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| ABSTRACT |
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| INTRODUCTION |
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Plasmodium ovale was long thought to be absent from southeast Asia. The first microscopic identifications of P. ovale were reported in the 1970s in countries surrounding Cambodia,69 including cases along the eastern and northwestern borders of Cambodia.1012 Molecular diagnosis methods have recently led to the identification of even more P. malariae and P. ovale infections in the southeast Asian region.1318 However, until now, P. ovale malaria has never been diagnosed in Cambodia.
We used a highly sensitive polymerase chain reaction (PCR)-based method based on the amplification of the small subunit (SSU) ribosomal RNA (rRNA) gene in conjunction with microscopy to study the prevalence of the four human malaria species in blood specimens from inhabitants of the Rattanakiri province of Cambodia (Incardona S and others, unpublished data). This led to the identification of P. ovale malaria cases in the area. The PCR products amplified from these P. ovale specimens were also cloned and sequenced. This showed a surprisingly high SSU rRNA gene sequence heterogeneity between different isolates and between different clones within each isolate, and novel P. ovale variants were detected. Previously published P. ovale SSU rRNA sequences are generally of high similarity, but some extent of variation has been reported for a small number of cases. The complete gene sequence of a Cameroonian isolate differs by 4% from other African and Asian isolates.19 One P. ovale variant was observed in several places in the southeast Asian region.13,15,18 More recent data with detailed molecular analysis of a small number of P. ovale isolates show sequence variations in the SSU rRNA gene as well, and the existence of P. ovale subpopulations with two major variant types (called the CDC type and the LS type) has been suggested.20,21 Nevertheless, compared with P. falciparum and P. vivax, few data about the SSU rRNA genes of P. ovale are available. The results described in this report show that large sequence heterogeneity can exist in the SSU rRNA gene of wild P. ovale isolates, even within a very limited geographic area, and within individual P. ovale isolates. This diversity can have consequences on the molecular species diagnosis using P. ovale-specific primers, but our findings also raise new questions regarding the clonality of P. ovale infections, and the eventual existence of polymorphic and/or stage-specific SSU rRNA gene copies.
| MATERIALS AND METHODS |
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For each enrolled individual, personal and clinical information was recorded, a finger prick blood sample was obtained, and thin and thick blood smears were prepared. Blood spots of approximately 25 µL were also collected on Whatman (Brentford, United Kingdom) 3M filter paper. The Giemsa-stained blood smears were examined at the National Center for Parasitology, Entomology and Malaria Control in Phnom Penh. The blood spots were analyzed by the Pasteur Institute of Cambodia.
This study was reviewed and approved by the National Ethics Committee of the Kingdom of Cambodia, and all participants gave informed consent.
Extraction of DNA and characterization of SSU rRNA sequences. Parasite DNA was extracted from dried blood spots in a 96-well plate format by using the QIAamp DNA blood 96 kit in combination with Qiagen ATL buffer (Qiagen, Hilden, Germany), using a slightly modified version of a previously described protocol.22 A nested PCR of the SSU rRNA genes was performed essentially as described.23 Briefly, 4 µL of DNA was amplified in a 50-µL reaction volume with the genus-specific primers rPLU1 and rPLU5. The cycling conditions were as follows: 94°C for 4 minutes, then 35 cycles at 94°C for 30 seconds, 55°C for 1 minute, 72°C for 1 minute, and a final extension at 72°C for 4 minutes. A Plasmodium-specific nested PCR was performed with the primers rPLU3 and rPLU4 and 2 µL of PCR product. The cycling conditions were the same as above, except that the annealing temperature was 62°C. For all samples that were positive, a species-specific nested PCR was performed in four separate 20-µL reactions with the four primer pairs rFAL1/rFAL2, rVIV1/ rVIV2, rMAL1/rMAL2, and rOVA1/rOVA2, 2 µL of the PCR product and an annealing temperature of 58°C. The nested PCR products were analyzed by agarose gel electrophoresis and staining with ethidium bromide. The results were interpreted without prior knowledge of the microscopy results. The species-specific nested PCR products were purified with the QIAquick PCR purification kit (Qiagen). The P. ovale-specific nested PCR products were cloned using the pGEM-T Vector System I kit (Promega, Madison WI). Double-strand sequencing was performed by Genome Express (Meylan, France) by using the P. ovale-specific forward primer rOVA1 and the Plasmodium-specific reverse primer 2 described by Kimura and others.24 Resulting sequences were aligned with previously published sequences from the Gen-Bank/EMBL/DDBJ database, using the CLUSTAL-W alignment program.25 Phylogenetic analysis was performed with the PHYLIP package version 3.6a3,26 using the DNAdist algorithm and the neighbor-joining method. The reliability of the tree was assessed by the bootstrap method with 1,000 replications.
| RESULTS |
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Three of the four P. ovale sequences (#14, #47, and #94) contained ambiguous signals at various positions of the SSU rRNA gene sequence (positions 853, 1134, and 1135; Figure 2
). The corresponding PCR fragments were therefore cloned, and four or five randomly selected clones per sample (clones A to E) were sequenced. Consistent with distinct SSU rRNA sequences previously co-amplified by PCR, two to four different haplotypes were identified for each PCR product, i.e., for each isolate. Comparison of the various P. ovale SSU rRNA sequences showed further sequence diversity, with a total of nine different haplotypes. The previously published P. ovale sequences CDC1 and CDC2 (accession numbers L48987 and L48986) were detected in 33% (5 of 15) of the Cambodian sequences (clones Cb 14A, B, D, and Cb 94A, E), whereas all other haplotypes corresponded to new variants of the P. ovale SSU rRNA gene. These new variants resembled either the CDC1 or the CDC2 sequences, with minor variations or combinations of the two haplotypes. In particular, the C to G mutation detected at position 1134 in four different clones (clones Cb 14C, Cb 47C and Cb 94B, D) had never been previously reported.
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A phylogenetic tree was generated based on the alignment of the P. ovale SSU rRNA sequences, and its reliability was tested by the bootstrap method. Consistent with the two types of sequences observed in the alignment, the P. ovale SSU rRNA sequences fell into two major genetic clusters, with a reliability of 94.1% (Figure 3
). Indeed, the two clones (CDC1 and CDC2) derived from the Nigerian I/CDC strain, as well as the SSU rRNA sequences obtained from the Cambodian samples #47 and #94, fell into these two genetic groups. In contrast, all SSU rRNA sequences obtained from sample #14 belonged to a single cluster.
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| DISCUSSION |
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Compared with microscopy, the molecular approach offers a clear advantage for the characterization of minor species in mixed infections.11,12,14 In our study, P. ovale was microscopically confirmed in only half of our samples, despite careful and lengthy examination of the slides. The low parasitemias of P. ovale and its presence in mixed infections make its microscopic identification very difficult, which is probably the main reason for its late discovery in Cambodia. Since this species was regularly reported in all surrounding countries, especially since the use of molecular diagnosis methods, we believe that P. ovale existed before in Cambodia but was simply overlooked. Further training of microscopists for the detection of this species on thin films is needed, and wherever possible molecular diagnosis methods should be used in combination with microscopy.
The sequencing of the P. ovale SSU rRNA PCR products provided undisputable confirmation of the species diagnosis in all four cases. It also showed unexpected sequence diversity, with the identification of nine different haplotypes, seven of which were novel. Cloning and sequencing showed up to four distinct P. ovale SSU rRNA sequences per sample. This is the first time that such high sequence diversity has been observed within individual P. ovale isolates, and it is particularly remarkable since the isolates all originated from a single village. Sequence variations in the SSU rRNA gene of P. ovale can have important implications on its molecular diagnosis with species-specific primers or probes. Indeed, failures of P. ovale and P. malariae detection because of minor nucleotide changes have been previously reported.15,16 For probe-hybridization methods, the risk of misdiagnosis could be reduced by using multiple species-specific probes and a separate assay with a genus-specific probe. Larger studies of the entire SSU rRNA gene in wild P. ovale isolates of different geographic origins would be useful to get a better knowledge of the actual molecular diversity of this species.
However, our results also raise the question of the origin of such a high sequence diversity in individual P. ovale isolates. It is unclear whether it reflects the presence of multiple clonal types of P. ovale in each isolate, or the existence of distinct gene copies co-amplified from a single parasite clone, or a combination of both.
Previous reports from southern Vietnam, Myanmar, Laos, and Thailand described a single variant form of the P. ovale SSU rRNA gene, and mixed infections with the normal and the variant forms were observed.13,15,18 Based on considerable sequence variations in the V7 and V8 regions of the SSU rRNA gene in different P. ovale isolates, the existence of P. ovale subspecies has even been evoked,27 and more recent data seem to support the existence of at least two types of P. ovale variants or subpopulations.20,21,28 According to these data, the sequences found in our study would rather belong to the "classic-type" variant, but with considerable variations within this subgroup and also within individual isolates. However, variations in the Plasmodium SSU rRNA sequence are not restricted to species, subspecies, or variants. It has been shown that four to eight genomic rDNA units exist in Plasmodium spp. that consist of two to three distinct developmentally expressed gene sets with specific sequence signatures.29 In particular, P. falciparum has A- and S- type SSU rRNA, being specifically transcribed during the asexual and sexual/ sporozoite stages, respectively.30 Plasmodium vivax has an additional O-type transcribed in the ookinete/oocyst stage.31 For P. malariae and P. ovale, only a single SSU rRNA gene type has been described. The copy number of the SSU rRNA gene in P. ovale is unknown. Based on the copy number in other Plasmodium species, it could be approximately 48 per genome.29 The primers used for our molecular analysis are specific for the SSU rRNA S-type in P. falciparum, for the SSU rRNA A-type in P. vivax,23 and for an unknown type in P. malariae and P. ovale. Some of the diversity observed in the Cambodian P. ovale SSU rRNA sequences might result from amplification of more than one SSU rRNA gene type per genome. This hypothesis is supported by the phylogenetic analysis of the P. ovale SSU rRNA sequences shown in Figure 3
. According to this analysis, the sequences derived from a single sample of the P. ovale reference strain NigerianI/ CDC,32 as well as those cloned from the Cambodian P. ovale isolates, divide into two major genetic clusters. Furthermore, the alignment with the A-, S- and O-type SSU rRNA genes of P. vivax, which is phylogenetically the closest Plasmodium to P. ovale,32 showed similar patterns in two stage-specific P. vivax sequences and in the two P. ovale sequence types. We therefore tend to conclude that more than one sequence type per genome could have been amplified from the Cambodian P. ovale isolates, but the extent of sequence variation between these gene copies would not necessarily be as big as between the A-, S-, or O- gene types of P. falciparum and P. vivax. The question of how many distinct rRNA gene units were amplified remains open. We observed up to four distinct haplotypes per sample, which may all represent distinct SSU rRNA units within a single genome. It has been reported that artifactual genetic diversity can be generated by recombination between templates of related sequences during PCR amplification.33 Indeed, the possibility that some of the P. ovale haplotypes were artifically produced by PCR-mediated recombination of at least two different sequence types cannot be ruled out. However, it seems not to be a major issue in our study, since the sequences of the P. falciparum, P. vivax, and P. malariae SSU rRNA perfectly matched the published reference sequences. In addition, only one of the nine observed SSU rRNA P. ovale haplotypes might actually have resulted from recombination of two other sequences in the same sample (Cb94B derived from Cb94A/E and Cb94D; Figure 2
). Another possibility to be considered is that the different SSU rRNA sequences could have originated from different P. ovale parasite clones. Given the low prevalence of P. ovale in the region, the probability of one patient being simultaneously infected with two or more genetically distinct P. ovale populations should be low, but it cannot be excluded that several P. ovale variants or subspecies are frequently transmitted together. The high sequence diversity observed in the examined isolates could even have resulted from a combination of polyclonality and intra-genomic variations. In summary, we conclude that substantial heterogeneity of P. ovale SSU rRNA sequences was observed between and within P. ovale isolates from northeastern Cambodia, and we suggest that SSU rRNA sequence diversity, usually interpreted as strain-to-strain variations, may well be due to variations among different SSU rRNA gene copies within a single genome. Further work is needed to examine this possibility, in particular sequence analysis of the P. ovale rRNA expressed at different developmental stages and analysis of the full P. ovale rDNA gene set.
Our results confirm that P. ovale is more prevalent in southeast Asia than previously suspected. This species probably remained undetected because of diagnosis difficulties. Indeed, PCR-based methods for the diagnosis of malaria have recently been introduced in Cambodia and proved useful for the detection of minor species and mixed infections. This is an important issue since interactions between species in the same patient may affect both the course and the severity of the infection, as well as the response to treatment.3437 Our observations call for larger community-based surveys, using microscopy and molecular diagnosis methods, to obtain more accurate information about the epidemiologic situation of malaria in Cambodia. Indeed, a precise estimate of the prevalences of the four malaria species and the frequency of mixed infections is required to optimize the medical treatments and malaria control measures according to the local characteristics of the disease.
Received April 7, 2004. Accepted for publication November 12, 2004.
Acknowledgments: We thank the staff of the National Center for Parasitology, Entomology and Malaria Control as well as the staff of the European Commission National Malaria Control Program for sample collection and for the initial examination of the blood slides.
Financial support: This work was supported by the PAL+ program of the French Ministry of Research and New Technologies.
Authors addresses: Sandra Incardona, Sophy Chy, Sina Nhem, and Rithy Sem, Institut Pasteur du Cambodge, 5 Boulevard Monivong, BP 983, Phnom Penh, Cambodia, Telephone: 855-23-368-036, Fax: 855-23-725-606, E-mails: sandra{at}pasteur-kh.org, chsophy{at}pasteur-kh.org, sandra{at}pasteur-kh.org, and srithy{at}pasteur-kh.org. Lim Chiv, Sean Hewitt, and Socheat Doung, National Center for Parasitology, Entomology and Malaria Control, 372 Boulevard Monivong/Rue 322, Phnom Penh, Cambodia, Telephone: 855-23-219-271, Fax: 855-23-219-271, E-mails: cnm{at}bigpond.com.kh, hewitt_se{at}hotmail.com, and socheatd{at}cnm.gov.kh. Odile Mercereau-Puijalon, Unité dImmunologie Moléculaire des Parasites, Centre National de la Recherche Scientifique, Unité de Recherche Associee 2581, Institut Pasteur, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France, Telephone: 33-1-45-68-86-23, Fax: 33-1-40-61-35-41, E-mail: omp{at}pasteur.fr. Thierry Fandeur, Unité Mixte de Recherche, Institut National de Recherche Agronomique dImmunologie Parasitaire, Faculté des Sciences Pharmaceutiques, 31 Avenue Monge, Parc Grandmont, 37200 Tours, France, E-mail: thierry.fandeur{at}univ-tours.fr.
Reprint requests: Sandra Incardona, Institut Pasteur du Cambodge, 5 Boulevard Monivong, BP 983, Phnom Penh, Cambodia.
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