Abstract
The eradication of Plasmodium parasites, responsible for malaria, is a daunting global public health task. It requires a comprehensive approach that addresses symptomatic, asymptomatic, and submicroscopic cases. Overcoming this challenge relies on harnessing the power of molecular diagnostic tools, as traditional methods like microscopy and rapid diagnostic tests fall short in detecting low parasitaemia, contributing to the persistence of malaria transmission. By precisely identifying patients of all types and effectively characterizing malaria parasites, molecular tools may emerge as indispensable allies in the pursuit of malaria elimination. Furthermore, molecular tools can also provide valuable insights into parasite diversity, drug resistance patterns, and transmission dynamics, aiding in the implementation of targeted interventions and surveillance strategies. In this review, we explore the significance of molecular tools in the pursuit of malaria elimination, shedding light on their key contributions and potential impact on public health.
Similar content being viewed by others
Data availability
No datasets were generated or analysed during the current study.
References
WHO World malaria report 2022 12/01/2023]; https://www.who.int/teams/global-malaria-programme/reports/world-malaria-report-2022
Muppidi P et al (2023) Diagnosis of cerebral malaria: tools to reduce Plasmodium falciparum associated mortality. Front Cell Infect Microbiol 13:1090013
WHO (2014) Severe malaria. Trop Med Int Health 19(Suppl 1):7–131
Miller LH et al (2002) The pathogenic basis of malaria. Nature 415(6872):673–679
Magallon-Tejada A et al (2016) Cytoadhesion to gC1qR through Plasmodium Falciparum Erythrocyte Membrane Protein 1 in severe Malaria. PLoS Pathog 12(11):e1006011
Gupta H, Wassmer SC (2021) Harnessing the potential of miRNAs in Malaria Diagnostic and Prevention. Front Cell Infect Microbiol 11:793954
Martianez-Vendrell X et al (2022) Factors affecting the performance of HRP2-Based Malaria Rapid Diagnostic tests. Trop Med Infect Dis, 7(10)
Galatas B, Bassat Q, Mayor A (2016) Malaria parasites in the Asymptomatic: looking for the Hay in the Haystack. Trends Parasitol 32(4):296–308
Chen I et al (2016) Asymptomatic malaria: a chronic and debilitating infection that should be treated. PLoS Med 13(1):e1001942
Naing C et al (2022) Detection of asymptomatic malaria in Asian countries: a meta-analysis of diagnostic accuracy. Malar J 21(1):50
Gupta H et al (2018) Drug-resistant polymorphisms and copy numbers in Plasmodium Falciparum, Mozambique, 2015. Emerg Infect Dis 24(1):40–48
Gupta H et al (2020) Effect of mass dihydroartemisinin-piperaquine administration in southern Mozambique on the carriage of molecular markers of antimalarial resistance. PLoS ONE 15(10):e0240174
Gupta H et al (2017) Molecular surveillance of pfhrp2 and pfhrp3 deletions in Plasmodium Falciparum isolates from Mozambique. Malar J 16(1):416
Galatas B et al (2020) Field performance of ultrasensitive and conventional malaria rapid diagnostic tests in southern Mozambique. Malar J 19(1):451
Mobegi VA et al (2014) Genome-wide analysis of selection on the malaria parasite Plasmodium Falciparum in West African populations of differing infection endemicity. Mol Biol Evol 31(6):1490–1499
Simam J et al (2018) Gene copy number variation in natural populations of Plasmodium Falciparum in Eastern Africa. BMC Genomics 19(1):372
Schaffner SF et al (2018) hmmIBD: software to infer pairwise identity by descent between haploid genotypes. Malar J 17(1):196
Spanakos G et al (2018) Genetic spatiotemporal anatomy of Plasmodium Vivax Malaria episodes in Greece, 2009–2013. Emerg Infect Dis 24(3):541–548
Patel JC et al (2014) Genetic evidence of importation of drug-resistant Plasmodium falciparum to Guatemala from the Democratic Republic of the Congo. Emerg Infect Dis 20(6):932–940
Daniels RF et al (2020) Evidence for reduced Malaria Parasite Population after Application of Population-Level Antimalarial Drug Strategies in Southern Province, Zambia. Am J Trop Med Hyg 103(2Suppl):66–73
Amir A et al (2018) Diagnostic tools in childhood malaria. Parasit Vectors 11(1):53
Amexo M et al (2004) Malaria misdiagnosis: effects on the poor and vulnerable. Lancet 364(9448):1896–1898
Das S et al (2018) Performance of an ultra-sensitive Plasmodium Falciparum HRP2-based rapid diagnostic test with recombinant HRP2, culture parasites, and archived whole blood samples. Malar J 17(1):118
Vernelen K et al (2018) Photo-based External Quality Assessment of Malaria rapid diagnostic tests in a non-endemic setting. PLoS ONE 13(8):e0201622
Roth JM et al (2016) Molecular malaria diagnostics: a systematic review and meta-analysis. Crit Rev Clin Lab Sci 53(2):87–105
Gavina K et al (2017) A sensitive species-specific reverse transcription real-time PCR method for detection of Plasmodium Falciparum and Plasmodium Vivax. Parasite Epidemiol Control 2(2):70–76
Varo R et al (2021) Diagnosis of clinical malaria in endemic settings. Expert Rev Anti Infect Ther 19(1):79–92
Mercereau-Puijalon O, Barale JC, Bischoff E (2002) Three multigene families in Plasmodium parasites: facts and questions. Int J Parasitol 32(11):1323–1344
Steenkeste N et al (2009) Towards high-throughput molecular detection of Plasmodium: new approaches and molecular markers. Malar J 8:86
Lazrek Y et al (2023) Molecular detection of human Plasmodium species using a multiplex real time PCR. Sci Rep 13(1):11388
Lucchi NW et al (2010) Real-time fluorescence loop mediated isothermal amplification for the diagnosis of malaria. PLoS ONE 5(10):e13733
Kersting S et al (2014) Rapid detection of Plasmodium falciparum with isothermal recombinase polymerase amplification and lateral flow analysis. Malar J 13:99
Schneider R et al (2021) Validation of a novel FRET real-time PCR assay for simultaneous quantitative detection and discrimination of human Plasmodium parasites. PLoS ONE 16(6):e0252887
Mens PF et al (2012) Direct blood PCR in combination with nucleic acid lateral flow immunoassay for detection of Plasmodium species in settings where malaria is endemic. J Clin Microbiol 50(11):3520–3525
Souza SS et al (2018) Photo-Induced Electron transfer real-time PCR for detection of Plasmodium Falciparum plasmepsin 2 Gene Copy Number. Antimicrob Agents Chemother, 62(8)
Cheng Z et al (2015) Capture and Ligation Probe-PCR (CLIP-PCR) for Molecular Screening, with application to active Malaria Surveillance for Elimination. Clin Chem 61(6):821–828
Hofmann N et al (2015) Ultra-sensitive detection of Plasmodium falciparum by amplification of multi-copy subtelomeric targets. PLoS Med 12(3):e1001788
Demas A et al (2011) Applied genomics: data mining reveals species-specific malaria diagnostic targets more sensitive than 18S rRNA. J Clin Microbiol 49(7):2411–2418
Lucchi NW et al (2012) A new single-step PCR assay for the detection of the zoonotic malaria parasite Plasmodium Knowlesi. PLoS ONE 7(2):e31848
Gupta H et al (2016) New molecular detection methods of malaria parasites with multiple genes from genomes. Acta Trop 160:15–22
Cunningham CH et al (2021) A novel CRISPR-based malaria diagnostic capable of Plasmodium detection, species differentiation, and drug-resistance genotyping. EBioMedicine 68:103415
Rao PN et al (2016) A method for Amplicon Deep Sequencing of Drug Resistance Genes in Plasmodium Falciparum Clinical isolates from India. J Clin Microbiol 54(6):1500–1511
Silva M et al (2022) Plasmodium Falciparum Drug Resistance genes pfmdr1 and pfcrt in vivo Co-expression during artemether-lumefantrine therapy. Front Pharmacol 13:868723
Nsanzabana C et al (2018) Tools for surveillance of anti-malarial drug resistance: an assessment of the current landscape. Malar J 17(1):75
Gupta H et al (2015) Categorical complexities of Plasmodium Falciparum malaria in individuals is associated with genetic variations in ADORA2A and GRK5 genes. Infect Genet Evol 34:188–199
da Silva C et al (2023) Targeted and whole-genome sequencing reveal a north-south divide in P. Falciparum drug resistance markers and genetic structure in Mozambique. Commun Biol 6(1):619
Smith-Aguasca R et al (2019) Mosquitoes as a feasible sentinel group for anti-malarial resistance surveillance by Next Generation sequencing of Plasmodium Falciparum. Malar J 18(1):351
Taylor SM et al (2013) Pooled deep sequencing of Plasmodium Falciparum isolates: an efficient and scalable tool to quantify prevailing malaria drug-resistance genotypes. J Infect Dis 208(12):1998–2006
Telele NF et al (2018) Pretreatment drug resistance in a large countrywide Ethiopian HIV-1 C cohort: a comparison of Sanger and high-throughput sequencing. Sci Rep 8(1):7556
Gruenberg M et al (2019) Amplicon deep sequencing improves Plasmodium Falciparum genotyping in clinical trials of antimalarial drugs. Sci Rep 9(1):17790
Beckmann JS, Estivill X, Antonarakis SE (2007) Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability. Nat Rev Genet 8(8):639–646
McCarroll SA, Altshuler DM (2007) Copy-number variation and association studies of human disease. Nat Genet 39(7 Suppl):S37–42
Cheeseman IH et al (2009) Gene copy number variation throughout the Plasmodium falciparum genome. BMC Genomics 10:353
Gresham D et al (2006) Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science 311(5769):1932–1936
Dharia NV et al (2009) Use of high-density tiling microarrays to identify mutations globally and elucidate mechanisms of drug resistance in Plasmodium Falciparum. Genome Biol 10(2):R21
Cheeseman IH et al (2016) Population structure Shapes Copy Number Variation in Malaria parasites. Mol Biol Evol 33(3):603–620
Kidgell C et al (2006) A systematic map of genetic variation in Plasmodium Falciparum. PLoS Pathog 2(6):e57
Witkowski B et al (2017) A surrogate marker of piperaquine-resistant Plasmodium Falciparum malaria: a phenotype-genotype association study. Lancet Infect Dis 17(2):174–183
Amato R et al (2017) Genetic markers associated with dihydroartemisinin-piperaquine failure in Plasmodium Falciparum malaria in Cambodia: a genotype-phenotype association study. Lancet Infect Dis 17(2):164–173
Gil JP, Krishna S (2017) pfmdr1 (Plasmodium Falciparum multidrug drug resistance gene 1): a pivotal factor in malaria resistance to artemisinin combination therapies. Expert Rev Anti Infect Ther 15(6):527–543
Srisutham S et al (2021) Measurement of gene amplifications related to drug resistance in Plasmodium falciparum using droplet digital PCR. Malar J 20(1):120
Fassbinder-Orth CA (2014) Methods for quantifying gene expression in ecoimmunology: from qPCR to RNA-Seq. Integr Comp Biol 54(3):396–406
Sepulveda N et al (2018) Global analysis of Plasmodium Falciparum histidine-rich protein-2 (pfhrp2) and pfhrp3 gene deletions using whole-genome sequencing data and meta-analysis. Infect Genet Evol 62:211–219
Beshir KB et al (2017) Plasmodium Falciparum parasites with histidine-rich protein 2 (pfhrp2) and pfhrp3 gene deletions in two endemic regions of Kenya. Sci Rep 7(1):14718
Flannery EL et al (2015) Next-generation sequencing of Plasmodium Vivax patient samples shows evidence of direct evolution in drug-resistance genes. ACS Infect Dis 1(8):367–379
Beghain J et al (2016) Plasmodium copy number variation scan: gene copy numbers evaluation in haploid genomes. Malar J 15:206
Sonden K et al (2015) Asymptomatic Multiclonal Plasmodium falciparum infections carried through the dry season Predict Protection against subsequent clinical Malaria. J Infect Dis 212(4):608–616
Pumpaibool T et al (2009) Genetic diversity and population structure of Plasmodium Falciparum in Thailand, a low transmission country. Malar J 8:155
Meyer CG et al (2002) Genetic diversity of Plasmodium Falciparum: asexual stages. Trop Med Int Health 7(5):395–408
Arnott A, Barry AE, Reeder JC (2012) Understanding the population genetics of Plasmodium Vivax is essential for malaria control and elimination. Malar J 11:14
Ingasia LA et al (2016) Genetic variability and population structure of Plasmodium Falciparum parasite populations from different malaria ecological regions of Kenya. Infect Genet Evol 39:372–380
Ghansah A et al (2014) Monitoring parasite diversity for malaria elimination in sub-saharan Africa. Science 345(6202):1297–1298
Mohd Abd Razak MR et al (2016) Genetic diversity of Plasmodium falciparum populations in Malaria Declining Areas of Sabah, East Malaysia. PLoS ONE 11(3):e0152415
Chenet SM et al (2012) Local population structure of Plasmodium: impact on malaria control and elimination. Malar J 11:412
Huijben S et al (2020) Counter-selection of Antimalarial Resistance polymorphisms by intermittent preventive treatment in pregnancy. J Infect Dis 221(2):293–303
Sundararaman SA et al (2013) Plasmodium falciparum-like parasites infecting wild apes in southern Cameroon do not represent a recurrent source of human malaria. Proc Natl Acad Sci U S A 110(17):7020–7025
Lin JT et al (2015) Using Amplicon Deep Sequencing To Detect Genetic Signatures of Plasmodium Vivax Relapse. J Infect Dis 212(6):999–1008
Levitt B et al (2017) Overlap extension barcoding for the Next Generation sequencing and genotyping of Plasmodium Falciparum in Individual patients in Western Kenya. Sci Rep 7:41108
Lerch A et al (2017) Development of amplicon deep sequencing markers and data analysis pipeline for genotyping multi-clonal malaria infections. BMC Genomics 18(1):864
Hathaway NJ et al (2018) SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing. Nucleic Acids Res 46(4):e21
Assefa SA et al (2014) estMOI: estimating multiplicity of infection using parasite deep sequencing data. Bioinformatics 30(9):1292–1294
Lerch A et al (2019) Longitudinal tracking and quantification of individual Plasmodium falciparum clones in complex infections. Sci Rep 9(1):3333
Tusting LS et al (2014) Measuring changes in Plasmodium Falciparum transmission: precision, accuracy and costs of metrics. Adv Parasitol 84:151–208
Hay SI, Smith DL, Snow RW (2008) Measuring malaria endemicity from intense to interrupted transmission. Lancet Infect Dis 8(6):369–378
Lyimo BM et al (2022) Potential opportunities and challenges of deploying Next Generation sequencing and CRISPR-Cas systems to Support Diagnostics and Surveillance towards Malaria Control and Elimination in Africa. Front Cell Infect Microbiol 12:757844
Nabet C et al (2016) Genetic diversity of Plasmodium Falciparum in human malaria cases in Mali. Malar J 15:353
Pothin E et al (2016) Estimating malaria transmission intensity from Plasmodium Falciparum serological data using antibody density models. Malar J 15:79
Baum E et al (2015) Submicroscopic and asymptomatic Plasmodium falciparum and Plasmodium Vivax infections are common in western Thailand - molecular and serological evidence. Malar J 14:95
Cook J et al (2015) Mass screening and treatment on the basis of results of a Plasmodium falciparum-specific rapid diagnostic test did not reduce malaria incidence in Zanzibar. J Infect Dis 211(9):1476–1483
Cordray MS, Richards-Kortum RR (2012) Emerging nucleic acid-based tests for point-of-care detection of malaria. Am J Trop Med Hyg 87(2):223–230
Notomi T et al (2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 28(12):E63
Polley SD et al (2010) Mitochondrial DNA targets increase sensitivity of malaria detection using loop-mediated isothermal amplification. J Clin Microbiol 48(8):2866–2871
Mori Y et al (2001) Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation. Biochem Biophys Res Commun 289(1):150–154
Sirichaisinthop J et al (2011) Evaluation of loop-mediated isothermal amplification (LAMP) for malaria diagnosis in a field setting. Am J Trop Med Hyg 85(4):594–596
Tao ZY et al (2011) Adaptation of a visualized loop-mediated isothermal amplification technique for field detection of Plasmodium Vivax infection. Parasit Vectors 4:115
Tayipto Y et al (2022) Serology for Plasmodium Vivax surveillance: a novel approach to accelerate towards elimination. Parasitol Int 87:102492
Fonseca AM et al (2019) VAR2CSA Serology to detect Plasmodium Falciparum transmission patterns in pregnancy. Emerg Infect Dis 25(10):1851–1860
Kartal L, Mueller I, Longley RJ (2023) Using serological markers for the Surveillance of Plasmodium Vivax Malaria: a scoping review. Pathogens, 12(6)
Morshed MG et al (2007) Molecular methods used in clinical laboratory: prospects and pitfalls. FEMS Immunol Med Microbiol 49(2):184–191
Akoniyon OP et al (2022) Whole genome sequencing contributions and challenges in Disease Reduction focused on Malaria. Biology (Basel), 11(4)
Funding
This work was supported by the Science and Engineering Research Board (SERB), India, under Award Number SRG/2022/000705 (HG). The content is solely the responsibility of the authors and does not necessarily represent the official views of the funders.
Author information
Authors and Affiliations
Contributions
HG and KS conceived the idea. SS, IG, and HG collected the literature. HG and SS generated the first draft of the study. HG, IG, and KS critically reviewed the manuscript. All authors have read and agreed to the published version of the manuscript.
Corresponding author
Ethics declarations
Ethics approval and consent to participate
Not applicable.
Competing interests
The authors declare no competing interests.
Additional information
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Gupta, H., Sharma, S., Gilyazova, I. et al. Molecular tools are crucial for malaria elimination. Mol Biol Rep 51, 555 (2024). https://doi.org/10.1007/s11033-024-09496-4
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s11033-024-09496-4