# Genetic Profiling of thePlasmodium falciparum Population Using Antigenic Molecular Markers

Authors: Purva Gupta; Ruchi Singh; Haris Khan; Adil Raza; Veena Yadavendu; R. M. Bhatt; Vineeta Singh
Journal: The Scientific World Journal
 (2014)

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## Abstract

About 50% of malaria infections in India are attributed toPlasmodium falciparum but relatively little is known about the genetic structure of the parasite populations. The molecular genotyping of the parasite populations by merozoite surface protein (msp1 and msp2) and glutamate-rich protein (glurp) genes identifies the existing parasite population in the regions which help in understanding the molecular mechanisms involved in the parasite’s drive for survival. This study reveals the genetic profile of the parasite population in selected regions across the country with varying degree of endemicity among them. We also report the prevalence of Pfcrt mutations in this parasite population to evaluate the pattern of drug resistance development in them.


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## Body

## 1. Introduction

Malaria parasites infect about 650 million people worldwide andP. falciparum alone leads to almost one million deaths per year making it the most virulent parasite causing malaria. It is pertinent to develop efficient means of controllingP. falciparum in areas to which malaria infections are highly endemic. Since malaria infections are endemic to India, it is necessary to characterize the parasite population and know the genotypic pattern of the circulating parasite populations [1]. The identification of multiclones in the population not only helps in assessing the parasite population dynamics but also provides insights into the existing population [2]. Previous studies have revealed high polymorphism inmsp1,msp2, andglurp genes from different regions to which malaria is endemic [3]. In a country like India to which malaria is endemic, continuous molecular surveillance of the field isolates is required to know the pattern of existing and emerging drug resistance. This knowledge is the key to effective malaria control programs.Genotyping theP. falciparum populations using antigenic genesmsp1,msp2, andglurp has been known to describe allelic variability within parasite populations and also to distinguish recrudescence from new infections ofP. falciparum disease [4]. Mostly these polymorphic markers (msp1 andmsp2) have been used to assess the multiplicity of infection (MOI) for detecting the number of clones per isolate. Block-2 ofmsp1 gene, block-3 or the central repetitive domain ofmsp2 gene, and RII repeat region ofglurp show large allelic polymorphism [5]. Inmsp1 gene three distinct allelic families K1, MAD20, and RO33 have been described whereasmsp2 gene consists of FC27 and IC3D7 families. Several genes ofP. falciparumhave shown extensive genetic polymorphism in genetic analysis and therefore have been extensively used as markers to study the genetic diversity and MOI [6, 7].Chloroquine (CQ) is the most widely used antimalarial drug butP. falciparum has established mechanisms to evade the drug pressure. It is not very clear how the CQ resistance (CQR) is implemented but point mutations inP. falciparum CQR transporter protein (Pfcrt), encoded by thepfcrt gene, have been shown to make the parasite less sensitive to CQ [8].The purpose of the present study was to genotype the parasite population inP. falciparum infections in India using antigenic polymorphic markersmsp1,msp2, andglurpand drug resistance gene, namely,Pfcrt, so as to assess the parasite population dynamics in the country.


## 2. Materials and Methods

### 2.1. Sample Collection

One hundred and seven symptomatic malaria blood samples were collected by finger prick method from different regions of India (Figure1); the details are given in Table 1. Only after the ethical clearance from the institute the collection ofP. falciparum infected blood samples was done. The collection of samples was carried out during the years 2009–2012.Table 1
Summary of theP. falciparum isolates collected from various regions across India.
S. number
Region
Total samples collected
Samples positive forP. falciparum by microscopy and RDT
P. falciparum monoinfections by PCR
1
Aligarh (ALG)
13
13
13
2
Ahmedabad (AHM)
9
9
9
3
Rajasthan (RAJ)
14
4
4
4
Chennai (CHE)
15
5
5
5
Raipur (RAP)
14
14
14
6
Rourkela (RKL)
20
20
13
7
Ranchi (RNC)
22
22
22
Total
107
87
80Figure 1
Map of India showing different regions from where malaria symptomatic samples were collected. The table specifies the number of samples collected from each region.


### 2.2.P. falciparum Detection and Diagnosis

Microscopy and rapid diagnostic tests (RDT) were used for the first line ofP. falciparum malaria diagnosis and bloodspots of infected samples were made on Whatman (number 3) filter paper for further molecular studies. The microscopically confirmedP. falciparum samples were then subjected to genotyping by different polymorphic markers.


### 2.3. DNA Isolation and PCR Analysis

Genomic DNA ofP. falciparum positive samples was isolated by QIAamp DNA Blood Mini Kit (Qiagen Inc.) according to manufacturer’s protocol. Mixed infections ofP. vivax andP. falciparum were confirmed by nested PCR assay of 18srRNA primers [9].


### 2.4. Molecular Genotyping

The singleP. falciparum infections after the species specific PCR were only considered for further molecular analysis. The repetitive polymorphic regions in different allelic families ofmsp1 (block 2),msp2 (block 3), and region II ofglurp genes were amplified by PCR. These alleles have conserved regions flanked by repeat sequences of variable regions [5]. The primary PCR amplification ofmsp1,msp2, andglurp genes comprised an initial step of 95°C for five minutes followed by 30 cycles of 95°C for 1 minute, 58°C for 2 minutes, 72°C for 2 minutes, and a final extension of 72°C for 5 minutes. The nested PCR cycling parameters forglurp were the same as the primary reaction but formsp1 andmsp2 the annealing temperature was 61°C in the nested PCR. The PCR products formsp1,msp2, andglurp were separated on 1.5% ethidium bromide stained agarose gels for visualization under UV illumination.The point mutations in thePfcrt gene were typed to study the polymorphisms in the drug resistance gene. InPfcrt gene ofP. falciparumthe primers amplifieda fragment of 450 bp which carries SNPs from 72–76 and 97 positions. Both primary and nested PCR amplifications consisted of an initial denaturation of 94°C for five minutes with 35 cycles of 94°C for 30 s, 55°C for 30 s, 72°C for 1.5 minutes, and a final extension of 72°C for 7 minutes. Restriction fragment length polymorphism (RFLP) was carried out for the amplified region ofpfcrt gene by enzymeApo I (New England BioLabs Inc.) for the detection of SNPs as described previously with slight modifications [1, 10].


## 2.1. Sample Collection

One hundred and seven symptomatic malaria blood samples were collected by finger prick method from different regions of India (Figure1); the details are given in Table 1. Only after the ethical clearance from the institute the collection ofP. falciparum infected blood samples was done. The collection of samples was carried out during the years 2009–2012.Table 1
Summary of theP. falciparum isolates collected from various regions across India.
S. number
Region
Total samples collected
Samples positive forP. falciparum by microscopy and RDT
P. falciparum monoinfections by PCR
1
Aligarh (ALG)
13
13
13
2
Ahmedabad (AHM)
9
9
9
3
Rajasthan (RAJ)
14
4
4
4
Chennai (CHE)
15
5
5
5
Raipur (RAP)
14
14
14
6
Rourkela (RKL)
20
20
13
7
Ranchi (RNC)
22
22
22
Total
107
87
80Figure 1
Map of India showing different regions from where malaria symptomatic samples were collected. The table specifies the number of samples collected from each region.


## 2.2.P. falciparum Detection and Diagnosis

Microscopy and rapid diagnostic tests (RDT) were used for the first line ofP. falciparum malaria diagnosis and bloodspots of infected samples were made on Whatman (number 3) filter paper for further molecular studies. The microscopically confirmedP. falciparum samples were then subjected to genotyping by different polymorphic markers.


## 2.3. DNA Isolation and PCR Analysis

Genomic DNA ofP. falciparum positive samples was isolated by QIAamp DNA Blood Mini Kit (Qiagen Inc.) according to manufacturer’s protocol. Mixed infections ofP. vivax andP. falciparum were confirmed by nested PCR assay of 18srRNA primers [9].


## 2.4. Molecular Genotyping

The singleP. falciparum infections after the species specific PCR were only considered for further molecular analysis. The repetitive polymorphic regions in different allelic families ofmsp1 (block 2),msp2 (block 3), and region II ofglurp genes were amplified by PCR. These alleles have conserved regions flanked by repeat sequences of variable regions [5]. The primary PCR amplification ofmsp1,msp2, andglurp genes comprised an initial step of 95°C for five minutes followed by 30 cycles of 95°C for 1 minute, 58°C for 2 minutes, 72°C for 2 minutes, and a final extension of 72°C for 5 minutes. The nested PCR cycling parameters forglurp were the same as the primary reaction but formsp1 andmsp2 the annealing temperature was 61°C in the nested PCR. The PCR products formsp1,msp2, andglurp were separated on 1.5% ethidium bromide stained agarose gels for visualization under UV illumination.The point mutations in thePfcrt gene were typed to study the polymorphisms in the drug resistance gene. InPfcrt gene ofP. falciparumthe primers amplifieda fragment of 450 bp which carries SNPs from 72–76 and 97 positions. Both primary and nested PCR amplifications consisted of an initial denaturation of 94°C for five minutes with 35 cycles of 94°C for 30 s, 55°C for 30 s, 72°C for 1.5 minutes, and a final extension of 72°C for 7 minutes. Restriction fragment length polymorphism (RFLP) was carried out for the amplified region ofpfcrt gene by enzymeApo I (New England BioLabs Inc.) for the detection of SNPs as described previously with slight modifications [1, 10].


## 3. Results

A total of 87 samples were microscopically confirmed out of which 80 were found to be positive forP. falciparummonoinfections by PCR assay. Out of these 80P. falciparummonoinfections, 67 samples were successfully analyzed by PCR formsp1, 71 samples formsp2, and 51 samples forglurp loci in the isolates.After the PCR assay, the classification of the alleles was done according to the number and size of fragments and the allelic family (Figure2). Themsp1 gene block-1 amplification for K1 allelic family was positive in 29 samples (36.25%) with five different allelic sizes ranging from 180 to 300 bp among which 200 bp allelic fragment was predominant. The other family MAD20 inmsp1was found in 32 samples (40.0%) depicting seven different allelic sizes within 100–300 bp and 200 bp was found to be the predominant allele size in this group. The RO33 family was detected in 17 samples (21.25%) having four distinct alleles with fragment sizes of 100–200 bp and its predominant allele was found to be 200 bp fragment (Figure 3(a)). Themsp2 amplification for FC27 family was positive in 37 isolates (46.25%) having seven different allele types ranging from 280 to 800 bp predominated by 300 bp fragment size. The IC3D7 allelic family was amplified in 45 isolates (56.25%) demarcated by nine different alleles spanning between 400 and 1150 bp fragments where 500 bp fragment was in majority (Figure 3(b)). Forglurp 51 samples (63.75%) were found to be positive for RII repeat region producing eight different sizes ranging between 700 and 1200 bp, among which 900 bp allele was found to be predominant (25.0%) (Figure 3(c)). The number of genotypes for each marker is shown in Tables 2 and 3.Table 2
Region-wise genetic diversity ofP. falciparum by msp1, msp2, and glurp.
S. number
Region
Number of samples (n)
PCR assay
msp1
msp2
glurp
K1
MAD20
RO33
Total
FC27
IC3D7
Total
1
Aligarh
13
2
7
3
12
9
5
14
10
2
Ahmedabad
9
1
2
4
7
7
5
12
8
3
Rajasthan
4
1
2
2
5
3
1
4
3
4
Chennai
5
2
4
3
9
3
1
4
3
5
Raipur
14
8
5
2
15
9
8
17
12
6
Rourkela
13
9
3
3
15
5
8
13
11
7
Ranchi
22
6
9
0
15
1
17
18
4Table 3
Summary of all the isolates positive for each allelic family formsp1, msp2, and glurp along with the number of alleles and the range of sizes of alleles.
Loci
Number of samples positive by PCR
Number of distinct alleles
Sizes of alleles (bp)
MSP-1
K1
29
5
180–300
MAD20
32
7
100–300
RO33
17
4
100–200
MSP-2
FC27
37
7
280–800
IC3D7
45
9
400–1150
GLURP
51
8
700–1200Figure 2
Gel picture showing the amplification ofP. falciparum msp1,msp2, andglurp genes. Lane 2 showsmsp1 allelic family K1, lanes 3 and 4 show allelic family MAD20, lanes 5 and 6 show allelic family RO33, lanes 7 and 8 showmsp2 allelic family FC27, lanes 9, 10, and 11 show family IC3D7, lanes 15, 16, and 17 showglurp gene amplification, lane 13 is the negative control, and lanes 1, 12, 14, and 18 show 100 bp DNA ladder.Genetic diversity ofP. falciparum bymsp1,msp2, andglurp genes. PCR amplification was represented by groups where PCR product size differed by 20 bp. (a) Genetic diversity bymsp1 gene. Blue bars denote the K1 allelic family, size ranging from 180 to 300 bp; red bars denote the MAD20 allelic family, size ranging from 100 to 220 bp; and green bars denote the RO33 allelic family, size ranging from 100 to 200 bp. (b) Genetic diversity bymsp2 gene. Blue bars denote the FC27 allelic family, size ranging from 280 to 800 bp and the red bars denote the IC3D7 allelic family, size ranging from 400 to 1150 bp. (c) Genetic diversity byglurp gene. Blue bars denote the RII repeat region of glurp gene, size ranging from 700 to 1200 bp.
(a)
(b)
(c)It was seen that 46.25% of the isolates studied were multiclonal in nature with two or more alleles present inmsp1,msp2, andglurp genes. Thirteen multiple alleles were seen inmsp1 (16.25%), 28 were found inmsp2 (35%), and two multiple alleles were seen inglurp (2.5%) genes showing more genotypic variation inmsp2 than inmsp1 andglurp. There was only one isolate from Rourkela, positive for all the allelic families ofmsp1 andmsp2. There were 21 distinct haplotype patterns observed among the parasite population and the prominent genotype pattern was MAD20 formsp1 and FC27 formsp2.MOI is calculated as the number of genotypes for a gene divided by the number of isolates with positive PCR amplification. For each region studied MOI of bothmsp1 andmsp2 was calculated whose results are shown in Figure 4.Figure 4
Graph showing comparison of MOI formsp1 andmsp2 genes in different regions of India. ALG: Aligarh, AHM: Ahmedabad, RAJ: Rajasthan, CHE: Chennai, RAP: Raipur, RKL: Rourkela, and RNC: Ranchi.A fragment of 450 bp inpfcrt gene was amplified for 80P. falciparum isolates out of which 68 samples showed successful amplification. Restriction sites forApo I enzyme are seen at codon 76 where K76T mutation was observed in 29.4% of the isolates.


## 4. Discussion

Though, for parasite genotyping,msp1,msp2, andglurp genes have been the recommended molecular markers for several drug efficacy studies, still the parasite population genetic profile has not been assessed systematically in a country to which malaria is endemic like India [6, 11, 12]. The field isolates in the present study have been genotyped using the polymorphic regions of these three genes in order to compare the diversity and the existing allelic frequencies.Themsp1andmsp2showed 16 each, andglurp markers showed eight allelic families in the studied parasite population. These findings indicate that, for detection of MOI,msp1 served as a better marker as MOI formsp1 was higher in comparison tomsp2. However it is noticeable thatglurp did not indicate the existing genetic pattern with lower frequency of diverse alleles [13]. This study shows the complex diversity existing in theP. falciparum field isolates in areas of the country where malaria is endemic. The diversity seen in these isolates is due to the complexity present in the parasite population.Previously it has been reported that a higher MOI was found in severe infections as compared to the mild type infections in studies from Uganda [14]. These findings were in tandem with studies from India, which showed a strong association between multiple genotype infections, significantly high MOI, and severity ofP. falciparum malaria [15, 16]. Findings from Yemen show a regional variation with a higher MOI in isolates from foothills/coastland areas as compared to those from the highlands [17]. Another study from India showed a high proportion of multiclonal isolates and high MOI in regions to whichP. falciparum is highly endemic [18]. Findings on the genetic pattern of these polymorphic genesmsp1,msp2, andglurp of field isolates are similar to the other studies reported elsewhere [3, 4]. Studying the dynamics of multiclone infections and MOI in relation to the host immunity, disease prevalence, genetic structure, and geographical distribution would allow us to know more about the virulence ofP. falciparum.We were able to identify 21 distinct genetic patterns among the parasite population indicative of the fact that a considerable amount of gene flow is ongoing between the different regions withP. falciparum infections. It would be interesting and of importance to link the genotypic pattern of the parasites with the clinical phenotype. The recent data ofmsp1,msp2, andglurp markers for drug efficacy studies are highly important in areas where malaria is endemic for understanding the treatment criteria [19]. These highly polymorphic surface proteins are vaccine candidate genes and monitoring these genes to understand their genetic diversity and structure would help us develop vaccines with cross-protection against a range of antigenic variants [13, 20].The studied drug resistance gene indicates that extensive mapping of this gene should be carried out in more areas in which malaria is endemic. The resistant mutants are the result of drug pressure and hence control programs should be devised in such a manner that they help in reducing the drug pressure and enhance the activity of antimalarials. This study indicates the high complexity and the diversity existing in theP. falciparum population in several areas of the country where malaria is endemic. The MOI was higher inmsp1 in this reported study, suggesting that the intensity of malaria transmission in these regions is high. This multiplicity of infection has definite implications not only in the drug resistant parasite but also in the outcome of the disease treatment. The diversity (MOI) in the parasite population was seen more in the rural areas like Rourkela and Ranchi than in urban areas like Ahmedabad and Aligarh. This difference in the genetic diversity could be attributed to the topographical and climatic changes in the environmental factors. This kind of study in addition to other molecular methods should be undertaken for monitoring the existing and emerging drug resistance patterns in malaria disease.



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