Mohammad Tauqeer Alam

Similar Trends of Pyrimethamine Resistance-Associated Mutations in Plasmodium vivax and P. falciparum

ABSTRACT The antifolate drugs sulfadoxine and pyrimethamine are commonly used to treat Plasmodium falciparum malaria. However, they can also affect the Plasmodium vivax parasite if it coexists with P. falciparum, as both species have common drug targets. Resistance to the antifolate drugs arises due to point mutations in the target enzymes of the respective parasite. To assess the cross-species impact of antifolate drug treatment, we describe here the dihydrofolate reductase (DHFR) mutations among field isolates of P. vivax and P. falciparum. The overall DHFR mutation rate for P. vivax was lower than that for P. falciparum. However, both species of Plasmodium followed similar trends of DHFR mutations. Similar to P. falciparum, the DHFR mutation rate of P. vivax also varied from region to region. It was lower in P. vivax-dominant regions but higher in the P. falciparum-dominated areas and highest where antifolates are used as the first line of antimalarial treatment. In conclusion, the antifolate treatment of falciparum malaria is proportionately affecting the DHFR mutations of P. vivax, suggesting that the drug should be used with caution to minimize the development of cross-species resistance in the field.

Sequence diversity and natural selection at domain I of the apical membrane antigen 1 among Indian Plasmodium falciparum populations

BackgroundThe Plasmodium falciparum apical membrane antigen 1 (AMA1) is a leading malaria vaccine candidate antigen. The complete AMA1 protein is comprised of three domains where domain I exhibits high sequence polymorphism and is thus named as the hyper-variable region (HVR). The present study describes the extent of genetic polymorphism and natural selection at domain I of the ama1 gene among Indian P. falciparum isolates.MethodsThe part of the ama 1 gene covering domain I was PCR amplified and sequenced from 157 P. falciparum isolates collected from five different geographical regions of India. Statistical and phylogenetic analyses of the sequences were done using DnaSP ver. 4. 10. 9 and MEGA version 3.0 packages.ResultsA total of 57 AMA1 haplotypes were observed among 157 isolates sequenced. Forty-six of these 57 haplotypes are being reported here for the first time. The parasites collected from the high malaria transmission areas (Assam, Orissa, and Andaman and Nicobar Islands) showed more haplotypes (H) and nucleotide diversity π as compared to low malaria transmission areas (Uttar Pradesh and Goa). The comparison of all five Indian P. falciparum subpopulations indicated moderate level of genetic differentiation and limited gene flow (Fixation index ranging from 0.048 to 0.13) between populations. The difference between rates of non-synonymous and synonymous mutations, Tajimas D and McDonald-Kreitman test statistics suggested that the diversity at domain I of the AMA1 antigen is due to positive natural selection. The minimum recombination events were also high indicating the possible role of recombination in generating AMA1 allelic diversity.ConclusionThe level of genetic diversity and diversifying selection were higher in Assam, Orissa, and Andaman and Nicobar Islands populations as compared to Uttar Pradesh and Goa. The amounts of gene flow among these populations were moderate. The data reported here will be valuable for the development of AMA1-based malaria vaccine.

Plasmodium vivax: Sequence polymorphism and effect of natural selection at apical membrane antigen 1 (PvAMA1) among Indian population

Present study describes the characterization of apical membrane antigen 1 (PvAMA1) polymorphisms among Indian Plasmodium vivax isolates. The partial PvAMA1 gene (covering domain I and domain II regions) sequenced from sixty-one (n=61) isolates in this study resulted into 49 haplotypes. Comparison with the previously available PvAMA1 sequences in the GenBank database revealed that 45 of these were new haplotypes that have never been reported till date. For further analyses, we also included 11 previously reported PvAMA1 sequences from India available in the database. Thus genetic diversity and effect of natural selection were analyzed both at domain I and domain II of this promising malaria vaccine candidate among 72 Indian P. vivax isolates. Non-synonymous mutations were found at 25 codons (16 at domain I and 9 at domain II) where 17 codons were dimorphic while rest of them (8 codons) were trimorphic. Thus codon polymorphisms were observed to be more at domain I as compared to domain II. Although the difference between the rate of non-synonymous (dN) and synonymous (dS) mutations was positive (dN-dS, 0.002+/-0.004SE) at domain II, it was not significantly different from each other (P=0.272), indicating tendency of stronger diversifying selection at this domain. The dN-dS difference for domain I (-0.006+/-0.009SE, P=0.268) and for entire 900 bp region (-0.002+/-0.005E, P=0.320) being negative and statistically insignificant suggests the role of both positive as well as purifying selection. Three-dimensional distributions of all polymorphic residues were mapped on a modeled PvAMA1 structure. Results suggested that almost all of the observed polymorphisms were located at one surface of the antigen. In conclusion, PvAMA1 antigen displays high diversity among Indian isolates with more diversifying selection at domain II. The result has significant value in malaria vaccine development using this antigen.

Genetic Variation in the Plasmodium falciparum Circumsporozoite Protein in India and Its Relevance to RTS,S Malaria Vaccine

RTS,S is the most advanced malaria vaccine candidate, currently under phase-III clinical trials in Africa. This Plasmodium falciparum vaccine contains part of the central repeat region and the complete C-terminal T cell epitope region (Th2R and Th3R) of the circumsporozoite protein (CSP). Since naturally occurring polymorphisms at the vaccine candidate loci are critical determinants of the protective efficacy of the vaccines, it is imperative to investigate these polymorphisms in field isolates. In this study we have investigated the genetic diversity at the central repeat, C-terminal T cell epitope (Th2R and Th3R) and N-terminal T cell epitope regions of the CSP, in P. falciparum isolates from Madhya Pradesh state of India. These isolates were collected through a 5-year prospective study aimed to develop a well-characterized field-site for the future evaluation of malaria vaccine in India. Our results revealed that the central repeat (63 haplotypes, n = 161) and C-terminal Th2R/Th3R epitope (24 haplotypes, n = 179) regions were highly polymorphic, whereas N-terminal non-repeat region was less polymorphic (5 haplotypes, n = 161) in this population. We did not find any evidence of the role of positive natural selection in maintaining the genetic diversity at the Th2R/Th3R regions of CSP. Comparative analysis of the Th2R/Th3R sequences from this study to the global isolates (n = 1160) retrieved from the GenBank database revealed two important points. First, the majority of the sequences (∼61%, n = 179) from this study were identical to the Dd2/Indochina type, which is also the predominant Th2R/Th3R haplotype in Asia (∼59%, n = 974). Second, the Th2R/Th3R sequences in Asia, South America and Africa are geographically distinct with little allele sharing between continents. In conclusion, this study provides an insight on the existing polymorphisms in the CSP in a parasite population from India that could potentially influence the efficacy of RTS,S vaccine in this region.

Extensive Genetic Diversity in the Plasmodium falciparum Na+/H+ Exchanger 1 Transporter Protein Implicated in Quinine Resistance

ABSTRACT The Plasmodium falciparum Na+/H+ exchanger (Pfnhe-1) locus at chromosome 13 and another locus at chromosome 9 have recently been proposed to influence quinine resistance. Here, we sequenced the ms4760 locus of the Pfnhe-1 gene from 244 P. falciparum isolates collected from five different regions of India. A total of 16 different ms4760 alleles (with one to five DNNND repeats) were observed among these isolates. Interestingly, areas with a high prevalence of chloroquine and sulfadoxine-pyrimethamine resistance showed more Pfnhe-1 DNNND repeats compared to low drug resistance areas. The extent of genetic diversity at the ms4760 locus also varied from one region to another, with expected heterozygosity values ranging from 0.47 to 0.88.

Therapeutic efficacy of chloroquine and sequence variation in pfcrt gene among patients with falciparum malaria in central India.

Objectives  To assess the therapeutic efficacy of chloroquine (CQ) treatment against uncomplicated Plasmodium falciparum infections in a tribal population of central India (Madhya Pradesh) and to investigate the prevalence of mutant P. falciparum chloroquine‐resistant transporter (pfcrt) gene in the parasite population.

Identification of two cryptic species in the Anopheles (Cellia) annularis complex using ribosomal DNA PCR-RFLP

Anopheles (Cellia) annularis Van der Wulp is a complex of two sibling species provisionally designated as species A and B and can only be differentiated on the basis of the paracentric inversion in the ovarian polytene chromosomes. To analyze the distribution of these two species and to develop a molecular method for the identification of these two cryptic species, we sequenced the ribosomal DNA internal transcribed spacer 2 (ITS2) and domain 3 (D3) of A. annularis specimens collected from Sonapur (Assam), Jabalpur (Madhya Pradesh), Ranchi (Jharkhand), and Ghaziabad (Uttar Pradesh). We did not find any sequence variation among the specimens collected from Assam, Madhya Pradesh, and Jharkhand states, whereas two types of sequences were obtained from the specimens collected from the state of Uttar Pradesh, which correspond to species A and B of the A. annularis complex. Species A was more prevalent among the all four regions studied. The ITS2 sequence of species A showed unique restriction sites for MvaI and Eco24I, while species B displayed HinfI and NruI sites. Similarly, the D3 sequence of species A showed unique restriction site for Alw26I, while species B showed a unique KpnI site. In this study, we report for the first time the development of ribosomal DNA polymerase chain reaction-restriction fragment length polymorphism methods for identifying these two cryptic species of the Annularis complex.

Genetic diversity in the C-terminal 42 kDa region of merozoite surface protein-1 of Plasmodium vivax (PVMSP-142) among Indian isolates

Plasmodium vivax merozoite surface protein 1 (PvMSP-1) is a leading malaria vaccine candidate. This protein is processed to give rise to various sized fragments during merozoite maturation. Here, we describe the analysis of genetic diversity in the 42 kDa C-terminal part of this protein among 33 Indian P. vivax isolates. A total of 27 haplotypes with 72 mutations and 0.0212+/-0.0005S.D. over all pi nucleotide diversity were observed among the isolates. Twenty-six of 27 haplotypes reported here were new as they have not been reported so far from any other country. The difference between non-synonymous (dN) and synonymous (dS) mutations was found to be positive (0.0081+/-0.0051) for the entire 42 kDa region. Further analysis revealed that 33 kDa (MSP-1(33)) fragment of the MSP-1(42) was highly polymorphic with pi nucleotide diversity 0.0290+/-0.0007S.D. The dN-dS for this region of MSP-1 was also positive (0.0114+/-0.0071S.E.). On the other hand, there was no non-synonymous mutation in the 19 kDa (MSP-1(19)) fragment of the MSP-1(42) and thus it was highly conserved. In conclusion, MSP-1(33) fragment was highly polymorphic and appeared to be under diversifying selection whereas there was no selection at MSP-1(19) region among the isolates. Present study will be helpful for the development of PvMSP-1 based vaccine against P. vivax malaria.

The type and mysorensis forms of the Anopheles stephensi (Diptera: Culicidae) in India exhibit identical ribosomal DNA ITS2 and domain-3 sequences

Anopheles (Cellia) stephensi Liston 1901 is one of the major malaria vectors in the Indian subcontinent, Iran, and the Middle East. Three races in this species, namely A. stephensi stephensi (type form), A. stephensi variety mysorensis, and A. stephensi intermediate form, have earlier been reported by several investigators. We describe here the sequencing of the ribosomal DNA internal transcribed spacer 2 (ITS2) and domain-3 (D3) loci of the A. stephensi type and variety mysorensis forms. We also sequenced field-collected adult specimens of this mosquito from three different regions of India. Both forms of A. stephensi showed identical ITS2 and D3 sequences. We did not find any intraspecies sequence variation among the 70 specimens sequenced in this study. In contrast to the eight ITS2 haplotypes observed among Iranian A. stephensi population, we found only one ITS2 haplotype in India. This is the first time to our knowledge that the sequence of the D3 locus of A. stephensi is being reported here. In conclusion, the type and variety mysorensis forms of A. stephensi exhibit identical nucleotide sequences at their ITS2 and D3 loci.

Cellular immune responses to recombinant Plasmodium vivax tryptophan-rich antigen (PvTRAg) among individuals exposed to vivax malaria

Plasmodium vivax, the most widespread species of human malaria parasite responsible for 70–80 million cases each year requires a vaccine. In recent years, many potential vaccine candidate antigens have been identified from P. vivax including PvTRAg. We describe here cellular immune response to recombinant PvTRAg expressed in Escherichia coli. The in vitro stimulation of PBMCs derived from P. vivax‐exposed individuals (n = 16) showed strong proliferative response (SI > 2·2) to PvTRAg as compared to PBMCs from normal healthy controls (n = 8). Although both Th1 (IFN‐γ, TNF‐α and IL‐12) and Th2 (IL‐4 and IL‐10) cytokines were secreted by the PBMCs of the P. vivax‐exposed individuals in response to PvTRAg, the overall response was more inclined towards Th2. In conclusion, recombinant PvTRAg was found to elicit strong cellular immune response among the P. vivax‐exposed individuals.