Genetic diversity in Plasmodium falciparum

Conserved Binding Regions Provide the Clue for Peptide-Based Vaccine Development: A Chemical Perspective

Synthetic peptides have become invaluable biomedical research and medicinal chemistry tools for studying functional roles, i.e., binding or proteolytic activity, naturally-occurring regions’ immunogenicity in proteins and developing therapeutic agents and vaccines. Synthetic peptides can mimic protein sites; their structure and function can be easily modulated by specific amino acid replacement. They have major advantages, i.e., they are cheap, easily-produced and chemically stable, lack infectious and secondary adverse reactions and can induce immune responses via T- and B-cell epitopes. Our group has previously shown that using synthetic peptides and adopting a functional approach has led to identifying Plasmodium falciparumconserved regions binding to host cells. Conserved high activity binding peptides’ (cHABPs) physicochemical, structural and immunological characteristics have been taken into account for properly modifying and converting them into highly immunogenic, protection-inducing peptides (mHABPs) in the experimental Aotus monkey model. This article describes stereo–electron and topochemical characteristics regarding major histocompatibility complex (MHC)-mHABP-T-cell receptor (TCR) complex formation. Some mHABPs in this complex inducing long-lasting, protective immunity have been named immune protection-inducing protein structures (IMPIPS), forming the subunit components in chemically synthesized vaccines. This manuscript summarizes this particular field and adds our recent findings concerning intramolecular interactions (H-bonds or π-interactions) enabling proper IMPIPS structure as well as the peripheral flanking residues (PFR) to stabilize the MHCII-IMPIPS-TCR interaction, aimed at inducing long-lasting, protective immunological memory.

Plasmodium falciparum msp2 Genotypes and Multiplicity of Infections among Children under Five Years with Uncomplicated Malaria in Kibaha, Tanzania

Genetic diversity of Plasmodium falciparum may pose challenges in malaria treatment and prevention through chemotherapy and vaccination. We assessed Plasmodium falciparum genetic diversity and multiplicity of infection (MOI) of P. falciparum infections and sort relationship of parasitaemia with P. falciparum msp2 genotypes as well as with the number of infecting clones. The study was carried out in Kibaha, Tanzania. Ninety-nine children under five years with uncomplicated malaria were recruited. Genetic diversity was analyzed by genotyping the msp2 gene using PCR-Restriction Fragment Length Polymorphism. Thirty-two different msp2 alleles were obtained. The msp2 3D7 allelic frequency was higher (48.1%) and more prevalent than FC27 (27.3%) (p < 0.05). Twenty-four percent of the infections were mixed alleles. The individuals with FC27 had high parasitemia compared to those with 3D7 alleles (p = 0.038). The mean MOI was low (1.4 clones, 95% CI 1.2–1.5). The P. falciparum population among children at Kibaha is composed of distinct P. falciparum clones, and parasites having 3D7 are more frequent than those with FC27 alleles. Individuals with parasite having FC27 alleles have high parasite densities suggesting that parasites with FC27 alleles may associate with severity of disease in Kibaha. Low MOI at Kibaha suggests low malaria transmission rate.

Plasmodium falciparum populations from northeastern Myanmar display high levels of genetic diversity at multiple antigenic loci

Levels of genetic diversity of the malaria parasites and multiclonal infections are correlated with transmission intensity. In order to monitor the effect of strengthened malaria control efforts in recent years at the China-Myanmar border area, we followed the temporal dynamics of genetic diversity of three polymorphic antigenic markers msp1, msp2, and glurp in the Plasmodium falciparum populations. Despite reduced malaria prevalence in the region, parasite populations exhibited high levels of genetic diversity. Genotyping 258 clinical samples collected in four years detected a total of 22 PCR size alleles. Multiclonal infections were detected in 45.7% of the patient samples, giving a minimum multiplicity of infection of 1.41. The majority of alleles experienced significant temporal fluctuations through the years. Haplotype diversity based on the three-locus genotypes ranged from the lowest in 2009 at 0.33 to the highest in 2010 at 0.80. Sequencing of msp1 fragments from 36 random samples of five allele size groups detected 13 different sequences, revealing an additional layer of genetic complexity. This study suggests that despite reduced prevalence of malaria infections in this region, the parasite population size and transmission intensity remained high enough to allow effective genetic recombination of the parasites and continued maintenance of genetic diversity.

The use of PCR genotyping in the assessment of recrudescence or reinfection after antimalarial drug treatment

In the past, assessment of drug efficacy against Plasmodium falciparum malaria has been performed by microscopy, screening for parasites in blood smears. However, in areas of high endemicity, reappearing parasites might be derived from new inoculations and could be classified falsely as treatment failures. Recently, a number of studies have used polymerase chain reaction (PCR) analysis of detectable parasites after drug administration to discriminate new infections from true recrudescence. The feasibility, high sensitivity and high resolution of this technique proves that it will be practical and highly valuable in studies on both drug resistance and vaccine efficacy as well as the testing of novel antimalarial drugs. In this article, Georges Snounou and Hans-Peter Beck discuss the uncertainties in the interpretation of data inherent to the technical limitations of the PCR technique, and the constraints imposed by the biology of the parasite. They suggest that although genotyping can provide strong evidence for differentiating between true recrudescence and reinfection, it must be interpreted with caution. They also propose strategies that might help minimize these uncertainties.

Initial characterization of Pf62, a novel protein of Plasmodium falciparum identified by immunoscreening

In order to find new antigens from Plasmodium falciparum, a complementary DNA (cDNA) library was constructed and screened. The study of expression library of P. falciparum was performed in an attempt to identify new antigens that could have potential relevance for the falciparum-malaria diagnosis and/or protection. Between the positive clones detected (ring erythrocyte surface antigen, merozoite erythrocyte surface antigen, RHOP H3, CSP, LSA), a new gene that correspond to a new protein (Pf62) was isolated and characterized. This antigen was useful for the diagnosis of malaria in enzyme-linked immunosorbent assay tests. The cDNA corresponding to this antigen and structure of the gene were characterized. Pf62 is a single copy gene that contains one exon. The Pf62 cDNA has an open reading frame of 1,599 nucleotides that code for a putative protein of 532 amino acids with a predicted molecular mass of 62 kDa. The polypeptide contains in the central section two regions of repeats of 21 and 19 amino acids, respectively. The localization of the Pf62 protein was performed by immunoblot, indirect immunofluorescence assay and immunoelectron microscopy. Pf62 is localized in the cytoplasm of the parasite and also on the surface of the infected erythrocyte. Serologic assays by using synthetic peptides designed from different antigenic regions of the Pf62 protein resulted in acceptable data of sensitivity and specificity in symptomatic malaria patients.

Acquired immunity to malaria

Naturally acquired immunity to falciparum malaria protects millions of people routinely exposed to Plasmodium falciparum infection from severe disease and death. There is no clear concept about how this protection works. There is no general agreement about the rate of onset of acquired immunity or what constitutes the key determinants of protection; much less is there a consensus regarding the mechanism(s) of protection. This review summarizes what is understood about naturally acquired and experimentally induced immunity against malaria with the help of evolving insights provided by biotechnology and places these insights in the context of historical, clinical, and epidemiological observations. We advocate that naturally acquired immunity should be appreciated as being virtually 100% effective against severe disease and death among heavily exposed adults. Even the immunity that occurs in exposed infants may exceed 90% effectiveness. The induction of an adult-like immune status among high-risk infants in sub-Saharan Africa would greatly diminish disease and death caused by P. falciparum. The mechanism of naturally acquired immunity that occurs among adults living in areas of hyper- to holoendemicity should be understood with a view toward duplicating such protection in infants and young children in areas of endemicity.

Genetic fingerprints of parasites causing severe malaria in a setting of low transmission in Sudan

In this study we intended to examine the extent of genetic diversity of Plasmodium falciparum parasites causing severe malaria (SM). For this purpose, 100 parasite isolates were obtained from patients with SM and uncomplicated malaria, from an area of low and unstable malaria transmission in Sudan. The diversity of infection (DOI) was estimated by relating the number of the different parasite genotypes that were detected to the total number of parasites that were genotyped (parasite population/subpopulation). We used different molecular markers individually (pfcrt-76, pfmr1-86, GLURP size and MSP2 family and size) and as a group to set a multilocus genetic profile for each parasite isolate. The DOI as estimated by MSP2 and GLURP was 0.553 and 0.435, respectively. However, combination of all four molecular markers (multilocus genetic profile) revealed a fingerprint pattern of genetic diversity with a DOI of 0.936, indicating that in SM infection, diversity is the rule and homogeny is the exception. Furthermore, our clinical data suggest that the virulence markers might also be more diverse than expected. In conclusion, the results are unexpected and overturn the assumption that parasites causing SM are a limited subpopulation of virulent parasites or of a clonal nature. However, it was more likely that there was a genetically unique parasite in each infection.

Liver stage antigen 3 isolated from a cDNA library of Plasmodium falciparum erythrocytic stages

An expression library of P. falciparum erythrocyte stages (clon Dd2) was constructed and immunoscreened with a sera pool from malaria patients. Isolated clones were analysed, and the liver stage antigen 3 (LSA-3) antigen was identified. The partial nucleotide sequence of LSA-3 has 1,623 bp. The open reading frame coded for the putative protein with 541 amino acid residues. We have demonstrated by reverse transcriptase polymerase chain reaction the transcription of the LSA-3 gene in ring form, trophozoite, and schizont, stages of asexual erythrocyte cycle.

Genomic heterogeneity in the density of noncoding single-nucleotide and microsatellite polymorphisms in Plasmodium falciparum

The density and distribution of single-nucleotide polymorphisms (SNPs) across the genome has important implications for linkage disequilibrium mapping and association studies, and the level of simple-sequence microsatellite polymorphisms has important implications for the use of oligonucleotide hybridization methods to genotype SNPs. To assess the density of these types of polymorphisms in P. falciparum, we sampled introns and noncoding DNA upstream and downstream of coding regions among a variety of geographically diverse parasites. Across 36,229 base pairs of noncoding sequence representing 41 genetic loci, a total of 307 polymorphisms including 248 polymorphic microsatellites and 39 SNPs were identified. We found a significant excess of microsatellite polymorphisms having a repeat unit length of one or two, compared to those with longer repeat lengths, as well as a nonrandom distribution of SNP polymorphisms. Almost half of the SNPs localized to only three of the 41 genetic loci sampled. Furthermore, we find significant differences in the frequency of polymorphisms across the two chromosomes (2 and 3) examined most extensively, with an excess of SNPs and a surplus of polymorphic microsatellites on chromosome 3 as compared to chromosome 2 (P=0.0001). Furthermore, at some individual genetic loci we also find a nonrandom distribution of polymorphisms between coding and flanking noncoding sequences, where completely monomorphic regions may flank highly polymorphic genes. These data, combined with our previous findings of nonrandom distribution of SNPs across chromosome 2, suggest that the Plasmodium falciparum genome may be a mosaic with regard to genetic diversity, containing chromosomal regions that are highly polymorphic interspersed with regions that are much less polymorphic.

Restricted genetic diversity of Plasmodium falciparum major merozoite surface protein 1 in isolates from Colombia

The merozoite surface protein 1 (MSP-1) gene of Plasmodium falciparum encodes a major immune target under development as a malaria vaccine. In this study, we typed MSP-1 variable regions of parasites obtained from Buenaventura, Colombia. Four MSP-1 gene types were detected corresponding to prototype and recombinant K1 and MAD20 block 4 sequences. In contrast to variability within block 4, blocks 2, 6, and 16-17 corresponded exclusively to the MAD20 allelic type. Most (80%) blood samples contained multiple MSP-1 gene types. The presence of four MSP-1 variants within block 4 against a MAD20 background indicates that current P. falciparum populations in Buenaventura are derived from parasites expressing K1 and MAD20 alleles, some of which underwent two recombination events within or flanking block 4. Restricted MSP-1 diversity appears to be relatively stable in Buenaventura and suggests that selection has resulted in the dominance of the MAD20 type in most of the polymorphic blocks with the exception of block 4.

The genetic structure of malaria parasite populations

The suggestion that a clonal population structure may typify Plasmodium populations has proved highly controversial. For the most part, existing population genetic data from wild populations contradict the idea and are consistent with randomly interbreeding populations. In this article, Andrew Read and Koren Day point out that these data could also be consistent with population subdivision and frequent nonrandom mating, which current sampling methods would be incapable of detecting.

The sticky secrets of sequestration

Sequestration, the adherence of infected erythrocytes containing the more mature stages of parasite development (trophozoites and schizonts) to the endothelial cells lining the capillaries and post-capillary venules, is characteristic of Plasmodium falciparum infections. In this review, Irwin Sherman and his colleagues discuss recent advances in the characterization of the adhesive molecules on the surface of malaria-infected erythrocytes and the receptors on the endothelium to which they bind.

Sequence diversity in the amino-terminal region of the malaria-vaccine candidate serine repeat antigen in natural Plasmodium falciparum populations

The amino-terminal region of the serine repeat antigen (SERA) of Plasmodium falciparum is a major malaria-vaccine candidate. Variation in this molecule is essentially dimorphic and alleles may be grouped into the types FCR3, K1 and Honduras1. The Honduras1-type is thought to be the product of homologous recombination between FCR3 and K1 alleles. Here we have examined patterns of sequence diversity in exon II of SERA gene, which encodes most of the amino-terminal region of the antigen, in wild P. falciparum isolates from Indonesia (n=60), Myanmar (n=10) and Thailand (n=14). Among the Indonesian isolates the FCR-3 type predominated (56/60), twenty of which we characterized as novel alleles. A new K1-type allele was also found. In Myanmar, however, all isolates displayed K1-type SERA sequences, which included one new allele. The Honduras1-type was not detected in both countries. In contrast, the 14 isolates from Thailand displayed all three allelic types, with one new Honduras1-type and three new K1-type alleles. On examining the global distribution of SERA alleles by combining previously published sequence data with our results, the FCR3-type alleles predominated in Indonesia, Brazil, and Solomon Islands, but were not found in wild isolates from Myanmar and Africa. Brazil was the only area where K1-type alleles were not found. The distribution of Honduras1-type alleles seems to be mostly restricted to parasite populations from Vietnam, Thailand and Africa. In the allelic families FCR3 and K1, most diversity resulted from variation in sequence and number of octamer repeat units and of allotypes encoding the stretch of serine residues. Sequence analysis indicated that both insertions and deletions of repetitive motifs (creating variation within dimorphic allelic families) and homologous recombination between alleles belonging to different allelic families (creating Honduras1-type alleles) play a role in generating new SERA alleles. Since repeat motifs in the amino-terminal region of SERA contain epitopes recognized by parasite-inhibitory antibodies, sequence variation in exon II may represent one of the parasite's immune-evasion strategies.

Genetic polymorphism of Plasmodium falciparum isolates from Loreto, Peru

Eight genotypes of Plasmodium falciparum were detected after analysing blood samples obtained from 30 Peruvian jungle-dwelling patients in Loreto, a high transmission area for P. falciparum, using amplification of the polymorphic marker gene GLURP (glutamate-rich protein). Genotypes I (GLURP450) and VIII (GLURP800) were the most common (15/30 and 13/30, respectively). This single copy gene showed 15 patients to be infected with a single genotype of P. falciparum; the other 15 were infected with mixed genotypes, one of them with 4 genotypes. These findings are compatible with a high genetic complexity of P. falciparum. Further investigations are needed, using this and other markers, in order to design malaria control measures in Peru.

The sequence of a 200 kb portion of a Plasmodium vivax chromosome reveals a high degree of conservation with Plasmodium falciparum chromosome 3

Within a 199,866 base pair (bp) portion of a Plasmodium vivax chromosome we identified a conserved linkage group consisting of at least 41 genes homologous to Plasmodium falciparum genes located on chromosome 3. There were no P. vivax homologues of the P. falciparum cytoadherence-linked asexual genes clag 3.2, clag 3.1 and a var C pseudogene found on the P. vivax chromosome. Within the conserved linkage group, the gene order and structure are identical to those of P. falciparum chromosome 3. This conserved linkage group may extend to as many as 190 genes. The subtelomeric regions are different in size and the P. vivax segment contains genes for which no P. falciparum homologues have been identified to date. The size difference of at least 900 kb between the homologous P. vivax chromosome and P. falciparum chromosome 3 is presumably due to a translocation. There is substantial sequence divergence with a much higher guanine+cytosine (G+C) content in the DNA and a preference for amino acids using GC-rich codons in the deduced proteins of P. vivax. This structural conservation of homologous genes and their products combined with sequence divergence at the nucleotide level makes the P. vivax genome a powerful tool for comparative analyses of Plasmodium genomes.

Population structure of Plasmodium falciparum isolates during an epidemic in southern Mauritania

While the population structure of Plasmodium falciparum is well analysed in selected areas with high malaria endemicity in East and West Africa, only limited data are available for low endemicity regions bordering the Saharan desert. This is one of the first studies for the Sahel, where atypically strong rainfalls in 1998 and 1999 led to a severe outbreak of falciparum malaria in south-east Mauritania. During a study on in vivo-drug resistance against chloroquine we collected blood samples of patients with fever in two medical centres located in non-endemic and hypoendemic areas. We analysed 386 samples by polymerase chain reaction for infection with P. falciparum, and 173 (45%) tested positive. The isolates were genotyped for three polymorphic genetic markers: merozoite surface protein 1 (MSP1), MSP2 and glutamate-rich protein (GLURP). Differences between the two regions could be shown in either number of clones per infection or in their distribution on the different allelic groups. While the mean minimal number of clones in the non-endemic region around Aioun was 1.57, blood samples collected in the hypoendemic region around Kobeni showed multiple infections with an average of 2.34 clones (P < 0.001). In addition, clear differences between endemic regions were apparent in three of the investigated allelic groups: RO33 of the MSP1 gene and FC and Indochina of the MSP2 gene.

Recent origin of Plasmodium falciparum from a single progenitor

Genetic variability of Plasmodium falciparum underlies its transmission success and thwarts efforts to control disease caused by this parasite. Genetic variation in antigenic, drug resistance, and pathogenesis determinants is abundant, consistent with an ancient origin of P. falciparum, whereas DNA variation at silent (synonymous) sites in coding sequences appears virtually absent, consistent with a recent origin of the parasite. To resolve this paradox, we analyzed introns and demonstrated that these are deficient in single-nucleotide polymorphisms, as are synonymous sites in coding regions. These data establish the recent origin of P. falciparum and further provide an explanation for the abundant diversity observed in antigen and other selected genes.

Evidence for clonal propagation in natural isolates of Plasmodium falciparum from Venezuela

We have analyzed 75 isolates of Plasmodium falciparum, collected in Venezuela during both the dry (November) and rainy (May-July) seasons, with a range of genetic markers including antigen genes and 14 random amplified polymorphic DNA (RAPD) primers. Thirteen P. falciparum stocks from Kenya and four other Plasmodium species are included in the analysis for comparison. Cross-hybridization shows that the 14 RAPD primers reveal 14 separate regions of the parasite's genome. The P. falciparum isolates are a monophyletic clade, significantly different from the other Plasmodium species. We identify three RAPD characters that could be useful as "tags" for rapid species identification. The Venezuelan genotypes fall into two discrete genetic subdivisions associated with either the dry or the rainy season; the isolates collected in the rainy season exhibit greater genetic diversity. There is significant linkage disequilibrium in each seasonal subsample and in the full sample. In contrast, no linkage disequilibrium is detected in the African sample. These results support the hypothesis that the population structure of P. falciparum in Venezuela, but not in Africa, is predominantly clonal. However, the impact of genetic recombination on Venezuelan P. falciparum seems higher than in parasitic species with long-term clonal evolution like Trypanosoma cruzi, the agent of Chagas' disease. The genetic structure of the Venezuelan samples is similar to that of Escherichia coli, a bacterium that propagates clonally, with occasional genetic recombination.

Mutation rates in the dihydrofolate reductase gene of Plasmodium falciparum

A new method has been established to define the limits on a spontaneous mutation rate for a gene in Plasmodium falciparum. The method combines mathematical modelling and large-scale in vitro culturing and calculates the difference in mutant frequencies at 2 separate time-points. We measured the mutation rate at 2 positions in the dihydrofolate reductase (DHFR) gene of 3D7, a pyrimethamine-sensitive line of P. falciparum. This line was re-cloned and an effectively large population was treated with a selective pyrimethamine concentration of 40 nM. We detected point mutations at codon-46 (TTA to TCA) and codon-108 (AGC to AAC), resulting in serine replacing leucine and asparagine replacing serine respectively in the corresponding gene product. The substitutions caused a decrease in pyrimethamine sensitivity. By mathematical modelling we determined that the mutation rate at a given position in DHFR was low and occurred at less than 2.5 x 10(-9) mutations/DHFR gene/replication. This result has important implications for Plasmodium genetic diversity and antimalarial drug therapy by demonstrating that even with low mutation rates anti-malarial resistance will inevitably arise when mutant alleles are selected under drug pressure.

Protection against Plasmodium falciparum malaria in chimpanzees by immunization with the conserved pre-erythrocytic liver-stage antigen 3

In humans, sterile immunity against malaria can be consistently induced through exposure to the bites of thousands of irradiated infected mosquitoes. The same level of protection has yet to be achieved using subunit vaccines. Recent studies have indicated an essential function for intrahepatic parasites, the stage after the mosquito bite, and thus for antigens expressed during this stage. We report here the identification of liver-stage antigen 3, which is expressed both in the mosquito and liver-stage parasites. This Plasmodium falciparum 200-kilodalton protein is highly conserved, and showed promising antigenic and immunogenic properties. In chimpanzees (Pan troglodytes), the primates most closely related to humans and that share a similar susceptibility to P. falciparum liver-stage infection, immunization with LSA-3 induced protection against successive heterologous challenges with large numbers of P. falciparum sporozoites.

Expression and characterisation of Plasmodium falciparum acidic basic repeat antigen expressed in Escherichia coli

The acidic basic repeat antigen (ABRA) of Plasmodium falciparum has been localised on the merozoite surface and in the parasitophorous vacuole. It is one of the antigens enriched in the clusters of merozoites formed with growth inhibitory immune serum and possesses chymotrypsin-like activity. Chymostatin, an inhibitor of chymotrypsin, inhibits malaria invasion as well as autoproteolysis of ABRA. Based on these characteristics of ABRA, it seems important for invasion and should be investigated as a target for vaccine and drug design. For the functional characterisation of this protein, the full-length mature ABRA protein and its fragments with/without the putative protease active site were cloned, expressed and purified from Escherichia coli. The polyclonal serum raised against recombinant ABRA fragment recognised a parasite protein with a mobility of 101 kDa in an immunoblot assay and showed immunofluorescence activity with a schizont-rich preparation of P. falciparum. Using a partially purified fragment containing the putative active site and fluorogenic and chromogenic substrates, we established that the protease activity of ABRA resides in the N-terminal portion of the protein and the highly charged C-terminal part of the protein is not required for this activity. The protease activity of ABRA was inhibited with serine protease inhibitors like chymostatin and phenyl methyl sulfonyl fluoride (PMSF) whereas leupeptin was not able to inhibit this enzyme activity. These results clearly indicated that ABRA is a protease with chymotrypsin-like specificity. This is the first report describing the expression and characterisation of recombinant ABRA protein.

Population structure of recrudescent Plasmodium falciparum isolates from western Uganda

It has been proposed that polymorphisms of the Merozoite Surface Protein 1 and 2 (MSP1 and MSP2) and the Glutamate Rich Protein (GLURP) genes can be considered as genetic markers for the genotyping of field populations of Plasmodium falciparum. During a field study on in vivo drug resistance against chloroquine, sulphadoxine/pyrimethamine (S/P) and cotrimoxazole in West Uganda, sensitive and resistant isolates were collected from patients by fingerprick for genotyping. 59 (72.8%) of the 81 P. falciparum samples isolated at day 0 showed multiclonal infection with 2-7 clones. Among the isolates we investigated, presence of the allelic family MAD20 of MSP1 at day 0 was significantly (P = 0.0041) associated with decreased resistance to antimalarials. Use of this method in a field study on in vivo drug resistance demonstrates another potential application of genotyping as a tool for epidemiological investigations.

Antigenic and genetic diversities of Babesia ovata in persistently infected cattle

Exploring the antigenic and genetic diversities of Babesia ovata, we obtained several field isolates from grazing cattle in the Okushiri island, Japan. Parasite isolation was greatly facilitated by using bovine red blood cell-substituted SCID mice (Bo-RBC-SCID mice), into which the blood samples of the cattle were inoculated. Isolates from different individuals within a herd of cattle were compared in immunoblot analysis with an anti-B. ovata serum and also in Southern blot analysis with a probe for the small subunit ribosomal RNA gene. In both analyses, the isolates exhibited banding patterns that were significantly different from each other. We were also able to obtain a series of parasite isolates from a single cow in different seasons of a nine months period, including winter when active vector ticks were not in the field environment. Different seasonal isolates showed different banding patterns in both immunoblot and Southern blot analyses. By contrast, these analyses detected little difference among the parasites that had been passed various times in Bo-RBC-SCID mice, where no specific immune responses should be generated. These results indicate that individual animals within a herd of cattle were infected with antigenically and genetically diversified populations of B. ovata, and that the parasites could persistently infect a single animal with dynamic change in their predominant subpopulations.

The biology of Plasmodium falciparum transmission stages

The most important function of any parasite is to secure transmission to new hosts. The gametocyte, the stage which has become developmentally committed to the sexual cycle, provides a critical link in the transmission of Plasmodium falciparum from the human host to the anopheline mosquito vector. It is therefore imperative that our determination to understand the biology of the gametocyte is greater than the technical obstacles which have resulted in the gametocyte being left very much out of the limelight by the intensive investigation of the asexual bloodstream parasite. Here we explore the areas of gametocyte biology which by nature of their relevance to control and pathology as well as basic biology, are the subjects of investigation in our laboratory. We also point out areas in need of particular attention.

Sequence analysis of the major piroplasm surface protein gene of benign bovine Theileria parasites in east Asia

Relatively benign Theileria parasites are widespread among cattle in East Asia. Although the parasites are presumed to be of the Theileria sergenti/Theileria buffeli/Theileria orientalis group, their taxonomic status and epidemiology have not been well defined. In the present study, theilerial DNA samples were collected from various East Asian countries, including Japan, Korea, Taiwan, and China. DNA sequences encoding a major piroplasm surface protein were amplified by polymerase chain reaction, followed by cloning into a plasmid vector. More than 20 DNA clones derived from parasite DNA of a single infected animal were examined for their restriction-fragment-length polymorphism, showing that they were classified into four major types. Sequence analysis revealed six types of DNA sequences encoding major piroplasm surface protein with homologies of between 75 and 91%. Of the six sequences, four were identical to those previously reported, while the other two appeared to be new sequences. Among the DNA clones derived from a single infected animal, two to three distinct sequences were often found. Phylogenetic analysis of the six major piroplasm surface protein sequences indicates that five of the six are closely related to each other, and that all are distantly related to the homologous genes of Theileria annulata and Theileria parva. The results suggest that, in addition to those described as T. sergenti/T. buffeli/T. orientalis, there may be some undefined Theileria species distributed in East Asia, and that many cattle are infected with mixed populations of geographically variable Theileria parasites.

Characterization of protective epitopes in a highly conserved Plasmodium falciparum antigenic protein containing repeats of acidic and basic residues

The delineation of putatively protective and immunogenic epitopes in vaccine candidate proteins constitutes a major research effort towards the development of an effective malaria vaccine. By virtue of its role in the formation of the immune clusters of merozoites, its location on the surface of merozoites, and its highly conserved nature both at the nucleotide sequence level and the amino acid sequence level, the antigen which contains repeats of acidic and basic residues (ABRA) of the human malaria parasite Plasmodium falciparum represents such an antigen. Based upon the predicted amino acid sequence of ABRA, we synthesized eight peptides, with six of these (AB-1 to AB-6) ranging from 12 to 18 residues covering the most hydrophilic regions of the protein, and two more peptides (AB-7 and AB-8) representing its repetitive sequences. We found that all eight constructs bound an appreciable amount of antibody in sera from a large proportion of P. falciparum malaria patients; two of these peptides (AB-1 and AB-3) also elicited a strong proliferation response in peripheral blood mononuclear cells from all 11 human subjects recovering from malaria. When used as carrier-free immunogens, six peptides induced a strong, boostable, immunoglobulin G-type antibody response in rabbits, indicating the presence of both B-cell determinants and T-helper-cell epitopes in these six constructs. These antibodies specifically cross-reacted with the parasite protein(s) in an immunoblot and in an immunofluorescence assay. In another immunoblot, rabbit antipeptide sera also recognized recombinant fragments of ABRA expressed in bacteria. More significantly, rabbit antibodies against two constructs (AB-1 and AB-5) inhibited the merozoite reinvasion of human erythrocytes in vitro up to approximately 90%. These results favor further studies so as to determine possible inclusion of these two constructs in a multicomponent subunit vaccine against asexual blood stages of P. falciparum.

Mating Patterns of Plasmodium falciparum

Recent empirical data have enabled a more informed debate over the extent of clonality in Plasmodium falciparum populations. Oocyst heterozygosity data reveal that the mating structure of malaria populations varies according to the transmission intensity. This finding provides a more detailed picture of the malaria mating structure than previous conclusions, which were based on indirect measures of population mating structure, ie. linkage disequilibrium analyses. In this article, Ric Paul and Karen Day discuss aspects of the genetic structure of malaria populations as evidenced by oocyst heterozygosity and linkage disequilibrium data. They address the difficulties of performing genetic analyses of malaria parasite population structure inherent in parasite sampling, why two identical parasites are rarely observed in the field and how features of the epidemiology determine parasite population structure.

A primary malarial infection is composed of a very wide range of genetically diverse but related parasites

To address the question of how many distinct parasites are injected when a mosquito bites, we have characterized isolates resulting most probably from a single sporozoite inoculum. We describe the direct and immediate cloning on hepatocyte feeder layers of a Thai and an African Plasmodium falciparum primary isolate and the characterization of 67 independent clones by four techniques totaling nine different markers. This led to three main conclusions: (a) both the phenotypic and genotypic markers revealed an unexpectedly large degree of diversity within the clones from a single isolate; (b) the clones are nonetheless genetically related; and (c) a single mosquito inoculum would most likely be sufficient to generate considerable isolate complexity in the absence of repeated exposure. This diversity, which has been greatly underestimated in previous studies, does not bode well for the development of successful malaria control means.

Malaria's Eve: evidence of a recent population bottleneck throughout the world populations of Plasmodium falciparum

We have analyzed DNA sequences from world-wide geographic strains of Plasmodium falciparum and found a complete absence of synonymous DNA polymorphism at 10 gene loci. We hypothesize that all extant world populations of the parasite have recently derived (within several thousand years) from a single ancestral strain. The upper limit of the 95% confidence interval for the time when this most recent common ancestor lived is between 24,500 and 57,500 years ago (depending on different estimates of the nucleotide substitution rate); the actual time is likely to be much more recent. The recent origin of the P. falciparum populations could have resulted from either a demographic sweep (P. falciparum has only recently spread throughout the world from a small geographically confined population) or a selective sweep (one strain favored by natural selection has recently replaced all others). The selective sweep hypothesis requires that populations of P. falciparum be effectively clonal, despite the obligate sexual stage of the parasite life cycle. A demographic sweep that started several thousand years ago is consistent with worldwide climatic changes ensuing the last glaciation, increased anthropophilia of the mosquito vectors, and the spread of agriculture. P. falciparum may have rapidly spread from its African tropical origins to the tropical and subtropical regions of the world only within the last 6,000 years. The recent origin of the world-wide P. falciparum populations may account for its virulence, as the most malignant of human malarial parasites.

Molecular basis for evasion of host immunity and pathogenesis in malaria

The article relates the ability of the malaria parasite Plasmodium falciparum to avoid a protective immune response, and to induce pathological changes, to the properties of specific parasite molecules. Cytoadherence and rosetting are important features of cerebral malaria and involve proteins located on the surface of the infected red blood cell. Proinflammatory cytokines, particularly tumour necrosis factor (TNF), play a role in protective immunity and in inducing pathology. Glycophosphatidyl inositol membrane anchors of parasite proteins possess insulin like activity and induce TNF synthesis. People subject to repeated infections in malaria endemic areas rarely develop complete or sterile immunity to malaria. They frequently carry small numbers of parasites in the blood, with little symptoms of the disease, illustrating a phenomenon termed semi-immunity. The basis for semi-immunity is incompletely understood. Malaria parasites are susceptible to several immunological effector mechanisms. The presence of extensive repetitive regions is a feature of many P. falciparum proteins. Available evidence suggests that the structural characteristics of the repeats and their location on the surface of parasite proteins promote immunogenicity. The repeats may help the parasite evade host immunity by (i) exhibiting sequence polymorphism, (ii) preventing the normal affinity and isotype maturation of an immune response, (iii) functioning possibly as B cell superantigens, (iv) generating predominantly thymus independent antibody responses, and (v) acting as a sink for binding protective antibodies. Sequence diversity in non-repetitive regions and antigenic variation in parasite molecules located on the surface of infected red blood cells also play a role in immune evasion. Some sequence homologies between parasite and human proteins may be due to molecular mimicry. Homologies in other instances can cause autoimmune responses. The immune evasion mechanisms of the parasite need to be considered in developing vaccines. Protective immunity and pathology may be delicately balanced in malaria.

Plasmodium falciparum sporozoite invasion is inhibited by naturally acquired or experimentally induced polyclonal antibodies to the STARP antigen

Antibody(Ab)-mediated inhibition of sporozoite invasion of hepatocytes is a mechanism that has been clearly demonstrated to act upon Plasmodium falciparum pre-erythrocytic stages in humans. Consequently we have analyzed the Ab response to a recently identified P. falciparum sporozoite surface protein, STARP, in malaria-exposed individuals and tested the inhibitory effect of these Ab upon hepatocyte invasion in vitro. STARP-specific IgG were detected in 90 and 61% of sera from regions where individuals were exposed to 100 and 1-5 infectious bites per year, respectively. These IgG were predominantly of the cytophilic IgG1 or IgG3 type. STARP and the major sporozoite surface protein, CS, elicited equivalent IgG levels in adults. When affinity purified from either African immune sera or the serum of an individual experimentally protected by irradiated sporozoite immunization, STARP-specific Ab prevented up to 90% of sporozoites from invading human hepatocytes. The dose-dependent and reproducible inhibition was more pronounced than that observed with human CS-specific Ab affinity purified under identical conditions. Substantial reduction of sporozoite invasion was also observed with Ab induced by artificial immunization with recombinant STARP protein and reactive with the native protein. Taken together with recent findings of human cytotoxic T lymphocytes specific for this antigen, these results promote the interest of studying the efficacy of STARP as a target for immune effector mechanisms operating upon pre-erythrocytic stages.

Evidence for distinct prototype sequences within the Plasmodium falciparum Pf60 multigene family

Using oligonucleotides derived from Pf60.1, a member of the Plasmodium falciparum Pf60 multigene family, numerous fragments were amplified from genomic and cDNA from the 3D7 P. falciparum clone. DNA sequencing showed that the various fragments presented considerable diversity, indicating that the 3D7 repertoire contains at least 20 distinct versions of the region analysed. The various sequences aligned with either of two prototype sequences. Characteristic of the A-type was the presence of a 21 bp motif, present in variable copy number, as well as a sequence homologous to the Babesia sp. RAP-1 consensus. The B prototype sequence did not present such features and substantially differed from the A-type, due to accumulation of point mutations and numerous triplet deletions. Consistent with the marked differences between both sub-families, individual members from each sub-family did not cross-hybridise, produced distinct multiple band patterns on Southern blots and distinct chromosome profiles. Numerous hybrid sequences were observed. Interestingly, most var genes and var-related unspliced cDNAs described so far are of A/B hybrid type. These data suggest that the family has evolved by successive amplifications from two ancestral copies, with accumulation of mutations, as well as recombination and/or gene conversion events.

The chromosomal organization of the Plasmodium falciparum var gene family is conserved

The var gene family of Plasmodium falciparum encodes the protein PfEMP1 which is located on the surface of infected erythrocytes and is the receptor that mediates binding to ligands on endothelial cells. This family of proteins is responsible for antigenic variation and differences in binding phenotype to ligands such as CD36 and ICAM1. We have compared the organization of the var gene family in three in vitro cloned lines of P. falciparum and show that most var genes are located in the subtelomeric region of each chromosome closely linked to the repetitive sequence rep20. While most chromosomes possess var genes in the subtelomeric region, in each in vitro cloned line there are some chromosomes that have deleted subtelomeric repetitive regions which include var genes. Comparison of the location of var genes in a field isolate showed that it does not have any detectable subtelomeric deletions as all chromosomes contain var genes and rep20 sequences. We have detected three chromosomes (4, 7 and 12) that contain var gene loci in more stable central regions and the position of these genes on chromosome 4 in the cloned lines analysed is conserved. The location of most of the var gene family in the subtelomeric region of the genome of P. falciparum has important implications for the generation of antigenic diversity of the PfEMP1 protein.

[Cloning and sequencing of p33 in a Korean isolate of Theileria sergenti]

The gene encoding the 33 kDa piroplasm surface protein of Theileria sergenti isolated in Korea was cloned and the nucleotide sequence was determined by dideoxy chain termination method. The cloned gene corresponds to 869 bp encoding an open reading frame 283 amino acids. Comparison of the sequence between Korean and Japanese isolates showed 99.4% homology rate in the nucleotide sequence and 98.9% homology rate in the amino acid sequence.

Antigenic variation and immune evasion in Plasmodium falciparum malaria

Plasmodium falciparum malaria is responsible for 2 million deaths each year. Even in endemic regions, immunity to malaria builds slowly and is rarely complete. Strategies such as antigenic variation and antigenic diversity are critical to a parasite's ability to evade the host immune response and infect previously exposed individuals. In this short review, the phenomenon of antigenic variation is discussed in relation to immune evasion and its impact on parasite pathogenesis. Recent advances in the understanding of the underlying molecular mechanisms of antigenic variation are examined and questions posed for future research.

Plasmodium falciparum malaria: some epidemiological implications of parasite and host diversity

Observations are accumulating concerning: (1) the antigenic diversity of Plasmodium falciparum; (2) the diversity of the genetic immuno-competence of human hosts; (3) the associations between these diversities and disease, protection and defined immune responses; and (4) the possible mechanisms of acquired protection at different steps of the host-parasite interaction. These observations have led to speculations concerning the distribution of disease, the acquisition of protection, and vaccination prospects. Speculations on the latter have varied from pessimism about the possibility of developing a vaccine that would protect most people against most parasites, to optimism based on the hypothesis that a local P. falciparum population is composed of a few discrete subpopulations. If this hypothesis is correct, it may be possible to prevent most severe disease with a narrow-spectrum vaccination against a virulent minority of the subpopulations, or transmission could be interrupted by a relatively low coverage of a broad-spectrum vaccination. A conceptual model that might accommodate the observations is outlined. Its plausibility and testability are considered, as well as some of its implications for the planning and interpretation of epidemiological surveys and intervention trials, and perhaps for selection of antigens for inclusion in vaccines.

Characterization of promoters and stable transfection by homologous and nonhomologous recombination in Plasmodium falciparum

Genetic studies of the protozoan parasite Plasmodium falciparum have been severely limited by the inability to introduce or modify genes. In this paper we describe a system of stable transfection of P. falciparum using a Toxoplasma gondii dihydrofolate reductase-thymidylate synthase gene, modified to confer resistance to pyrimethamine, as a selectable marker. This gene was placed under the transcriptional control of the P. falciparum calmodulin gene flanking sequences. Transfected parasites generally maintained plasmids episomally while under selection; however, parasite clones containing integrated forms of the plasmid were obtained. Integration occurred by both homologous and nonhomologous recombination. In addition to the flanking sequence of the P. falciparum calmodulin gene, the 5' sequences of the P. falciparum and P. chabaudi dihydrofolate reductase-thymidylate synthase genes were also shown to be transcriptionally active in P. falciparum. The minimal 5' sequence that possessed significant transcriptional activity was determined for each gene and short sequences containing important transcriptional control elements were identified. These sequences will provide considerable flexibility in the future construction of plasmid vectors to be used for the expression of foreign genes or for the deletion or modification of P. falciparum genes of interest.

Current status of the Plasmodium falciparum genome project

The Plasmodium falciparum Genome Project is a collaborative effort by many laboratories that will provide detailed molecular information about the parasite, which may be used for developing practical control measures. Initial goals are to prepare an electronically indexed clone bank containing partially sequenced clones representing up to 80% of the parasite's genes and to prepare an ordered set of overlapping clones spanning each of the parasite's 14 chromosomes. Currently, clones of genomic DNA, prepared as yeast artificial chromosomes, are arranged into contigs covering approximately 70% of the genome of parasite clone 3D7, gene sequence tags are available from more than contigs covering approximately 70% of the genome of parasite clone 3D7, gene sequence tags are available from more than 20% of the parasite's genes, and approximately 5% of the parasite's genes are tentatively identified from similarity searches of entries in the international sequence databases. A total of > 0.5 Mb of P. falciparum sequence tag data is available. The gene sequence tags are presently being used to complete YAC contig assembly and localize the cloned genes to positions on the physical map in preparation for sequencing the genome. Routes of access to project information and services are described.

Molecular genetic approaches to parasite identification: their value in diagnostic parasitology and systematics

A wide range of approaches is available to parasitologists to aid in specific parasite identification and to formulate phylogenetic relationships. This review emphasises the usefulness of molecular genetic techniques, especially DNA-based procedures, in addressing problems of identification, characterisation and phylogeny of parasites. It should be stressed that an understanding of the various DNA approaches, techniques and target genes most likely to be effective in addressing key issues in diagnostic parasitology and systematics is still developing. Nevertheless, DNA methods clearly have great potential with regard to specificity and sensitivity, and applications will increase further with technological advance. Indeed, because of the minimal requirements for material, PCR-based methods especially should prove of immense value in future studies with parasites.

Antigenic variation and the within-host dynamics of parasites

Many parasites exhibit antigenic variation within their hosts. We use mathematical models to investigate the dynamical interaction between an antigenically varying parasite and the host's immune system. The models incorporate antigenic variation in the parasite population and the generation of immune responses directed against (i) antigens specific to individual parasite variants and (ii) antigens common to all the parasite variants. Analysis of the models allows us to evaluate the relative importance of variant-specific and cross-reactive immune responses in controlling the parasite. Early in the course of infection within the host, when parasite diversity is below a defined threshold value (the value is determined by the biological properties of the parasite and of the host's immune response), the variant-specific immune responses are predominant. Later, when the parasite diversity is high, the cross-reactive immune response is largely responsible for controlling the parasitemia. It is argued that increasing antigenic diversity leads to a switch from variant-specific to cross-reactive immune responses. These simple models mimic various features of observed infections recorded in the experimental literature, including an initial peak in parasitemia, a long and variable duration of infection with fluctuating parasitemia that ends with either the clearance of the parasite or persistent infection.

Antigenic alteration in major piroplasm surface proteins of Theileria sergenti during infection

Theileria sergenti piroplasms were purified from different parasitemia peaks of cattle infected with parasitized erythrocytes or sporozoites during persistent infection. Their reactivities with monoclonal antibodies 13F5 and C9, which recognize 23 kDa and 32 kDa piroplasm surface proteins, respectively, were analyzed. Antigenic differences were observed among parasites from different parasitemia peaks during persistent infection when cattle were infected with sporozoites. Results of two-dimensional polyacrylamide gel electrophoresis showed that the 23 and 32 kDa proteins were expressed in all samples tested, regardless of their reactivities with the monoclonal antibodies. In contrast, parasites obtained from cattle inoculated with parasitized erythrocytes showed no antigenic alteration over a 2 month observation period. The results suggest that antigenic alteration of T. sergenti during persistent infection is related to whether the parasites proliferate through extraerythrocytic schizont stage in cattle or sporozoite and other sexual stages in tick vector.

Gene flow and cross-mating in Plasmodium falciparum in households in a Tanzanian village

The diversity of the genes encoding 2 merozoite surface proteins (MSP-1 and MSP-2) of Plasmodium falciparum has been examined in parasites infecting members of 4 households in a village in Tanzania. The polymerase chain reaction (PCR) was used to characterize allelic variants of these genes by the sizes and sequences of regions of tandemly repeated bases in each gene. In each household extensive polymorphism was detected among parasites in the inhabitants and in infected mosquitoes caught in their houses. Similar frequencies of the alleles of these genes were observed in all households. Capture-recapture data indicated that both Anopheles gambiae and A. funestus freely dispersed among households in the hamlet. The results confirm that cross-mating and gene flow occur extensively among the parasites, and are discussed within the context of spatial clustering of natural populations of P. falciparum.

Mating patterns in malaria parasite populations of Papua New Guinea

Description of the genetic structure of malaria parasite populations is central to an understanding of the spread of multiple-locus drug and vaccine resistance. The Plasmodium falciparum mating patterns from madang, Papua New Guinea, where intense transmission of malaria occurs, are described here. A high degree of inbreeding occurs in the absence of detectable linkage disequilibrium. This contrasts with other studies, indicating that the genetic structure of malaria parasite populations is neither clonal nor panmictic but will vary according to the transmission characteristics of the region.

PCR typing of field isolates of Plasmodium falciparum

We report on an analysis of the constraints of PCR typing of field Plasmodium falciparum isolates by using a few highly polymorphic markers, MSA-1, MSA-2, TRAP, and CS. We show that the reactions are specific for the P. falciparum species. The detection threshold (minimum number of parasites required to detect a visible band by ethidium bromide) differed from one marker to the other and, within one locus, from one primer combination to the other. Importantly, the various MSA-1 and MSA-2 reference alleles were amplified with the same efficiency. Amplification from reconstituted allele mixtures indicated that at certain allele ratios, the most abundant allele interfered with the amplification of the less abundant one. An analysis of nine isolates collected from patients with acute malaria in Dielmo, Senegal, during a transmission season when the inoculation rate was one infective bite every second night is presented and discussed. All samples contained more than one parasite type. A significant polymorphism was observed for the four markers. Novel TaqI restriction fragment length polymorphisms were found for the TRAP gene, and TRAP gene typing alone allowed a distinction between the various isolates. MSA-1 and MSA-2 gave multiple band patterns specific for each sample.

Vaccine development from a commercial point of view

The development of a commercial vaccine comprises distinct stages. Initiation of a research project is triggered by demands from the market. If commercial and technical requirements are met, a feasibility study is carried out. Research is started, and aimed at formulating the product profile (what the product looks like). The product profile is subject to requirements set by the market (e.g. whether the product will fit into existing vaccination schedules) and very often technical aspects affect the product profile (e.g. whether the freeze-dried product is easy to reconstitute). Only after a cost-profit analysis is positive, the development phase is entered. During this phase, experiments are carried out to obtain registration. After the product has been registered it is ready for production and marketing. Only few vaccines for hemoparasitic diseases have reached the market. These comprise: attenuated parasites (Toxoplasma gondii, Eimeria species); killed vaccines (Anaplasma marginale) and subunit vaccines (Babesia canis). Factors relating to the product potential of these vaccines are discussed.