaria eradication

“…Malaysia H 34 Purifying selection 2 clusters were identified Yap et al (2017) [ 143 ] Merozoite surface protein 1 42 kDa region ( msp1 42 ) Erythrocyte invasion Pen. Malaysia, Sabah, Thailand, India H, Macaque 39 Purifying selection within Malaysia isolates – Chua et al (2017) [ 144 ] Apical membrane antigen 1 ( ama1 ) Erythrocyte invasion Sabah H 36 Purifying selection – De Silva et al (2017) [ 145 ] Merozoite surface protein 1 ( msp3 ) Erythrocyte invasion Pen. Malaysia H 48 Purifying selection in Domain B 2 clusters were identified Ahmed et al (2018) [ 146 ] msp1 Erythrocyte invasion Pen.…”