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

Abstract

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.

Background

Plasmodium vivax is the main species causing malaria in the Middle East, Asia, the West Pacific, and Central and South America, where billions of people are at risk [1, 2]. In the Americas, the number of malaria cases gradually declined from 2000 to 2012 due to the improvement and intensification of control measures. In 2012, 469,369 new malaria cases were reported, which represents a 72 % reduction compared to the year 2000 [3, 4]. In 2008, 20,833 cases were reported in Mesoamerica (from Southern Mexico to Panama), of which 11.3 % corresponded to Mexico. Around the world there are countries that have advanced to the pre-elimination phase, while others have reported little decline or even an increase in the number of malaria cases [5, 6]. To contribute to better control efforts and accelerate malaria elimination, more knowledge is needed about the parasites circulating in each region. In this sense, analysis of the evolutionary forces that shape malaria antigen diversity can be useful for monitoring and designing vaccines, describing transmission dynamics, and conducting epidemiological surveillance.

The Plasmodium merozoite invades reticulocytes in a few seconds by a series of complex interactions. The merozoite surface protein 1 (MSP1) participates in the initial adhesion to the reticulocyte and the apical membrane antigen 1 (AMA1) into parasite reorientation [7–9]. Then the Duffy binding protein (DBP) irreversible binds at the time of reticulocyte invasion [10]. In P. vivax the MSP1 of 200 kb is coded by a gene located in chromosome 7 and is comprised of variable and semi-conserved blocks. This protein is processed into fragments of 83, 30, 38 and 42 kDa [11]. At the time of invasion, the carboxyl fragment of 42 kDa is further processed into two fragments of 33 and 19 kDa (MSP1₃₃ and MSP1₁₉). Both fragments are immunogenic, capable of inducing antibodies that block merozoite invasion [12]. AMA1 is an antigen of 66 kDa, coded by a gene located in chromosome 9 and secreted by micronemes. The ecto-cytoplasmic region is comprised of three domains (I, II and III) and 16 cysteine residues [13]. The crystal structure of AMA1 shows that domains I and II have a structure similar to the PAN adhesive motive and participate in reticulocyte adhesion, and that domain I is more variable than domain II [8]. DBP is an integral membrane protein of 140 kDa coded by a gene located in chromosome 6 and comprised of seven domains: a signal peptide, two cysteine-rich domains flanking the amino N-cys and carboxyl C-cys (II and VI), three hydrophobic domains (III - V) and one trans-membrane domain (VII) [14]. Domain II (DBP_II), which comprises 170 amino acids flanked by cisterns 4 and 7 (within residues 291 and 460), binds the Duffy antigen on the reticulocyte surface. This domain also presents high molecular polymorphism, but the precise site of interaction seems to be more conserved [14, 15]. These merozoite proteins induce antibodies capable of blocking reticulocyte invasion. MSP1 seems to be the most immunogenic, evidenced by the fact that a large number of patients developed antibodies against it after the primary blood infection [16, 17]. Apparently, AMA1 is the second most immunogenic [18, 19] and DBP the least [20, 21].

In southern Mexico, previous studies have shown that P. vivax comprises a unique genetic population, such as the association of vector compatibility to Pvs25-28 protein polymorphisms [22] and to subpopulations defined by microsatellite markers [23]. By analysis of msp1 block icb5-6 from this region, divergent lineages of Sal 1 or Belem strains were distinguished [24]. To gain further insights into the evolutionary genetics of P. vivax merozoite vaccine candidates, the genetic diversity of ama1_I-II, dbp_II and msp1₄₂ fragments was analyzed in parasites from southern Mexico and compared to other geographic origins.

Methods

This study was approved by the Ethics Committee of the National Institute of Public Health in Mexico (INSP, according to the initials in Spanish). Informed consent was obtained from all adult patients and the guardians of minors.

The specific area of southern Mexico herein studied is its Pacific coastal plain, defined as Jurisdiction VII of the State of Chiapas. This jurisdiction comprises 4644.07 km² and during the period of the present study (2006–2007) had a population of 710,716 inhabitants. Its altitude ranges from sea level to mountainous regions of about 4000 m above sea level, and has a great climactic and biological diversity. In the State of Chiapas, malaria transmission has been persistent but fluctuating. Since the 1980’s, when over 20, 000 cases were reported per year, malaria transmission has been declining. In the late 1990’s, there were about 1000 cases reported per year [25]. In Jurisdiction VII of the Chiapas State only 167 cases were reported in 2005. After hurricane Stan hit the region in October of 2005, the anti-malarial brigades did not have access to the affected areas for at least four months. As a result, the number of malaria cases increased in 2006 to 646 and in 2007 to 644 (data from the local malaria control program, Sanitary Jurisdiction VII).

P. vivax blood samples

During 2006 and 2007, malaria symptomatic patients living in Jurisdiction VII and diagnosed with P. vivax infection by microscopy were invited to donate 5 ml of venous blood. The DNA from infected blood samples was extracted using a commercially available QIAamp DNA blood minikit (Qiagen, USA), following the manufacturer’s instructions. From 200 μL of heparinized infected blood, two hundred microliters of soluble DNA were obtained.

PCR amplification and DNA sequencing

The msp1₄₂ gene fragment of approximately 1.2 kb was amplified using primers msp1-5´AAGCTTAGAGGACTACGACAAAG -3' and msp1-3´GTCGAAGGATTCGAACGAGCTCG 5'. The PCR was prepared as follows: 60 mM de Tris-SO₄, 18 mM ammonium sulphate, 2 mM of MgSO₄, 0.2 mM of dNTPs, 0.4 μM of each primer, 1U Platinum Taq DNA polymerase High Fidelity (Invitrogen, Carlsbad, CA) and 1–4 μL of genomic DNA, for a final PCR volume of 50 μL. The reaction was run at 95 °C for 5 min, followed by 35 cycles of 95 °C for 60 s, 60 °C for 60 s and 72 °C for 75 s, and a final extension at 72 °C for 10 min.

The ama1_I-II gene fragment of approximately 1.1 kb was amplified using primers ama1f-5'-TCCAGCTGGAAGATGTCCTG-3' and ama1r-5'-CCGCCCTTTTCTCTACACAG-3'. The PCR was prepared as aforementioned and the reaction was run at 95 °C for 5 min, followed by 35 cycles of 95 °C for 60 s, 61 °C for 60 s and 72 °C for 75 s, and a final extension at 72 °C for 10 min.

The dbp_II gene fragment of approximately 1.2 kb was amplified by polymerase chain reaction (PCR) using the following primers: dbpf-5' GATAAAACTGGGGAGGAAAAAGAT 3' and dbpr-5' CTTATCGGATTTGAATTGGTGGC 3'. The PCR was prepared as aforementioned and the reaction was run at 94 °C for 3 min, followed by 35 cycles of 94 °C for 40 s, 58 °C for 40 s and 72 °C for 1.5 min, and a final extension at 72 °C for 5 min.

The amplified products were examined in agarose gels at 1 % and stained with 0.2 μg/ml ethidium bromide using a Midicell primo electrophoresis chamber (Thermo EC330, New York, USA). The 100 bp ladder was used as a molecular marker (Invitrogen Corporation, Carlsbad, CA). The gel image was obtained in a photo documentation UV system (LMS-20E Bio-Doc-it, Upland, CA).

The amplified products, estimated by visual observation, were purified using a MinElute PCR purification kit (Qiagen, Valencia, CA), following the manufacturer’s instructions. The purified products were sequenced using forward and reverse primers for merozoite genes in a Taq FS Dye Terminator Cycle Fluorescence-Based Sequencer (Perkin Elmer/Applied Biosystems Model 3730) at the Biotechnology Institute of the National Autonomous University of Mexico at Cuernavaca (Morelos, Mexico). The quality of pherograms with the forward and reverse nucleotide sequences was verified manually and by using Bioedit v7.1.3 software. Consensus sequences were obtained for each gene fragment and were submitted to the NCBI GenBank [accession numbers: KP759780–KP759884].

Data analysis

The consensus sequences were aligned to the corresponding reference gene strains Sal 1 and Belem, respectively, as follows: for dbp_II, XM_001608337.1 and EU395587; for ama1_I-II, XM_001615397 and EU395595; for msp1₄₂, XM_001614792.1 and AF435594. DNA polymorphism was analyzed for the three gene fragments. The number of segregating sites (polymorphic) (S), number of mutations or nucleotide changes (M), number of haplotypes (H), haplotype diversity (Hd), nucleotide and genetic diversity (Pi; π, Theta; θ), and their corresponding standard deviations (SD) were calculated with DnaSP v5.1 software [26]. Haplotype frequencies for each gene fragment and for combined haplotypes were examined over time.

To explore the genetic relationship between the haplotypes of each merozoite gene, and how these haplotypes show up in the parasite isolates, a minimum spanning haplotype network was constructed for each gene fragment using TCS 1.21 [27] and Median Joining Network in PopArt 1.7 [28].

To determine how selective forces influence the haplotype relationship, the minimum number of recombination events (Rm) was estimated by the four-gamete test [29]. D’ and R² indexes of linkage disequilibrium were determined by non-random association between nucleotide variants within the gene fragments using DnaSP. To test the neutral theory of evolution, Tajima’s D values were calculated. Positive values correspond to positive or balancing selection, whereas negative values correspond to negative or purifying selection [30]. In coding regions, an excess of non-synonymous relative to synonymous changes is a clear signal of positive selection. Different levels of positive selection have been reported in other geographic sites for msp1₄₂ [31–33], ama1_I-II [13, 34] and dbp_II [35, 36]. Hence, the dN-dS difference between the rate of the average number of non-synonymous (dN) and synonymous (dS) nucleotide changes was calculated for each gene fragment of the distinct parasite groups by using the alternate hypothesis (HA: dN > dS). For this purpose, we used Nei-Gojobori’s method [37] and bootstrap variance estimation with 1000 replicates for the Z-test of selection (p < 0.05) in MEGA v6.0 software [38].

Finally, Wright’s fixation statistics (F_ST) [39] indexes were calculated to determine the degree of differentiation of P. vivax in southern Mexico based on each merozoite gene (dbp_II, msp1₄₂ and ama1_I-II), using DNA sequences of parasites from different geographic origins, by using the model of two parameters of Kimura 2P in DnaSP [26, 40]. F_ST values range from 0 to 1, high values indicate considerable degree of differentiation between parasite populations.

Homologous DNA sequences from other geographic sites were obtained from the NCBI GenBank: Msp1₄₂. For South Korea (SK), n = 200: JQ446312-JQ446322 [41], HQ171934-HQ171941 [42], and AF435635-AF435638 [11]. For Turkey (TUR), n = 30: AB564559-AB564588 [43]. For Thailand (THL), n = 93: AF435595-AF435615 [11], GQ890917-GQ890974 [44], AF199393- AF199404, and AF199408- AF199410 [45]. For Singapore (SNG), n = 50: GU971656-GU971705 [46]. For India-Bangladesh (IND-BNG), n = 35: EU430452-EU430479 [31], KF612323 [47], AF435639, and AF435616-AF435620 [11]. For Brazil (BRZ), n = 11: AF435622-25, 27, 29, 30, 31,[11] and AF199405-7 [45]. For Sri Lanka (SLK), n = 106: AJ292349-AJ292359 and GU175174-GU175268 [32]. For Myanmar (MYN), n = 28: JX490129-JX490156 (Zhou and Chen, unpublished). For Cambodia (CAM), n = 44: JX461286-JX461310, JX461312, JX461313, and JX461315- JX461332 [48]. Ama1_I-II: For THL, n = 231: FJ784891-FJ785121 [49]. For Venezuela (VNZ), n = 73: EU346015-EU346087 [34]. For IND, n = 56: EF025187-EF025197 [50] and EU282774-EU282822 [51]. For SLK, n = 23: EF218679-EF218701 [13]. For Iran (IRN), n = 83: JX624732-35 [52], KF422636-681, and KF422636-KF422681 [53]. For Papua New Guinea (PNG), n = 102: KC702402-KC702503 [54]. Dbp_II: For MYN, n = 54: JN255576-JN255587 [55]. For SK n = 111: JN989472-JN989484 [56], AF215737-AF215738 [57], AF220657-AF220663, AF220668 [58], DQ156522, DQ156523, and DQ156515 (Lim and Ayala, unpublished). For PNG, n = 201: AF289480-AF289483, AF289635-AF289640, AF289642-AF289645, AF289647-AF289653, AF291096 [59], AF469515-AF469602 [60], AY970837-AY970925 [61], and DQ156519 (Lim and Ayala, unpublished). For THL, n = 30: EF219451, EF368159-EF368180, EF379127, EF379128, and EF379130-EF379134 [35]. For BRZ, n = 122: EU812839-EU812960 [62]. For IND, n = 95: DQ156514, DQ156516 (Lim and Ayala, unpublished), FJ491142-FJ491144, FJ491146-FJ491161, FJ491163-FJ491169, FJ491171-FJ491173, FJ491175-FJ491218, FJ491221-FJ491234, and FJ491236-FJ491241 (Prajapati and Joshi, unpublished). For Colombia (COL), n = 17: U50575-U50591 [63]. For SLK, n = 100: GU143914-GU144013 [64]. For IRN, n = 130: EU860430-EU86038 [65], KF318358, KF318359 KF791921, and KF791923-KF791926 [66].

Results

Genetic polymorphism of P. vivax merozoite genes in SMX

From 35 P. vivax isolates (2006, n = 17; 2007, n = 18), gene fragments dbp_II, ama1_I-II and msp1₄₂ were amplified and the consensus nucleotide sequence obtained. Although several P. vivax isolates had codons or nucleotide fragments that resembled either Sal 1 or Belem, none was identical to either of these sequences. The msp1₄₂ sequence was more polymorphic than that of dbp_II or ama1_I-II (Table 1).

Table 1.

Comparison of P. vivax merozoite gene diversity among isolates from southern Mexico, 2006–2007

Parameter	Gene fragment
	msp1 42	ama1 I-II	dbp II
bp	1071	885	1104
1n, polymorphic sites	52	14	14
n, nucleotide changes	59	14	14
2π (SD)	0.01716 (0.00179)	0.00745 (0.00039)	0.00304 (0.00062)
3Θw (SD; nr, fr)	0.01178 (0.00381, 0.00163)	0.00384 (0.00150, 0.00103)	0.00308 (0.00120, 0.00082)
n, haplotypes	9	7	8
4Hd (SD)	0.783 (0.051)	0.723 (0.057)	0.556 (0.094)
Tajima’s D test (P value)	1.0408 (>0.10)	3.0416 (<0.01)	- 0.0459 (>0.10)

bp, base pairs; ¹Number; ²Nucleotide diversity (all nucleotide sites); ³nr, no recombination, and fr, free recombination; ⁴Haplotype diversity; SD, standard deviation

The msp1₄₂ gene fragment of 1072 bp (codons 1353–1710) had 52 polymorphic sites, in which 59 nucleotide changes were detected. All nucleotide changes were detected in subfragment msp1₃₃ (nucleotides 4060–4875), and five of these were synonymous. Subfragment msp1₁₉ was conserved (Table 1; Additional file 1). Nine haplotypes were resolved and the haplotype diversity (Hd) was higher than that found for dbp_II.

Fourteen polymorphic sites and seven haplotypes were detected among the 35 isolates for the ama1_I-II gene fragment of 885 bp (Table 1). Domain I had 11 nucleotide changes (within codons 125–243) and domain II three (within codons 244–460). Compared to the Sal 1 sequence, three additional polymorphisms were detected, with one synonymous change at codon 137 Pro (cca → ccc), and two nonsynonymous changes at codons 145 Glu/Ala (gaa → gca) and 277 Glu/Lys (gag → aag). These variant codons resembled the sequence of the Belem strain (Additional file 2).

A gene fragment of 1,104 pb was obtained for dbp_II. Fourteen polymorphic sites and mutations were detected within codons 191–558. The only synonymous change, at codon 530 (aac → aat), was found in two isolates. Most of the diversity indexes were lower than those estimated for ama1_I-II and msp1₄₂ (Table 1; Additional file 3).

Temporal distribution of single and combined haplotypes

P. vivax haplotypes were detected at a different frequency over time (Fig. 1; Additional file 4). The highest number of haplotypes for all three gene fragments (dbp_II, ama1_I-IIand msp1₄₂) was found in 2006, when all eight dbp_II and seven of the ama1_I-II haplotypes were detected. Meanwhile, only three dbp_II and four ama1_I-II haplotypes were identified in 2007. For msp1_42, eight of nine total haplotypes were detected in 2006. In addition, of 16 combined haplotypes (dbp_II-ama1_I-II-msp1₄₂), 13 were detected in 2006 and seven in 2007 (four of them were found in both years). For the three haplotypes exclusively detected in 2007, haplotype A was significantly more frequent (59 %) than the others (p = 0.00024) and was detected from January to September.

Fig. 1.

Monthly distribution of P. vivax dbp _II - ama1 _I-II - msp1 ₄₂ combined haplotypes in southern Mexico, 2006–2007. Each haplotype is indicated by a different color. Of 16 combined haplotypes, 13 were detected in 2006 and seven in 2007. Four were common to both years, while nine were exclusive to 2006 and three to 2007. The most frequent combined haplotype (in green) was only detected during 2007

Haplotype relationships for different merozoite genes and the haplotype configuration for P. vivax isolates in SMX

Each gene fragment produced a haplotype network with a different pattern (Fig. 2). 1) The SMX dbp_II network was the simplest; the haplotypes were separated by one to three mutational steps. From a highly frequent haplotype (dh1; 65.7 %), two branches emerged, and the most distant haplotypes (dh3 or dh4) were separated in opposite directions by eight and eleven mutational steps, respectively. Rather than a network, a straight-line pattern was observed. 2) For SMX ama1_I-II, the highly frequent haplotype (ah1; 45.7 %) and another four formed a loop, with 3 - 5 mutational steps in between. From haplotype ah5 there was a branch connecting more divergent haplotypes, ah2 and ah6. 3) The SMX msp1₄₂ network was more complex than that of ama1_I-II. Several haplotypes (mh2, mh3 and mh5) were apparently separated from the most frequent haplotype (mh1; 40 %) by numerous mutational steps. The triangle-like structures suggest the presence of different selective forces. Sign of  local divergence was detected in all three gene fragments, and it was more apparent in msp1₄₂. Haplotypes mh6, mh7 and mh8 seemed to have appeared by a mutation from other more frequent haplotypes. Haplotype mh6 had a nonsynonymous change exclusive to SMX at codon 1625 Lys/Glu (aag → gag). A total of 16 different dbp_II - ama1_I-II- msp1₄₂ haplotype arrangements were displayed (indicated by colors in Fig. 2). That is, P. vivax isolates with haplotype dbp_II dh1 could be accompanied by different and highly divergent ama1_I-II and msp1₄₂ haplotypes; for example, ah1, ah2, ah3 or ah6, and mh2, mh3 or mh5 and so on.

Fig. 2.

Haplotype networks of P. vivax genes encoding merozoite surface proteins in southern Mexico, 2006–2007. The haplotype network for each gene marker is shown. Each circle represents one haplotype and the circle size indicates frequency. The mutational steps are indicated by the short marks crossing the connection lines. Each color indicates a particular combined haplotype (dbp _II- ama1 _I-II-msp1 ₄, n = 16; coded by letters A → P). For example, isolates in dark green had the combined haplotype dh1-ah1-mh1, which was highly frequent and only detected in 2007. Meanwhile, isolates in intense pink and orange had a very different configuration (dh1, ah2 and mh3 or mh5), and haplotypes G, N, O and P had a distinctive and unique configuration

Recombination and linkage disequilibrium

Rm values were higher for msp1₄₂ than ama1_I-II and dbp_II (Table 2). All three gene markers were under linkage disequilibrium, with D’ values polarized to the upper and lower sides of the graph (−1.0 or 1.0). For msp1₄₂, a set of values ranged from 0.5 to −0.25, and the R² regression line started from ~0.35 (the lowest value for the three gene fragments) and decreased slowly with nucleotide distance. The graph shows the significant values of Fisher’s exact test; 203 significant comparisons were detected using the Bonferroni correction; R² values were above 0.5. For dbp_II, R² regression started at ~0.58 and sharply decreased to zero; with the Bonferroni correction only 18 comparisons were significant; R² values were above 0.45. For ama1_I-II, on the other hand, the R² regression line showed a subtle increase across the nucleotide distance; 74 significant comparisons were found with the Bonferroni correction; R² values were above 0.378 (Fig. 3).

Table 2.

Natural selection and recombination of P. vivax genes encoding merozoite proteins

Merozoite gene fragment	Geographic origin	N	dN-dS				Recombination Rm
			*Synonymous	*Non-synonymous	Z-test	p
msp1 42	SMX	35	6	34	1.276	0.102	9
	Global	632	21	88	2.755	0.007	22
ama1 I-II	SMX	35	1	13	2.157	0.016	3
	Global	607	15	36	1.562	0.121	17
dbp II	SMX	35	0	10	3.161	0.001	1
	Global	896	34	125	2.587	0.005	18

SMX, southern Mexico; N, number of sequences; Rm, minimal number of recombination events. msp1 ₄₂, 981pb; ama1 _I-II, 780pb; dbp _II, 663pb. *Codons with multiple evolutionary paths were excluded from the analysis

Fig. 3.

Linkage disequilibrium (D’ and R² indexes) in P. vivax merozoite gene fragments: a) msp1 ₄₂ , b) ama1 _I-II and c) dbp _II. Significant D’ values for all gene fragments were mostly polarized to the upper and lower range (from −1.0 to 1.0), except in msp1 ₄₂. R² values were high and diminished with nucleotide distance in dbp _II and msp1 ₄₂, while remaining high in ama1 _I-II. Circles in grey indicate a significant non-random association between nucleotide variants at different polymorphic sites, according to Fisher’s exact test at a 95 % confidence level

Natural selection

Tajima’s D value was positive for msp1₄₂ and ama1_I-II, although statistical significance existed only for ama1_I-II. The value for dbp_II was near neutrality (Table 1). For all gene fragments, non-synonymous nucleotide changes were more numerous than synonymous ones, and dN-dS values were consistently above 1.0 (Table 2). Unlike msp1₄₂, highly significant dN-dS values were detected for ama1_I-II and dbp_II.

Genetic comparison of P. vivax merozoite genes from SMX to other geographic sites

In SMX, the highest nucleotide diversity (π) was for msp1₄₂, followed by ama1_I-II and finally dbp_II (Table 1). The genetic and nucleotide diversity for SMX msp1₄₂ was lower than that found in all other sites (e.g., BRZ, IND and MYN) except TUR and SK (Additional file 5a). Similarly, the nucleotide diversity of SMX ama1_I-II was lower than that for all other locations except VNZ (Additional file 5b), while the SMX dbp_II fragment showed the lowest diversity of all locations (Additional file 5c). In contrast, Asian parasites were the most diverse for these three gene markers.

A sample of 35 isolates is acceptable for diversity analysis [67]. There were similar or smaller samples than SMX and from high transmission regions and the diversity results were as high as expected (e.g. BRZ, IND and MYN for msp1₄₂; THL, IND and SLK for ama1_I-II; COL and THL for dbp_II) (Additional file 5). There were differences in the number of exclusive haplotypes detected in each gene fragment; msp1₄₂ and ama1_I-II > dbp_II (Additional file 6). For SMX dbp_II, many haplotypes (including the very frequent ones) were shared with BRZ and sites outside the Americas. Two ama1_I-II haplotypes were only detected in VNZ (ah3 and ah4). Meanwhile, the most abundant msp1₄₂ (mh1) haplotype was also detected in BRZ, TUR and SK, and mh3 was also found in THL. Haplotype mh6 was only detected in one isolate and had one nonsynonymous change exclusive for SMX.

The Rm value of nine found for SMX msp1₄₂ was slightly lower than the range of 10 to 13 calculated for other locations (SLK was the exception, with a value of 23; Additional file 7). Similarly, Rm values for ama1_I-II and dbp_II (three and one, respectively) were significantly lower in SMX than those found for other locations (ranging from six to eleven, p = 0.0008, and from five to ten, p = 0.0003, respectively; Additional file 7).

Similar to SMX, a significant positive dN-dS was detected in P. vivax ama1_I-II from VNZ, PNG and SLK, but this parameter was not significant for IRN or IND parasites. Globally, positive selection was not significant (Table 2). However, this lack of significance may be due to the low value (0.368; p = 0.357) and large sample size (231 isolates) of THL parasites (Additional file 7). Indeed, the global analysis without THL resulted in a significantly positive dN-dS value (2.291, p = 0.012). For msp1₄₂ of P. vivax parasites, this parameter had a significant positive value in most countries, except SMX, TUR and BRZ, and to a lesser extent SLK (Additional file 7).

Genetic differentiation of P. vivax based on merozoite gene markers

F_ST values for P. vivax merozoite genes varied between intra and inter-continental regions, and there was no relation to geographic origin (Table 3). For msp1₄₂, F_ST values were from 0.0918 to 0.2859 between SMX parasites and those of other geographic origins. In fact, the lowest values were between the parasites of SMX and those of BRZ, IND-BNG and SLK. Interestingly, the highest F_ST values were observed (0.2977–0.5069) between TUR and other geographic sites, except between TUR and SMX (the lowest value, 0.1332).

Table 3.

F_ST indexes for P. vivax based on merozoite genes; values between southern Mexico and other geographic sites are in bold

a msp1 42
	SMX	BRZ	TUR	SK	SNG	THL	CAM	IND-BAN	MYN
BRZ	0.1065
TUR	0.1332	0.3554
SK	0.2859	0.2229	0.5069
SNG	0.2370	0.2754	0.4064	0.3221
THL	0.1817	0.1129	0.3803	0.2760	0.1007
CAM	0.1710	0.0806	0.3637	0.2279	0.1366	0.0093
IND-BAN	0.0978	0.0427	0.3074	0.1139	0.1273	0.0476	0.0266
MYN	0.1754	0.0968	0.3596	0.2189	0.0966	−0.0081	−0.0042	0.0192
SLK	0.0918	0.0377	0.2977	0.2099	0.1531	0.0365	0.0374	0.0119	0.0267
b ama1 I-II
	SMX	VNZ	IRN	IND	SLK	THL
VNZ	0.1881
IRN	0.0799	0.1220
IND	0.1080	0.1395	0.0066
SLK	0.1402	0.1682	0.0830	0.0740
THL	0.1983	0.1580	0.1133	0.0934	0.0850
PNG	0.2374	0.2859	0.1194	0.0803	0.1738	0.1993
c dbp II
	SMX	COL	BRZ	IRN	IND	SLK	SK	THL	MYN
COL	0.3157
BRZ	0.2269	0.1386
IRN	0.2255	0.1812	0.0487
IND	0.2476	0.1640	0.0132	0.0668
SLK	0.2652	0.1755	0.0303	0.0923	0.0260
SK	0.2601	0.2992	0.1327	0.1895	0.1222	0.1263
THL	0.1767	0.1922	0.0616	0.1414	0.0764	0.0873	0.1369
MYN	0.2040	0.2364	0.0840	0.1484	0.0810	0.0982	0.1286	0.0016
PNG	0.2799	0.2057	0.1260	0.1745	0.1483	0.1376	0.2252	0.1205	0.1452

SMX, southern Mexico; IRN, Iran; IND, India; BRZ, Brazil; COL, Colombia; PNG, Papua New Guinea; SLK, Sri Lanka; THL, Thailand; SK, South Korea; MYN, Myanmar; VNZ, Venezuela; SNG, Singapore; BNG, Bangladesh; TUR, Turkey; CAM, Cambodia

The values for ama1_I-II were from 0.0799 to 0.2374 between SMX parasites and those of other geographic origins. The lowest value was between SMX and IRN, while the highest values were found when comparing SMX or VNZ to PNG. SMX vs THL or VNZ showed similar values (0.1983 vs 0.1881, respectively). It is notable that P. vivax dbp_II produced high F_ST values between SMX and many other locations (0.1767–0.3157). Strikingly, the highest value was between SMX and COL, which was greater than that found between SMX and PNG or SK. The latter results are in agreement with the values for ama1_I-II (between SMX and PNG). The F_ST value between SMX and THL was similar for the three merozoite genes (0.1767–0.1983). Regarding SMX vs IND-SLK, there were low F_ST values for ama1_I-II (0.108) and msp1₄₂ (0.097), but a higher value for dbp_II (0.247). However, only in SMX were the three merozoite genes analyzed simultaneously (in the same parasite sample).

Discussion

In Mexico the problem of malaria transmission has existed for a long time, and since the 1950’s the number of cases has been recorded. In the 80’s more than 100,000 cases were reported each year, at which time malaria was widespread in most of the country. From 2000 onwards, transmission has been gradually decreasing, now reduced to residual foci. Presumably, this is due to vector control, case detection and drug delivery [68]. In the last decade, Mexico has advanced to the pre-elimination phase [69]. The remaining P. vivax could correspond to parasites with genetic and biological characteristics that have allowed them to persistent in the affected regions. In the Americas, the scant information available on the diversity of the main merozoite vaccine candidates is fragmented e.g., msp1₄₂ [11] and dbp_II [62] from BRZ, ama1_I-II from VEN [34], and dbp_II from COL [63].

Figure 4 summarizes the differences between three merozoite genes of P. vivax in SMX. The present study evidences limited genetic diversity for msp1₄₂  > ama1_I-II  > dbp_II. This low variation was previously detected for other makers such as pvs25-28 [22] and the circumsporozoite gene [70]. Different biological and socioeconomic factors contribute to the maintenance of certain P. vivax diversity, including the rate of hypnozoite and asymptomatic blood infections, early gametocyte development, and the delay in diagnosis and treatment [71, 72]. These factors were probably magnified after hurricane Stan devastated the SMX region. Also, since 1999 in Mexico, malaria medication has been comprised of single doses of CQ and PQ in an intermittent monthly scheme. This medication scheme did not affect the hypnozoite prevalence per se [73, 74]. Therefore, most of the haplotypes detected in 2006 might correspond to the activation of genetically different hypnozoites in the region. After antimalarial measures reached these areas, fewer haplotypes were detected in 2007. Only those whose frequency was favored managed to prevail.

Fig. 4.

Summary of the genetic characteristics of P. vivax merozoite genes participating sequentially in erythrocyte invasion in southern Mexico. The parasite sample was obtained after hurricane Stan caused an increase in P. vivax transmission. MSP1₄₂ participates in the initial adhesion to the reticulocyte, AMA1_I-II in re-orientation, and DBP_II in the moment that invasion initiates Ref. [7–9]

The haplotype networks arrangement of msp1₄₂, ama1_I-II, dbp_II suggested the presence of recombination and local diversification in these gene fragments in SMX. The greater complexity of the msp1₄₂ network might be due to the high degree of recombination defined by the Rm value and linkage disequilibrium indexes. Multiple haplotype configurations were found in this hypo-endemic region, and probable aggravated in other locations with more complex epidemiology and higher transmission. Such finding evidenced the importance of evaluating the manner that multivalent vaccines components are evolving in the affected regions.

There is evidence that recombination events occur in P. vivax during meiotic and mitotic reproduction [32, 36]. Accordingly, it has been described that the mosaic structure of these merozoite genes resulted from recombination across the dbp_II [75], msp1 [11] and ama1_I-II [34] gene sequences. Even in a low transmission setting, a high recombination rate for the P. vivax msp1 gene occurs [11]. In SMX, the results suggest a moderate recombination rate for msp1₄₂in the P. vivax sample. The presence of mixed genotype infections is a prerequisite for the generation of new recombinant haplotypes during meiosis in the mosquito midgut. In SMX, about 5–10 % of mixed infections were previously detected [23, 73]. Whether or not msp1₄₂ recombinants were generated in SMX, they prevailed and local diversification probably occurred.

The nucleotide diversity found between SMX P. vivax merozoite genes and those at other locations could have been influenced by different historical, epidemiological and ecological transmission dynamics. For example, in SLK, with low and unstable transmission, recombination events in this gene fragment were reportedly numerous [13, 64, 76]. The chances of generating a recombinant were higher in SLK than SMX because 69 % of infections had more than one genotype [77].

These merozoite proteins are exposed to the host-specific immune response, which causes selective pressure likely results in an evasive parasite response [62, 78, 79]. At least in SMX, recombination events maintain nucleotide diversity in msp1₄₂ as a function of immune evasion and likely counteract the low degree of positive selection. The latter is evidenced by the lower dN-dS value for msp1₄₂ than for ama1_I-II and dbp_II. Unlike in SMX, in most geographic locations the dN-dS value for msp1₄₂ was highly significant.

Because of being processed on the merozoite surface, MSP1 is presumably more exposed to the immune system than AMA1 and DBP (Fig. 4). Studies in BRZ have reported that in response to natural infection, a higher proportion of individuals had detectable antibodies against MSP1 than AMA1: 95 vs 72.7 % [78] and 90.5 vs 57 % [80]. In addition, 58.3 % [79] and 65 % [18] of the antibody response was reported to be against domain II of AMA1 (AMA1_II). On the other hand, DBP is only secreted at the time of invasion [15], and thus induces a weak and short-lasting antibody response [62], which in one study was detected in 44.5 % of primary infected individuals [78]. To evade the immune response, genes encoding for antigenic proteins accumulate non-synonymous mutations, which leads to an increase in diversity. In this study, values of dN-dS and Tajima’s D suggest that balancing selection [81] might have maintained the frequency of the ama_I-II haplotype in P. vivax from SMX, as has been suggested for other geographic sites such as SLK [13], IND [51], MYN [82], VNZ [34] and Honduras [83]. Patterns of diversifying selection were also suggested for ama1_I-II in VNZ [34] and COL [75].

Although Tajima’s D value was negative for dbp_II in SMX, no departure from neutrality was evidenced. Meanwhile, the dN-dS value (3.16) was highly significant and the absence of recombination may be indicative of a recent selective sweep. It has been reported that haplotype specific immunity existed for DBP_II [84]. Residues N417K, W437R and I503K were involved in antigenic drift; the resulting variant haplotypes KRK and NRK evaded antibodies induced by the Sal 1 sequence [14]. This type of polymorphisms are highly frequent at the global level [85]. In SMX, the haplotype bearing variant residues KRK was significantly more frequent (85 %). However, it is unknown whether its transmission was actually favored by other polymorphisms or by other genetic and/or biological factors. On the other hand, because dbp_II had the lowest nucleotide diversity, there were a large number of globally shared, closely related haplotypes. Hence, this gene fragment may be under functional and/or structural restrictions, as previously suggested by others [86] (Fig. 4).

The F_ST values of the current study indicate that all merozoite gene fragments evidence a certain degree of P. vivax genetic differentiation in SMX. Consistently higher values were obtained for dbp_II, which showed almost no recombination and no significant departure from neutrality, resulting in little diversity. However, if antigenic drift was operating in this gene fragment, it may have rendered few divergent dbp_II haplotypes and biased the F_ST values. A similar effect was observed for msp1₄₂ in TUR parasites [43]. Notwithstanding, in order to elucidate P. vivax differentiation and the degree of gene flow in SMX, it would be necessary to analyze mitochondrial markers. The existence of genetic flow between Central and South American regions, which has been suggested [87], is an important factor to be taken into account for malaria control and elimination.

Conclusions

The aforementioned results of the present study provide insights into merozoite vaccine candidates in Mesoamerica. Several factors should be considered to design and monitor monovalent and multivalent formulates, including the fluctuation of haplotype frequency, differences in intensity of recombination and natural selection of vaccine components [88–90]. In addition, the current findings can also facilitate the establishment of a molecular baseline for epidemiological surveillance.

Abbreviations

P. vivax

Plasmodium vivax

DBP

duffy binding protein

MSP1

merozoite surface protein 1

AMA1

apical membrane antigen 1

dbp_II

domain II of the duffy binding protein gene

ama1_I-II

domain I and II of the apical membrane antigen 1 gene

msp1₄₂

carboxyl fragment of 42 kD of the merozoite surface protein 1 gene

Rm

minimal number of recombination events

SMX

southern Mexico

TUR

Turkey

BRZ

Brazil

SLK

Sri Lanka

THL

Thailand

MYN

Myanmar

VEN

Venezuela

COL

Colombia

IRN

Iran

IND

India

PNG

Papua New Guinea

SK

South Korea

SNG

Singapore

BNG

Bangladesh

CAM

Cambodia

Additional files

Additional file 1: ^{(12.3KB, xlsx)}

P. vivax dbp _II polymorphism in isolates from southern Mexico, 2006–2007. (XLSX 12 kb)

Additional file 2: ^{(12.3KB, xlsx)}

P. vivax ama1 _I-II polymorphisms in isolates from southern Mexico, 2006–2007. (XLSX 12 kb)

Additional file 3: ^{(14KB, xlsx)}

P. vivax msp1 ₄₂ polymorphisms in isolates from southern Mexico, 2006–2007. (XLSX 13 kb)

Additional file 4: ^{(41.3KB, docx)}

P. vivax dbp _II , ama1 _I-II and msp1 ₄₂ ; haplotypes detected in southern Mexico, 2006–2007. (DOCX 41 kb)

Additional file 5: ^{(48.8KB, docx)}

Comparison of the genetic diversity of P. vivax merozoite proteins between southern Mexico and other geographic sites. (DOCX 48 kb)

Additional file 6: ^{(39.7KB, docx)}

P. vivax merozoite genes: shared haplotypes between southern Mexico and other geographic sites. (DOCX 39 kb)

Additional file 7: ^{(47.3KB, docx)}

Natural selection and minimal number of recombination events for P. vivax merozoite proteins from different geographic origins. (DOCX 47 kb)