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EVALUATION of MALARIA DIAGNOSTIC METHODS, EFFICACY of ARTEMETHER- LUMEFANTRINE THERAPY and GENETIC DETERMINANTS of Plasmodium Falciparum RESISTANCE

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EVALUATION of MALARIA DIAGNOSTIC METHODS, EFFICACY of ARTEMETHER- LUMEFANTRINE THERAPY and GENETIC DETERMINANTS of Plasmodium Falciparum RESISTANCE i EVALUATION OF MALARIA DIAGNOSTIC METHODS, EFFICACY OF ARTEMETHER- LUMEFANTRINE THERAPY AND GENETIC DETERMINANTS OF Plasmodium falciparum RESISTANCE BY AYOGU, EBERE EMILIA REG. NO: PG/PhD/10/57517 DEPARTMENT OF CLINICAL PHARMACY AND PHARMACY MANAGEMENT, FACULTY OF PHARMACEUTICAL SCIENCES UNIVERSITY OF NIGERIA, NSUKKA A THESIS SUBMITTED TO THE SCHOOL OF POST GRADUATE STUDIES OF THE UNIVERSITY OF NIGERIA, NSUKKA FOR THE AWARD OF DEGREE OF DOCTOR OF PHILOSOPHY (IN CLINICAL PHARMACY) ii CERTIFICATION Ebere Emilia Ayogu, a post graduate student in the Department of Clinical Pharmacy and Pharmacy Management with registration number PG/PhD/10/57517 has satisfactorily completed the requirements for the award of the degree of Doctor of Philosophy in Clinical Pharmacy and Pharmacy Management. The work embodied in this thesis is original and has not been submitted in part or full for any diploma or degree in this or any other University. ------------------------------------------ --------------------------------------- Prof. Chinwe V. Ukwe Prof. J.M. Okonta (Supervisor) (Head of Department) -------------------------------------------- ------------------------------------ Date Date iii DEDICATION This thesis is dedicated to my husband, Hon. Ayogu, Felix Victor who has laid down all necessary resources to see me through my academic pursuit from undergraduate to present. iv ACKNOWLEDGEMENT I am forever grateful to Almighty God who in His infinite goodness granted me bountiful blessings, good health and wisdom through out the period of this research. My sincerest thanks go to my supervisor, Prof Chinwe V. Ukwe for supervising my work in and out of academic sessions. I wish to appreciate my Head of Department, Prof J.M Okonta for his encouragement through out my research period. I also thank Prof C Nze Aguwa for his fatherly advice and encouragement from my under graduate days to present. I am indebted to Dr Emmanuel Nna, CEO Safety Molecular Pathology Laboratory (SMPL) for providing a standard molecular laboratory where all investigations were carried out and for statistically analyzing my results. I also thank all the staff of SMPL for their dedicated contributions to the successful completion of all molecular testing. I am very grateful to the staff of District Hospital Nsukka, Bishop Shanahan Annex, Enugu Ezike and Cottage Hospital Ugbuawka for allowing me access to the clinic and patients and in a special way the Laboratory Scientist that helped me in sample collection. This study would not have been feasible without the patients that consented to participate. I thank them all especially those who completed their follow up visits. I can not conclude without mentioning the untiring efforts of my senior colleague, Dr (Mrs) Petra Nnamani, for accepting me as a sister and leaving her doors open for me even at odd times. I also want to appreciate my professional colleagues and staff in the Department of Clinical Pharmacy and Pharmacy Management for their support. My warmest regard goes to my parents, Sir Titus and Dame Augustina Omeh, my siblings Ngo, Agidi, Equi, Chia, Bukas and Emebroda for being there for me in times of difficulty and happiness. I am also grateful to my brother in-law Hon Kentus Eze, for providing a comfortable accommodation for me through out my stay in Enugu. Finally, to my kids, NG, Dudu, Mimi, Onyi, Neche and my sister-in-law Amaka. I acknowledge your love and patience especially through out the numerous weeks I was absent from home. To Rev. Frs Norbet Attah and Christopher Ugwuta for their prayers and Mr Kenneth Ugwu, I say thanks a lot. To all others who in one way or the other contributed to the success of this work I say may God reward them all. v LIST OF ABBREVIATIONS ABBREVIATIONS MEANINGS A + T Adenine + Thymine AA Amino acids A-A Artesunate-amodiaquine AAH+ Protonated Amino acids ACPR Adequate clinical and parasitological response ACR Adequate clinical response ACTs Artemisinin Combination Therapies AFLPD Amplified fragment length polymorphism detection AL Artemether-lumefantrine Ala/Phe Alanine/Phenylalanine ALRTI Acute lower respiratory tract infection ALS Amyotrophic lateral sclerosis Arg Arginine ART Artemisinin Asn/Thr Asparagine/Threonine ASO Allele specific oligonucleotide BCRR Basic case reproduction rate CD Chlorproguanil- dapsone CD36 Cluster of differentiation 36 cDNA Complimentary DNA CNV Copy number variation CQ Chloroquine CQH+ Protonated Chloroquine CQR Chloroquine – resistant CQS Chloroquine - sensitive Cys Cystein DARC Duffy antigen receptor for chemokines dATP Deoxyriboadenosine triphosphate vi dCTP Deoxyribocytosine triphosphate dGTP Deoxyriboguanine triphosphate DHA Dihydro-artemisinin DHFR Dihydrofolate reductase DHP Dihydropteroate DHPPP 2-amino-4-hydroxy-6- hydroxymethyl-7, 8 dihydropteridine pyrophosphate DHPS Dihydropteroate synthase dNTPs Deoxyribonuclease triphosphates dTTP Deoxyribotyrosine triphosphate DV Digestive vacuole EANMAT East African Network for Monitoring Antimalarial Treatment ECs Endothelial cells EEO Electro-endosmosis EIR Entomological inoculation rate ETF Early treatment failure G + C Guanine + Cytosine G6PD Glucose-6-phosphate dehydrogenase gDNA Genomic DNA GFI Genotype failure index Glu Glutamine Gly Glycine GPI Glycosylphosphatidylinositol Hb Hemoglobin HIV Human immuno-virus HLA Human leukocyte antigen HRP II Histidine rich protein II ICAM-1 Intercellular Adhesion Molecule 1 IE Infected erythrocyte IIe Iso-leucine IPA Isopropanol-acetic acid IPT Intermittent preventive treatment iRBC Infected red blood cell IRS Indoor residual spraying ITNs Insecticide treated nets vii LCF Late clinical failure LD Linkage disequilibrium Leu Leucine LTF Late treatment failure MDGs Millennium Development Goals MLP Multi-locus probe MQ Mefloquine mRNA messenger RNA MSP Merozoite surface proteins msp 1 and 2 Merozoites surface protein 1 and 2 NNATP Nigerian National Antimalarial Treatment Policy NO Nitric oxide npcRNAs Non protein-coding RNAs NPV Negative predictive values NSPM Non-synonymous point mutations p-ABA p-aminobenzoic acid PCR Polymerase chain reaction PCT Parasite clearance time PfATPase b Plasmodium falciparum adenosine triphosphatase b Pfcrt Plasmodium falciparum chloroquine resistance transporter, PFGE Pulsed field gel electrophoresis Pfmdr 1 Plasmodium falciparum multidrug resistant gene1 Pgh1 P-glycoprotein homologue 1 pLDH Plasmodium enzyme lactate dehydrogenase PPM Parasite plasma membrane PPV Positive predictive values PVM Parasitophorous vacuolar membrane QN Quinine RAPD Random amplified polymorphic detection RBM Roll Back Malaria RDT Rapid diagnostic test RFLP Restriction fragment length polymorphism RNA Ribo nucleic acid SAO South-East Asian ovalocytosis viii SDS Sodium docecyl sulphate SERCA2+ Sarco/endoplasmic reticulum Ca2+ SGOT Serum glutamic oxaloacetic transaminase SLP Single locus probe SMPL Safety Molecular Pathology Laboratory SNPs Single nucleotide polymorphisms snRNAs Small nucleolar RNAs SOD1 Superoxide dismutase 1 SP Sulfadoxine – pyrimethamine TAREs Telomere-associated repetitive elements TE Tris EDTA THF Tetrahydrofolate Thr/Ser Threonine/Serine Tm Melting temperature tRNA Transport RNA TV Transport vesicles UNICEF United Nation International Children Emergency Fund UNTH University of Nigeria Teaching Hospital UTL Useful therapeutic life UV Ultraviolet Val Valine WHO World Health Organization ix LIST OF FIGURES Figure 1.1: Lifecycle of Plasmodium falciparum- - - - - - 7 Figure 1.2: The pathophysiology of P. falciparum infection - - - - 16 Figure 1.3: The process of DNA amplification by PCR, showing denaturation, annealing and extension - - - - - - - - - - - 61 Figure 1.4: The process of DNA amplification and quantification by Real Time PCR - - 64 Figure 2.1: Preparation of 2 % agarose gel - - - - - - - 89 x LIST OF TABLES Table 1.1: Degree of exposure and pattern of host morbidity - - - - - 25 Table 2.1: Course of AL treatment - - - - - - - - 78 Table 2.2 Classification of Treatment responses based on PCT- - - - - 85 Table 2.3 Classification of treatment responses based on therapeutic efficacy- - - 86 Table 3.1: Patients’ characteristics - - - - - - - - 98 Table 3.2: Comparison of RDT with microscopy - - - - - - 99 Table 3.3: Comparison of RDT with PCR - - - - - - - 100 Table 3.4: Comparison of microscopy with PCR - - - - - - 101 Table 3.5: Cost and turn around time of diagnostic methods - - - - - 102 Table 3.6: Temperature distributions among patients on follow days - - - - 103 Table 3.7: Mean parasite densities on follow up days - - - - - - 104 Table 3.8: Classification of treatment outcome based on parasite clearance time - - 105 Table 3.9: Clinical and parasitological PCR uncorrected responses on days 14 post treatment - 106 Table 3.10: Clinical and parasitological PCR uncorrected responses on days 28 post treatment - 107 Table 3.11: Distribution of mean parasite clearance time among patients’ characteristics - 108 Table 3.12: Parasite clearance time and treatment outcome - - - - - 109 Table 3.13: Polymorphic gene investigated, mutation sites, primer sequences, PCR conditions and restriction enzymes - - - - - - - - - 110 Table 3.14: Frequencies of Pfmdr 1 mutations and co-mutations among the patients and their restriction enzymes - - - - - - - - - 111 Table 3.15: Comparison of prevalence of Pfmdr1 mutations in patients with sensitivity, mild, moderate and severe resistance - - - - - - - - 112 Table 3.16: Comparison of prevalence of Pfmdr 1 mutations in patients that failed treatment and those that responded to treatment- - - - - - -
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