Intragenic recombination in the 3' portion of the merozoite surface protein 1 gene of Plasmodium vivax

Spatiotemporal Changes in Plasmodium vivax msp142 Haplotypes in Southern Mexico: From the Control to the Pre-Elimination Phase

For 20 years, Plasmodium vivax has been the only prevalent malaria species in Mexico, and cases have declined significantly and continuously. Spatiotemporal genetic studies can be helpful for understanding parasite dynamics and developing strategies to weaken malaria transmission, thus facilitating the elimination of the parasite. The aim of the current contribution was to analyze P. vivax-infected blood samples from patients in southern Mexico during the control (1993–2007) and pre-elimination phases (2008–2011). Nucleotide and haplotype changes in the pvmsp142 fragment were evaluated over time. The majority of multiple genotype infections occurred in the 1990s, when the 198 single nucleotide sequences exhibited 57 segregating sites, 64 mutations, and 17 haplotypes. Nucleotide and genetic diversity parameters showed subtle fluctuations from across time, in contrast to the reduced haplotype diversity and the increase in the R2 index and Tajima’s D value from 2008 to 2011. The haplotype network consisted of four haplogroups, the geographical distribution of which varied slightly over time. Haplogroup-specific B-cell epitopes were predicted. Since only high-frequency and divergent haplotypes persisted, there was a contraction of the parasite population. Given that 84% of haplotypes were exclusive to Mesoamerica, P. vivax flow is likely circumscribed to this region, representing important information for parasite surveillance.

A Chimeric Plasmodium vivax Merozoite Surface Protein Antibody Recognizes and Blocks Erythrocytic P. cynomolgi Berok Merozoites In Vitro

Research on erythrocytic Plasmodium vivax merozoite antigens is critical for identifying potential vaccine candidates in reducing P. vivax disease. However, many P. vivax studies are constrained by its inability to undergo long-term culture in vitro Conserved across all Plasmodium spp., merozoite surface proteins are essential for invasion into erythrocytes and highly expressed on erythrocytic merozoites, thus making it an ideal vaccine candidate. In clinical trials, the P. vivax merozoite surface protein 1 (PvMSP1-19) vaccine candidate alone has shown to have limited immunogenicity in patients; hence, we incorporate the highly conserved and immunogenic C terminus of both P. vivax merozoite surface protein 8 (PvMSP8) and PvMSP1-19 to develop a multicomponent chimeric protein rPvMSP8+1 for immunization of mice. The resulted chimeric rPvMSP8+1 antibody was shown to recognize native protein MSP8 and MSP1-19 of mature P. vivax schizonts. In the immunized mice, an elevated antibody response was observed in the rPvMSP8+1-immunized group compared to that immunized with single-antigen components. In addition, we examined the growth inhibition of these antibodies against Plasmodium cynomolgi (Berok strain) parasites, which is phylogenetically close to P. vivax and sustains long-term culture in vitro Similarly, the chimeric anti-rPvMSP8+1 antibodies recognize P. cynomolgi MSP8 and MSP1-19 on mature schizonts and showed strong inhibition in vitro via growth inhibition assay. This study provides support for a new multiantigen-based paradigm rPvMSP8+1 to explore potential chimeric vaccine candidates against P. vivax malaria using sister species P. cynomolgi.

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.

Low genetic diversity in the locus encoding the Plasmodium vivax P41 protein in Colombia's parasite population

Background

The development of malaria vaccine has been hindered by the allele-specific responses produced by some parasite antigens’ high genetic diversity. Such antigen genetic diversity must thus be evaluated when designing a completely effective vaccine. Plasmodium falciparum P12, P38 and P41 proteins have red blood cell binding regions in the s48/45 domains and are located on merozoite surface, P41 forming a heteroduplex with P12. These three genes have been identified in Plasmodium vivax and share similar characteristics with their orthologues in Plasmodium falciparum. Plasmodium vivax pv12 and pv38 have low genetic diversity but pv41 polymorphism has not been described.

Methods

The present study was aimed at evaluating the P. vivax p41 (pv41) gene’s polymorphism. DNA sequences from Colombian clinical isolates from pv41 gene were analysed for characterising and studying the genetic diversity and the evolutionary forces that produced the variation pattern so observed.

Results

Similarly to other members of the 6-Cys family, pv41 had low genetic polymorphism. pv41 3′-end displayed the highest nucleotide diversity value; several substitutions found there were under positive selection. Negatively selected codons at inter-species level were identified in the s48/45 domains; p41 would thus seem to have functional/structural constraints due to the presence of these domains.

Conclusions

In spite of the functional constraints of Pv41 s48/45 domains, immune system pressure seems to have allowed non-synonymous substitutions to become fixed within them as an adaptation mechanism; including Pv41 s48/45 domains in a vaccine should thus be carefully evaluated due to these domains containing some allele variants.

Electronic supplementary material

The online version of this article (doi:10.1186/1475-2875-13-388) contains supplementary material, which is available to authorized users.

Low genetic diversity and functional constraint in loci encoding Plasmodium vivax P12 and P38 proteins in the Colombian population

Background

Plasmodium vivax is one of the five species causing malaria in human beings, affecting around 391 million people annually. The development of an anti-malarial vaccine has been proposed as an alternative for controlling this disease. However, its development has been hampered by allele-specific responses produced by the high genetic diversity shown by some parasite antigens. Evaluating these antigens’ genetic diversity is thus essential when designing a completely effective vaccine.

Methods

The gene sequences of Plasmodium vivax p12 (pv12) and p38 (pv38), obtained from field isolates in Colombia, were used for evaluating haplotype polymorphism and distribution by population genetics analysis. The evolutionary forces generating the variation pattern so observed were also determined.

Results

Both pv12 and pv38 were shown to have low genetic diversity. The neutral model for pv12 could not be discarded, whilst polymorphism in pv38 was maintained by balanced selection restricted to the gene’s 5′ region. Both encoded proteins seemed to have functional/structural constraints due to the presence of s48/45 domains, which were seen to be highly conserved.

Conclusions

Due to the role that malaria parasite P12 and P38 proteins seem to play during invasion in Plasmodium species, added to the Pv12 and Pv38 antigenic characteristics and the low genetic diversity observed, these proteins might be good candidates to be evaluated in the design of a multistage/multi-antigen vaccine.

Genetic diversity and selection in three Plasmodium vivax merozoite surface protein 7 (Pvmsp-7) genes in a Colombian population

A completely effective vaccine for malaria (one of the major infectious diseases worldwide) is not yet available; different membrane proteins involved in parasite-host interactions have been proposed as candidates for designing it. It has been found that proteins encoded by the merozoite surface protein (msp)-7 multigene family are antibody targets in natural infection; the nucleotide diversity of three Pvmsp-7 genes was thus analyzed in a Colombian parasite population. By contrast with P. falciparum msp-7 loci and ancestral P. vivax msp-7 genes, specie-specific duplicates of the latter specie display high genetic variability, generated by single nucleotide polymorphisms, repeat regions, and recombination. At least three major allele types are present in Pvmsp-7C, Pvmsp-7H and Pvmsp-7I and positive selection seems to be operating on the central region of these msp-7 genes. Although this region has high genetic polymorphism, the C-terminus (Pfam domain ID: PF12948) is conserved and could be an important candidate when designing a subunit-based antimalarial vaccine.

Genetic polymorphism and natural selection in the C-terminal 42 kDa region of merozoite surface protein-1 among Plasmodium vivax Korean isolates

Background

The carboxy-terminal 42 kDa region of Plasmodium vivax merozoite surface protein-1 (PvMSP-1₄₂) is a leading candidate antigen for blood stage vaccine development. However, this region has been observed to be highly polymorphic among filed isolates of P. vivax. Therefore it is important to analyse the existing diversity of this antigen in the field isolates of P. vivax. In this study, the genetic diversity and natural selection in PvMSP-1₄₂ among P. vivax Korean isolates were analysed.

Methods

A total of 149 P. vivax-infected blood samples collected from patients in Korea were used. The region flanking PvMSP-1₄₂ was amplified by PCR, cloned into Escherichia coli, and then sequenced. The polymorphic characteristic and natural selection of PvMSP-1₄₂ were analysed using the DNASTAR, MEGA4 and DnaSP programs.

Results

A total of 11 distinct haplotypes of PvMSP-1₄₂ with 40 amino acid changes, as compared to the reference Sal I sequence, were identified in the Korean P. vivax isolates. Most of the mutations were concentrated in the 33 kDa fragment (PvMSP-1₃₃), but a novel mutation was found in the 19 kDa fragment (PvMSP-1₁₉). PvMSP-1₄₂ of Korean isolates appeared to be under balancing selection. Recombination may also play a role in the resulting genetic diversity of PvMSP-1₄₂.

Conclusions

PvMSP-1₄₂ of Korean P. vivax isolates displayed allelic polymorphisms caused by mutation, recombination and balancing selection. These results will be useful for understanding the nature of the P. vivax population in Korea and for development of a PvMSP-1₄₂ based vaccine against P. vivax.

Genetic characteristics of polymorphic antigenic markers among Korean isolates of Plasmodium vivax

Plasmodium vivax, a protozoan malaria parasite of humans, represents a major public health concern in the Republic of Korea (= South Korea). However, little is known about the genetic properties and population structures of the P. vivax isolates circulating in South Korea. This article reviews known polymorphic genetic markers in South Korean isolates of P. vivax and briefly summarizes the current issues surrounding the gene and population structures of this parasite. The critical genetic characteristics of major antigens of the parasite, such as circumsporozoite protein (CSP), merozoite surface protein 1 (MSP-1) and MSP-3, Duffy binding protein (DBP), apical membrane antigen 1 (AMA-1), and GAM-1, are also discussed.

AA. A comparative study of the genetic diversity of the 42kDa fragment of the merozoite surface protein 1 in Plasmodium falciparum and P. vivax

We investigated the genetic diversity of the 42kDa fragment of the merozoite surface protein 1 (MSP-1) antigen in Plasmodium falciparum and P. vivax, as well as in non-human primate malarial parasites. This fragment undergoes a proteolytic cleavage generating two fragments of 19kDa (MSP-1(19)) and 33kDa (MSP-1(33)) that are critical in erythrocyte invasion. We found that overall the MSP-1(33) fragment exhibits greater genetic diversity than the MSP-1(19) regardless of the species. We have found evidence for positive natural selection only in the human malaria parasites by comparing the rate of non-synonymous versus synonymous substitutions. In addition, we found clear differences between the two major human malaria parasites. In the case of P. falciparum, positive natural selection is acting on the MSP-1(19) region while the MSP-1(33) is neutral or under purifying selection. The opposite pattern was observed in P. vivax. Our results suggest different roles of this antigen in the host-parasite immune interaction in each of the major human malarial parasites.

Plasmodium vivax genetic diversity: microsatellite length matters

The Plasmodium vivax genome is very diverse but has a relatively low abundance of microsatellites. Leclerc et al. had shown that these di-nucleotide repeats have a low level of polymorphism, suggesting a recent bottleneck event in the evolutionary history of P. vivax. By contrast, in a recent paper, Imwong et al. show that there is a very high level of microsatellite diversity. The difference in these results is probably due to the set array lengths chosen by each group. Longer arrays are more diverse than are shorter ones because slippage mutations become exponentially more common with an increase in array length. These studies highlight the need to consider carefully the application and design of studies involving microsatellites.

Immunogenicity of a recombinant protein containing the Plasmodium vivax vaccine candidate MSP1(19) and two human CD4+ T-cell epitopes administered to non-human primates (Callithrix jacchus jacchus)

One of the most promising vaccine candidates against the erythrocytic forms of malaria is the 19 kDa C-terminal region of the merozoite surface protein 1 (MSP1(19)). As part of our studies aimed at the development of a Plasmodium vivax malaria vaccine, we characterized the immunogenic properties of a new bacterial recombinant protein containing the P. vivax MSP1(19) and two helper T-cell epitopes, the synthetic universal pan allelic DR epitope (PADRE) and a new internal MSP1 P. vivax epitope (DYDVVYLKPLAGMYK). We found that the recognition of His6MSP1(19)-DYDVVYLKPLAGMYK-PADRE was as good as the recognition of His6MSP1(19) indicating that the presence of the T-cell epitopes PADRE and DYDVVYLKPLAGMYK did not modify the MSP1(19) epitopes recognized by human IgG. The recombinant protein His6MSP1(19)-DYDVVYLKPLAGMYK-PADRE proved to be highly immunogenic in marmosets (Callithrix jacchus jacchus) when administered in incomplete Freund's adjuvant. However, when administered in other adjuvant formulations such as Quil A, CpG ODN 2006 or MPL/TDM, antibody titers to MSP1(19) were significantly lower. Among these three adjuvants, Quil A proved to be the most efficient one generating antibody titers significantly higher than the others. These results indicated that under the circumstances evaluated, adjuvants were key for the immunogenicity of the recombinant protein His6MSP1(19)-DYDVVYLKPLAGMYK-PADRE.

Diversity and natural selection in Plasmodium vivax Duffy binding protein gene

The Plasmodium vivax Duffy binding protein (DBP) binds to the Duffy blood group antigen on the surface of erythrocytes and is essential for invasion. Natural immunity develops to this protein making it an important vaccine candidate. Genetic diversity within and between populations was compared in 100 dbp sequences from isolates obtained from Papua New Guinea, Colombia, and South Korea. The cysteine-rich region II, that contains the binding domain, has the highest diversity compared to the rest of the dbp gene and appears to be under strong selective pressure based on statistical tests comparing rates of non-synonymous (K(n)) to synonymous mutations (K(s)) among P. vivax isolates and to those of closely related species. By contrast, meiotic recombination was not found to be significant for maintaining genetic diversity. A comparison of the patterns of nucleotide diversity within dbpII to that of genes encoding homologous erythrocyte binding proteins of Plasmodium knowlesi predict critical binding residues juxtaposed to polymorphic B- and T-cell epitopes. Phylogenic analysis and measurement of nucleotide diversity between and within the different geographic populations support emergence of distinct allelic families suggestive of divergent selection of alleles between populations. Development of a P. vivax DBP-based vaccine must take into account regions of high diversity within the molecule and alleles that show distinct geographic differences.

Expression, polymorphism analysis, reticulocyte binding and serological reactivity of two Plasmodium vivax MSP-1 protein recombinant fragments

Among the four parasite species causing malaria in humans, Plasmodium vivax prevails on both the Asian and the American continents. Several antigens from this parasite's erythrocytic stages have been characterised and some of them are considered to be good vaccine candidates. The P. vivax merozoite surface protein-1 (PvMSP-1) is a 200 kDa antigen, thought to mediate the initial contact between the merozoite and the erythrocyte. An effective blockage of this interaction could be important in anti-malarial vaccine design. This study analyses the genetic polymorphism, binding to both reticulocytes and erythrocytes, antigenicity and immunogenicity of two recombinant proteins belonging to the 33 kDa PvMSP-1 proteolytic fragment. Both regions showed very low genetic variation, bound reticulocytes with higher affinity than erythrocytes, were recognised by naturally P. vivax-infected patient sera and were immunogenic when used to immunise rabbits, making them good vaccine candidates against P. vivax, to be further preclinically tested in the Aotus monkey model.

Mosaic organization and heterogeneity in frequency of allelic recombination of the Plasmodium vivax merozoite surface protein-1 locus

The organization and allelic recombination of the merozoite surface protein-1 gene of Plasmodium vivax (PvMsp-1), the most widely prevalent human malaria parasite, were evaluated in complete nucleotide sequences of 40 isolates from various geographic areas. Alignment of 31 distinct alleles revealed the mosaic organization of PvMsp-1, consisting of seven interallele conserved blocks flanked by six variable blocks. The variable blocks showed extensive variation in repeats and nonrepeat unique sequences. Numerous recombination sites were distributed throughout PvMsp-1, in both conserved blocks and variable block unique sequences, and the distribution was not uniform. Heterozygosity of PvMsp-1 alleles was higher in Asia (0.953 +/- 0.009) than in Brazil (0.813 +/- 0.047). No identical alleles were shared between Asia and Brazil, whereas all but one variable block nonrepeat sequence found in Brazil occurred in Asia. These observations suggest that P. vivax populations in Asia are ancestral to Brazilian populations, and that PvMsp-1 has heterogeneity in frequency of allelic recombination events. Recurrent origins of new PvMsp-1 alleles by repeated recombination events were supported by a rapid decline in linkage disequilibrium between pairs of synonymous sites with increasing nucleotide distance, with little linkage disequilibrium at a distance of over 3 kb in a P. vivax population from Thailand, evidence for an effectively high recombination rate of the parasite. Meanwhile, highly reduced nucleotide diversity was noted in a region encoding the 19-kDa C-terminal epidermal growth factor-like domain of merozoite surface protein-1, a vaccine candidate.

Diversity in the thrombospondin-related adhesive protein gene (TRAP) of Plasmodium vivax

We analyzed 22 clinical isolates of Plasmodium vivax from Thailand and 17 from Brazil to investigate the extent of sequence variation in the thrombospondin-related adhesive protein of Plasmodium vivax (PvTRAP), a homologue of P. falciparum TRAP (PfTRAP) which has been considered to be a promising vaccine candidate. In total 54 haplotypes were identified from 73 distinct gene clones. Coexistence of different PvTRAP in circulation occurred in 10 and 13 isolates from Thailand and Brazil, respectively. Forty out of 48 substituted nucleotides are non-synonymous changes. Most of the substituted residues reside in the von Willebrand factor type A-domain (region II), a sulfated glycosaminoglycan-binding domain (region III) and a proline-rich region (region IV). All nucleotide substitutions are dimorphic. Two haplotypes from Thailand contain an inserted sequence encoding aspartic acid-serine-proline in the proline-rich region. Sequence analysis has revealed that nucleotide diversity in PvTRAP is low although Brazilian isolates display a higher degree of variation than those from Thailand. Phylogenetic construction using the neighbor joining method has shown that most of the Thai and the Brazilian isolates appear to be mainly clustered into distinct groups. Significantly greater than expected values of the mean number of non-synonymous (d(n)) than synonymous (d(s)) nucleotide substitutions per site were observed in regions II and III of PvTRAP. Analysis of the published PfTRAP sequences has shown a similar finding in regions II and IV suggesting that positive selection operates on the regions. Hence, different regions in PvTRAP and PfTRAP could be under different pressures in terms of immune selection, structural and/or functional constraints.