Population genetic analyses inferred a limited genetic diversity across the pvama-1 DI domain among Plasmodium vivax isolates from Khyber Pakhtunkhwa regions of Pakistan

Background

Plasmodium vivax apical membrane antigen-1 (pvama-1) is an important vaccine candidate against Malaria. The genetic composition assessment of pvama-1 from wide-range geography is vital to plan the antigen based vaccine designing against Malaria.

Methods

The blood samples were collected from 84 P. vivax positive malaria patients from different districts of Khyber Pakhtunkhwa (KP) province of Pakistan. The highly polymorphic and immunogenic domain-I (DI) region of pvama-1 was PCR amplified and DNA sequenced. The QC based sequences raw data filtration was done using DNASTAR package. The downstream population genetic analyses were performed using MEGA4, DnaSP, Arlequin v3.5 and Network.5 resources.

Results

The analyses unveiled total 57 haplotypes of pvama-1 (DI) in KP samples with majorly prevalent H-14 and H-5 haplotypes. Pairwise comparative population genetics analyses identified limited to moderate genetic distinctions among the samples collected from different districts of KP, Pakistan. In context of worldwide available data, the KP samples depicted major genetic differentiation against the Korean samples with Fst = 0.40915 (P-value = 0.0001), while least distinction was observed against Indian and Iranian samples. The statistically significant negative values of Fu and Li’s D* and F* tests indicate the evidence of population expansion and directional positive selection signature. The slow LD decay across the nucleotide distance in KP isolates indicates low nucleotide diversity. In context of reference pvama-1 sequence, the KP samples were identified to have 09 novel non-synonymous single nucleotide polymorphisms (nsSNPs), including several trimorphic and tetramorphic substitutions. Few of these nsSNPs are mapped within the B-cell predicted epitopic motifs of the pvama-1, and possibly modulate the immune response mechanism.

Conclusion

Low genetic differentiation was observed across the pvama-1 DI among the P. vivax isolates acquired from widespread regions of KP province of Pakistan. The information may implicate in future vaccine designing strategies based on antigenic features of pvama-1.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07798-1.

Genetic Diversity and Selection of Plasmodium vivax Apical Membrane Antigen-1 in China-Myanmar Border of Yunnan Province, China, 2009-2016

Plasmodium vivax apical membrane antigen-1 (PvAMA-1) is an important vaccine candidate for vivax malaria. However, antigenic variation within PvAMA-1 is a major obstacle to the design of a global protective malaria vaccine. In this study, we analyzed the genetic polymorphism and selection of the PvAMA-1 gene from 152 P. vivax isolates from imported cases to China, collected in the China–Myanmar border (CMB) area in Yunnan Province (YP) during 2009–2011 (n = 71) and 2014–2016 (n = 81), in comparison with PvAMA-1 gene information from Myanmar (n = 73), collected from public data. The overall nucleotide diversity of the PvAMA-1 gene from the 152 YP isolates was 0.007 with 76 haplotypes identified (Hd = 0.958). Results from the population structure suggested three groups among the YP and Myanmar isolates with optimized clusters value of K = 7. In addition, YP (2014–2016) isolates generally lacked some K components that were commonly found in YP (2009–2011) and Myanmar. Meanwhile, PvAMA-1 domain I is found to be the dominant target of positive diversifying selection and most mutation loci were found in this domain. The mutation frequencies of D107N/A, R112K/T, K120R, E145A, E277K, and R438H in PvAMA-1 were more than 70% in the YP isolates. In conclusion, high genetic diversity and positive selection were found in the PvAMA-1 gene from YP isolates, which are significant findings for the design and development of PvAMA-1-based malaria vaccine.

Low levels of genetic diversity associated with evidence of negative selection on the Babesia bovis apical membrane antigen 1 from parasite populations in Thailand

Babesia bovis, a parasite infecting cattle and buffalo, continues to spread throughout the developing world. The babesial vaccine was developed to be a sustainable alternative treatment to control the parasite. However, genetic diversity is a major obstacle for designing and developing a safe and effective vaccine. The apical membrane antigen 1 (AMA-1) is considered to be a potential vaccine candidate antigen among immunogenic genes of B. bovis. To gain a more comprehensive understanding of B. bovis AMA-1 (BbAMA-1), three B. bovis DNA samples were randomly selected to characterize in order to explore genetic diversity and natural selection and to predict the antigen epitopes. The sequence analysis revealed that BbAMA-1 has a low level of polymorphism and is highly conserved (95.46-99.94%) among Thai and global isolates. The majority of the polymorphic sites were observed in domains I and III. Conversely, domain II contained no polymorphic sites. We report the first evidence of strong negative or purifying selection across the full length of the gene, especially in domain I, by demonstrating a significant excess of the average number of synonymous (dS) over the non-synonymous (dN) substitutions. Finally, we also predict the linear and conformational B-cell epitope. The predicted B-cell epitopes appeared to be involved with the amino acid changes. Collectively, the results suggest that the conserved BbAMA-1 may be used to detect regional differences in the B. bovis parasite. Importantly, the limitation of BbAMA-1 diversity under strong negative selection indicates strong functional constraints on this gene. Thus, the gene could be a valuable target vaccine candidate antigen.

Diversity and evolutionary genetics of the three major Plasmodium vivax merozoite genes participating in reticulocyte invasion in southern Mexico

Background

Reported malaria cases in the Americas had been reduced to about one-half million by 2012. To advance towards elimination of this disease, it is necessary to gain insights into how the malaria parasite is evolving, including the emergence, spread and persistence of new haplotypes in affected regions. In here, the genetic diversity of the three major P. vivax merozoite genes was analyzed.

Methods

From P. vivax-infected blood samples obtained in southern Mexico (SMX) during 2006–2007, nucleotide sequences were achieved for: the 42 kDa carboxyl fragment of the merozoite surface protein-1 (msp1₄₂), domains I-II of the apical membrane antigen-1 (ama1_I-II), and domain II of the Duffy binding protein (dbp_II). Gene polymorphism was examined and haplotype networks were developed to depict parasite relationships in SMX. Then genetic diversity, recombination and natural selection were analyzed and the degree of differentiation was determined as F_ST values.

Results

The diversity of P. vivax merozoite genes in SMX was less than that of parasites from other geographic origins, with dbp_II < ama1_I-II < msp1₄₂. Ama1_I-II and msp1₄₂ exposed the more numerous haplotypes exclusive to SMX. While, all dbp_II haplotypes from SMX were separated from one to three mutational steps, the networks of ama1_I-II and msp1₄₂ were more complex; loops and numerous mutational steps were evidenced, likely due to recombination. Sings of local diversification were more evident for msp1₄₂. Sixteen combined haplotypes were determined; one of these haplotypes not detected in 2006 was highly frequent in 2007. The Rm value was higher for msp1₄₂than for ama1_I-II, being insignificant for dbp_II. The dN-dS value was highly significant for ama1_I-II and lesser so for dbp_II. The F_ST values were higher for dbp_II than msp1₄₂, and very low for ama1_I-II.

Conclusions

In SMX, P. vivax ama1_I-II, dbp_II and msp1₄₂ demonstrated limited diversity, and exhibited a differentiated parasite population. The results suggest that differential intensities of selective forces are operating on these gene fragments, and probably related to their timing, length of exposure and function during reticulocyte adhesion and invasion. Therefore, these finding are essential for mono and multivalent vaccine development and for epidemiological surveillance.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-015-1266-7) contains supplementary material, which is available to authorized users.