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Single Nucleotide Polymorphism of SSU rRNA Gene among Plasmodium Knowlesi Isolates of Sabah

Fread Anderios1*, Daw Khin Saw Naing2, Zaw Lin3, Nor Amalina Emran3
  1. Diseases Section, Sabah State Public Health Laboratory, Kota Kinabalu, Sabah, Malaysia
  2. Department of Community & Family Medicine, School of Medicine, Universiti Malaysia Sabah, Malaysia
  3. Department of Pathodiagnostics, School of Medicine, Universiti Malaysia Sabah, Malaysia
Corresponding Author: Fread Anderios, Diseases Section, Sabah State Public Health Laboratory, Kota Kinabalu, Sabah, Malaysia, E-mail: [email protected]
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Abstract

Background: The advent of PCR (Polymerase Chain Reaction) assays helped in correctly identifying Plasmodium knowlesi, which was previously misdiagnosed by microscopy as Plasmodium malarie in Sabah, Malaysia. The PCR-based diagnosis of P. knowlesi in Sabah is currently using a set of oligonucleotide primers namely Pmk8 and Pmk9 that target one of the parasite’s small subunit rRNA (SSU rRNA) genes. PCR also helped in discovering a variant form of P. malariae which has a deletion of 19 bp and seven substitutions of base pairs in the target sequence of the small-subunit rRNA gene among isolates of Sichuan province of China and Thai Myanmar Border. The sequences of eight isolates identified as P knowlesi in Kapit, Sarawek were not identical, showing within-species polymorphisms. Thus the possibility of variation in the DNA sequence of SSU rRNA gene of P knowlesi isolates was expected.

Aim & Objectives: To determine the within-species polymorphism of the fifth human malaria species among Sabah population in relation to geographical regions.

Methods: The samples of P.knowlesi isolates, sent to the Sabah State Public Health Laboratory from the districts with P. knowlesi high prevalence, were included. In 10 samples, which gave positive in PCR with Pmk8 and Pmk9 primers in Nest 2 PCR, the Nest 1 PCR products were analysed by automated sequencer for DNA sequence to find out genetic variation of SSU rRNA of P.knowlesi.

Results/Findings: All 10 samples showed SNPs (single nucleotide polymorphism) at 14 nucleotides when compared with the same gene of Standard Strain of P knowlesi. The locations of SNPs were quite similar to the SNPs found in Kapit Division of Sarawek, Malaysia. No typical SNPs pattern in each geographical region could be identified. However, SNPs in each region have only 2-3 nucleotides in difference.

Study Limitations: SSU rRNA gene is 2096 bp in length. However, Nest 1 product sequenced in this study is only 1622 bp in length that this study could not describe the variation in the sequence of the whole gene. Conclusion: There exists a somewhat similar regional pattern of Single Nucleotide Polymorphism in the sequence of SSU rRNA gene of P.knowlesi isolates from Sabah, Malaysia. It is recommended to conduct further studies, involving the whole gene sequence and covering a larger amount of samples derived from different geographic regions of Sabah.

Keywords

SSU rRNA gene, Single Nucleotide Polymorphism, P knowlesi, PCR, Sabah,

INTRODUCTION

Traditionally, only 4 Plasmodium species have been known to cause malaria in humans: P. falciparum, P. vivax, P. ovale, and P. Malariae[1].. At the beginning of this new millennium, P. knowlesi has been accepted as the fifth Plasmodium species that can cause human malaria [2]. It was previously believed to be a purely zoonotic species prevalent among the long tailed macaques . Human infection with P knowlesi was reportedly possible under experimental conditions. The first natural infection of P knowlesi in a human was reported in 1965 in a man who returned to the USA after visiting peninsular Malaysia [3]. It was reported that as much as 70% of malaria infections in government hospitals in Borneo are the result of P. knowlesi infection. [4]. Similar infections have been reported in Thailand, the Philippines, Singapore and Myanmar[3,5].
Although the current reported incidence of P. knowlesi infection in humans is relatively low, the possibility of mis-speciation by microscopy should be taken into account. Since the knowlesi species are indistinguishable to the more benign type of human malaria, P. malariae, most cases were diagnosed and treated as P. malariae[2,3,6].. However, in contrast to P. malariae, P. knowlesi cases need immediate and aggressive treatment because of its rapid replication rate and the resultant high level of parasitemia[4]. False identification of species might lead to severe and fatal infection[7]..
Sabah is the second largest state of Malaysia situated on the Borneo Island. With a population of nearly 3 million dispersed in a total land area of 74,500 sq meters, only about 22 % of land area is occupied [8].. Most of the uninhabited area of Sabah state is densely covered with tropical forest forming the natural habitat for primates as well as vector mosquitoes. In recent decades, expansion of agricultural activities led to increase man-monkey-mosquito contacts allowing P. knowlesi to enjoy the hospitality of human host.
In Malaysia as well as in most of the Asian countries, microscopy is still the method of choice for the diagnosis of malaria, especially in endemic areas as it is inexpensive and rapid method of detection. At best, the sensitivity of detection by microscopy is approximately 10- 30 parasites/μl of blood[6]. The malaria control programme is well aware that incorrect speciation is common and mixed infections and low levels of parasitaemia may be missed by microscopy.
To overcome some of the limitations of microscopy for detection of malaria, PCR assays have been developed for the detection and identification of malaria parasites. These methods have been proved to be more sensitive and specific than microscopy. Some are reported to detect as few as one parasite/μl of blood[6]. However, to attain such sensitivity, blood samples collected from the individuals need to be processed immediately or stored at low temperatures. Thus nested PCR assays as an alternative to real time PCR have been attempted. The nested PCR assay involved sequential amplification for each blood sample screened. In the first PCR (nest 1) amplification, Plasmodium genus-specific primers were used for small subunit rRNA (SSU rRNA) gene of Plasmodium species. The product of nest 1 amplification then served as DNA template for four separate second PCR nest 2 amplifications with primers specific for each of each malaria species[6]..
Since 2007, PCR services were available for all public hospitals around Sabah[9]. The PCR-based diagnosis of P. knowlesi in Sabah is currently using a set of oligonucleotide primers namely Pmk8 and Pmk9 that target one of the parasite’s small subunit rRNA (ssu rRNA) genes. Most Plasmodia species have two or three distinct SSU rRNA genes that are differently expressed during it’s life cycle. The Pmk8 and Pmk9 primers target the SSU rRNA expressed during the sexual stage of the parasite[6]..
PCR helped in discovering seven novel variants in Plasmodium ovale isolates in Cambodia, rediscovering P. malariae infections at two foci in the Sichuan province of China, discovering a variant form of P. malariae which has a deletion of 19 bp and seven substitutions of base pairs in the target sequence of the small-subunit rRNA gene, discovering the same sequence variations in P. malariae isolates collected along the Thai-Myanmar border, suggesting a wide distribution of this variant form from southern China to Southeast Asia[10].

RATIONALE & OBJECTIVE

Thus the possibility of variation in the DNA sequence of SSU rRNA gene of P knowlesi isolates was expected. The sequences of eight isolates identified as P knowlesi in Kapit , Sarawek were not identical showing within species polymorphisms[6]. In 2009 study on geographical and ethnic distribution of P. knowlesi in Sabah, the areas most commonly affected by P.knowlesi were related to tourist attraction sites of Sabah[9].. As ecotourism is in rising trend, the P.knowlesi infections among human population need to be effectively prevented and series of epidemiological studies are underway. Study of genetic variations may find out the possible marker for epidemiological purpose. This study aimed at discovering the genetic variation of SSU rRNA gene of P. knowlesi isolates in different geographical areas of Sabah.

METHODS

 Samples

Twenty samples of P.knowlesi isolates sent to Sabah State Public Health Laboratory from the district hospitals of Sabah were studied for genetic variation.

 Preparation of the DNA template

The DNA templates for the nested PCR assay were prepared from the whole blood using DNA isolation kit.

 Oligonucleotide Primers

Oligonucleotide primers were designed based on the Plasmodium small subunit ribosome RNA (SSU rRNA) genes. In this study, genus–specific primers rPLU1 and rPLU5 were used. For nest 2 PCR Pkm8 and Pkm9 primers were used to get diagnosis of knowlesi malaria[6].

 Nested PCR assay

 Nest 1 amplification was done as follow:
♦ step1, 94°c for 4 mins;
♦ step 2, 94°c for 30secs
♦ step 3, 55°c for 1 min
♦ step 4,72°c for 1 min
♦ repeat step 2-4 for 35 cycles
♦ Two μl of nest 1 product served as DNA template for nest 2 amplifications
 Nest 2 amplification condition was identical to those of nest 1 except that the annealing temperature in step 3 was 58°c for species-specific primers.
 The PCR products of nest 2 amplifications were analyzed by gel electrophoresis[6].

 DNA sequencing

 In samples, which gave positive in PCR with Pmk8 and Pmk9 primers in Nest 2 PCR, Nest 1 PCR products were analysed by automated sequencer for DNA sequence to find out genetic variation of SSU rRNA of P.knowlesi

RESULTS

Nest (1) product (Fig.1) of the isolates, in which Nest (2) product showed positive with 153bp DNA band (Fig.2), were sequenced for studying of genetic variation of SSU rRNA gene of P. knowlesi isolates. Nineteen isolates from five districts of Sabah States were studied.
Single Nucleotide Polymorphisms in SSU rRNA gene of Sabah P. knowlesi isolates, which were consistent with isolates of Sarawak, were found at nucleotide no. 192, 278, 279 280, 663, 678, 785, 797 and 1534. However, the polymorphic nucleotides were not the same for Sabah and Sarawak isolates. Some nucleotides, ie; no. 192, 279, 785, 797 and 1534 were same for all isolates tested but had different SNP with Standard strain. Some nucleotides: no. 278, 280, 663, 678 did not have SNP in all isolates (Fig.3).
At three continuous nucleotides at position 278, 279, & 280 of SSU rRNA gene of Standard Strain, Isolates of Sabah showed SNPs in comparison with SSU rRNA gene of Standard Strain. This phenomenon also occurred in Sarawak isolates. Genetic variation in these three nucleotide positions is typical for P. knowlesi isolates of Sabah and Sarawak isolates (Fig. 4).
At Nucleotide No. 678 of SSU rRNA gene, Ranau isolates were highly consistent with nucleotide C when compared with isolates from other districts. This consistency may be typical of isolates of Ranau (Fig.5).
There were many SNPs patterns of Sabah isolates which were not the same position as Sarawak isolates. There were 15 SNPs, out of which one Keningau isolate H08 had 13 SNPs when compared with isolates from other isolates. These SNPs were common between nucleotide no. 830 and 1565 of SSU rRNA gene.

DISCUSSION

In this study it was tried to find out that the genetic variation pattern of SSU rRNA gene of P.knowlesi isolates from Sabah to reveal important clues for future epidemiological studies. According to the previous literatures on P.malariae and P.ovale, there was relatively constant genetic variation in SSU rRNA gene and it was epidemiologically possible to trace the source and stream of transmission.
For the diagnosis of P. knowlesi isolates, Nested PCR assay was used in Sabah Public Health Laboratory. Nest (1) product of P. knowlesi isolates were studied for DNA sequence. Because this DNA size is 1622 excluding primers, it was possible to study the genetic variation to some extent.
According to the results, genetic variation patterns of this gene from Sabah isolates were similar to Sarawak isolates to some extent. The difference in these two studies between Sabah and Sarawak was that isolates were taken from five different districts of Sabah while Sarawak study focused only on Kapit division. Kapit division had a large focus of knowlesi malaria.
Three continuous nucleotides at position 278, 279 and 280 had SNPs and this was characteristic of both Sabah and Sarawak isolates to compare with this gene of standard strain. This characteristic will be important molecular epidemiological marker when compared with DNA sequence of SSU rRNA gene of P.knowlesi isolates from other regions of the world.
At Nucleotide No. 678 of SSU rRNA gene, Ranau isolates were highly consistent with nucleotide C when compared with isolates from other districts. Because there was one exception with isolate H31, this nucleotide C consistency will change if more isolates were studied for SNPs at this position. If this consistency is still present after studying more isolates, it can be the possible marker for Ranau isolates.
One Keningau isolate had 13 SNPs between nucleotide no. 830 and 1565 and this characteristic of the isolate may need further information so that SSU rRNA gene of other isolates of this district should be sequenced to draw a conclusion.

CONCLUSION

In this study on genetic variation pattern of SSU rRNA gene of P.knowlesi isolates, no SNPs pattern in each geographical region were constant. It is found that Isolates have more different SNPs when compared with standard strain than when compared among them.
In this study, to identify the genetic variation of SSU rRNA gene by using Nest 1 product, the SNPs in this gene of P.knowlesi were investigated. The SSU rRNA gene is 2096 bp in length. However, Nest 1 product sequenced in this study is only 1622 bp in length. Therefore it is necessary to sequence the whole gene to draw a firm conclusion. The next step in studying the variation of whole SSU rRNA gene will be designing the new primers for another set of PCR and sequencing.
For further research, plans are underway to study more isolates from each region for genetic variation including SNPs. Circumsporozoital (csp) gene and mitochondrial cox1 gene will be studied for understanding the epidemiology and origin of P.knowlesi infections in Sabah.
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