Dr
Vito Baraka
Current Organisation
NIMR
Current Job Title
Research Scientist
Biography
Publications
INTRODUCTION:Herpes Simplex virus type 2 (HSV-2) infection is associated with an increased risk of human immunodeficiency virus type 1 (HIV-1) acquisition and transmission. Individuals co-infected with HIV-1 and HSV-2 may have longer lasting, more frequent and severe outbreaks of herpes symptoms. Previous studies have assessed HSV-2 seroprevalence and associated risk factors in adult populations. However, there is limited data on the HSV-2 seroprevalence among adolescents and youth living with HIV-1. The study aimed to determine the HSV-2 seroprevalence and associated risk factors among adolescents and youth living with HIV-1 at referral hospital setting in Northern Tanzania. METHODOLOGY:A cross-sectional survey was conducted between February and July 2017 among HIV-1-infected individuals aged 10-24 years attending the Child -Centred Family Care Clinic at Kilimanjaro Christian Medical Centre. Blood specimens from 180 individuals were collected for ELISA-based detection of HSV-2 antibodies. Associations between risk factors and HSV-2 seroprevalence were analysed by univariate and multivariate logistic regression models. RESULTS:The overall HSV-2 seroprevalence was 18% (32/180). A significant HSV-2 seroprevalence was noted among adolescents and youth, who reported having had sexual intercourse than those who never had sexual intercourse (28.9% vs 13.3%, p = 0.02). Youths aged 20-24 had six folds higher risk of HSV-2 seroprevalence compared to those aged 10-14 years (AOR = 5.97 95% CI 1.31 - 27.19, p = 0.02). CONCLUSIONS:Our study found that HSV-2 seroprevalence increased by age among adolescents and youth living with HIV-1. Age-specific approaches might play an important role in interventions targeting HSV-2 infection.
BACKGROUND:Day 7 plasma lumefantrine concentration is suggested as a predictor for malaria treatment outcomes and a cut-off of ≥ 200 ng/ml is associated with day 28 cure rate in the general population. However, day 7 lumefantrine plasma concentration can be affected by age, the extent of fever, baseline parasitaemia, and bodyweight. Therefore, this study assessed the usefulness of day 7 lumefantrine plasma concentration as a predictor of malaria treatment outcome in under-fives children treated with generic or innovator drug-containing artemether-lumefantrine (ALu) in Tanzania. METHODS:This study was nested in an equivalence prospective study that aimed at determining the effectiveness of a generic ALu (Artefan®) in comparison with the innovator's product (Coartem®). Children with uncomplicated malaria aged 6-59 months were recruited and randomized to receive either generic or innovator's product. Children were treated with ALu as per World Health Organization recommendations. The clinical and parasitological outcomes were assessed after 28 days of follow up. PCR was performed to distinguish recrudescence and re-infections among children with recurrent malaria. Analysis of day 7 lumefantrine plasma concentration was carried out using a high-performance liquid chromatographic method with UV detection. RESULTS:The PCR corrected cure rates were 98.7% for children treated with generic and 98.6% for those treated with the innovator product (p = 1.00). The geometric mean (± SD) of day 7 plasma lumefantrine concentration was 159.3 (± 2.4) ng/ml for the generic and 164 (± 2.5) ng/ml for the innovator groups, p = 0.87. Geometric mean (± SD) day 7 lumefantrine plasma concentration between cured and recurrent malaria was not statistically different in both treatment arms [158.5 (± 2.4) vs 100.0 (± 1.5) ng/ml, (p = 0.28) for generic arm and 158.5 (± 2.3) vs 251.2 (± 4.2) ng/ml, (p = 0.24) for innovator arm]. Nutritional status was found to be a determinant of recurrent malaria (adjusted hazardous ratio (95% confidence interval) = 3(1.1-8.2), p = 0.029. CONCLUSION:Using the recommended cut-off point of ≥ 200 ng/ml, day 7 plasma lumefantrine concentration failed to predict malaria treatment outcome in children treated with ALu in Tanzania. Further studies are recommended to establish the day 7 plasma lumefantrine concentration cut-off point to predict malaria treatment outcome in children.
Background. Sub-Saharan Africa has the highest burden of malaria in the world. Artemisinin-based combination therapies (ACTs) have been the cornerstone in the efforts to reduce the global burden of malaria. In the effort to facilitate early detection of resistance for artemisinin derivatives and partner drugs, WHO recommends monitoring of ACT’s efficacy in the malaria endemic countries. The present systematic meta-analysis study summarises the evidence of therapeutic efficacy of the commonly used artemisinin-based combinations for the treatment of uncomplicated P. falciparum malaria in Sub-Saharan Africa after more than a decade since the introduction of the drugs.
Methods.Fifty two studies carried out from 2010 to 2020 on the efficacy of artemether-lumefantrine or dihydro-artemisinin piperaquine or artesunate amodiaquine in patients with uncomplicated P. falciparum malaria in Sub-Saharan Africa were searched for using the Google Scholar, Cochrane Central Register of controlled trials (CENTRAL), PubMed, Medline, LILACS, and EMBASE online data bases. Data was extracted by two independent reviewers. Random analysis effect was performed in STATA 13. Heterogeneity was established using I2 statistics.
Results.Based on per protocol analysis, unadjusted cure rates in malaria infected patients treated with artemether-lumefantrine (ALU), artesunate-amodiaquine (ASAQ) and dihydroartemisinin-piperaquine (DHP) were 89%, 94% and 91% respectively. However, the cure rates after PCR correction were 98% for ALU, 99% for ASAQ and 99% for DHP.
Conclusion.The present meta-analysis reports the overall high malaria treatment success for artemether-lumefantrine, artesunate-amodiaquine and dihydroartemisinin-piperaquine above the WHO threshold value in Sub-Saharan Africa.
Background. It has been more than 20 years since the malaria epidemiologic shift to school-aged children was noted. In the meantime, school-aged children (5–15 years) have become increasingly more vulnerable with asymptomatic malaria prevalence reaching up to 70%, making them reservoirs for subsequent transmission of malaria in the endemic communities. Intermittent Preventive Treatment of malaria in schoolchildren (IPTsc) has proven to be an effective tool to shrink this reservoir. As of 3rd June 2022, the World Health Organization recommends IPTsc in moderate and high endemic areas. Even so, for decision-makers, the adoption of scientific research recommendations has been stifled by real-world implementation challenges. This study presents methodology, challenges faced, and mitigations used in the evaluation of the implementation of IPTsc using dihydroartemisinin-piperaquine (DP) in three councils (Handeni District Council (DC), Handeni Town Council (TC) and Kilindi DC) of Tanga Region, Tanzania so as to understand the operational feasibility and effectiveness of IPTsc on malaria parasitaemia and clinical malaria incidence.
Methods. The study deployed an effectiveness-implementation hybrid design to assess feasibility and effectiveness of IPTsc using DP, the interventional drug, against standard of care (control). Wards in the three study councils were the randomization unit (clusters). Each ward was randomized to implement IPTsc or not (control). In all wards in the IPTsc arm, DP was given to schoolchildren three times a year in four-month intervals. In each council, 24 randomly selected wards (12 per study arm, one school per ward) were chosen as representatives for intervention impact evaluation. Mixed design methods were used to assess the feasibility and acceptability of implementing IPTsc as part of a more comprehensive health package for schoolchildren. The study reimagined an existing school health programme for Neglected Tropical Diseases (NTD) control include IPTsc implementation.
Results. The study shows IPTsc can feasibly be implemented by integrating it into existing school health and education systems, paving the way for sustainable programme adoption in a cost-effective manner.
Conclusions. Through this article other interested countries may realise a feasible plan for IPTsc implementation. Mitigation to any challenge can be customized based on local circumstances without jeopardising the gains expected from an IPTsc programme. Trial registration clinicaltrials.gov, NCT04245033. Registered 28 January 2020, https://clinicaltrials.gov/ct2/show/NCT04245033
Background
. Tanzania started a countrywide lymphatic filariasis elimination programme in 2000 adopting the mass drug administration (MDA) strategy. The drug used for the programme was the combination of ivermectin and albendazole. However, there is limited information on the current epidemiological trend of the infections, where MDA implementation is ongoing. The present study aimed at assessing the current status of Bancroftian filariasis infection rate and morbidity where MDA has been distributed and administered for over eight rounds.
Methodology
. The study was a cross-sectional descriptive study involving 272 individuals (>18 years) from endemic communities in Tanga region where MDA has been implemented. Clinical, sociodemographic, and circulating filarial antigen (CFA) test was undertaken using immune chromatographic card test according to the manufacturer's instructions.
Results
. A total of 472 individuals were screened: 307/472 (65.1%) were males while 165/472 (34.9%) were females. The overall prevalence of CFA was 5.51%, that of hydrocoele was 73.2%, and that of lymphoedema was 16.0%. The prevalence of hydrocoele combined with lymphoedema was 5.5%.
Conclusion
. Our findings demonstrate a considerable reduction in filarial infection. However, there is clear evidence of ongoing transmission despite the 8 rounds of MDA. It is unlikely that the annual MDA would interrupt filarial transmission; therefore, additional strategies are needed to accelerate lymphatic filariasis control and elimination.
BACKGROUND:Malaria in pregnancy increases the risk of deleterious maternal and birth outcomes. The use of ≥ 3 doses of sulfadoxine-pyrimethamine (SP) for intermittent preventive treatment of malaria (IPTp-SP) is recommended for preventing the consequences of malaria during pregnancy. This study assessed the effect of IPTp-SP for prevention of malaria during pregnancy in low transmission settings. METHODS:A cross-sectional study that involved consecutively selected 1161 pregnant women was conducted at Mwananyamala regional referral hospital in Dar es Salaam. Assessment of the uptake of IPTp-SP was done by extracting information from antenatal clinic cards. Maternal venous blood, cord blood, placental blood and placental biopsy were collected for assessment of anaemia and malaria. High performance liquid chromatography with ultraviolet detection (HPLC-UV) was used to detect and quantify sulfadoxine (SDX). Dried blood spots (DBS) of placental blood were collected for determination of sub-microscopic malaria using polymerase chain reaction (PCR). RESULTS:In total, 397 (34.2%) pregnant women reported to have used sub-optimal doses (≤ 2) while 764 (65.8%) used optimal doses (≥ 3) of IPTp-SP at the time of delivery. The prevalence of placental malaria as determined by histology was 3.6%. Submicroscopic placental malaria was detected in 1.4% of the study participants. Women with peripheral malaria had six times risk of maternal anaemia than those who were malaria negative (aOR, 5.83; 95% CI 1.10-30.92; p = 0.04). The geometric mean plasma SDX concentration was 10.76 ± 2.51 μg/mL. Sub-optimal IPTp-SP dose was not associated with placental malaria, premature delivery and fetal anaemia. The use of ≤ 2 doses of IPTp-SP increased the risk of maternal anaemia by 1.36-fold compared to ≥ 3 doses (aOR, 1.36; 95% CI 1.04-1.79; p = 0.02). CONCLUSION:The use of < 2 doses of IPTp-SP increased the risk of maternal anaemia. However, sub-optimal doses (≤ 2 doses) were not associated with increased the risk of malaria parasitaemia, fetal anaemia and preterm delivery among pregnant women in low malaria transmission setting. The use of optimal doses (≥ 3 doses) of IPTp-SP and complementary interventions should continue even in areas with low malaria transmission.
Background
Aedes aegypti (Diptera: Culicidae) is the main vector of the dengue virus globally. Dengue vector control is mainly based on reducing the vector population through interventions, which target potential breeding sites. However, in Tanzania, little is known about this vector's habitat productivity and insecticide susceptibility status to support evidence-based implementation of control measures. The present study aimed at assessing the productivity and susceptibility status of A. aegypti mosquitoes to pyrethroid-based insecticides in Dar es Salaam, Tanzania.
Methods
An entomological assessment was conducted between January and July 2015 in six randomly selected wards in Dar es Salaam, Tanzania. Habitat productivity was determined by the number of female adult A. aegypti mosquitoes emerged per square metre. The susceptibility status of adult A. aegypti females after exposure to 0.05% deltamethrin, 0.75% permethrin and 0.05% lambda-cyhalothrin was evaluated using the standard WHO protocols. Mortality rates were recorded after 24 h exposure and the knockdown effect was recorded at the time points of 10, 15, 20, 30, 40, 50 and 60 min to calculate the median knockdown times (KDT
50
and KDT
95
).
Results
The results suggest that disposed tyres had the highest productivity, while water storage tanks had the lowest productivity among the breeding habitats Of A. aegypti mosquitoes. All sites demonstrated reduced susceptibility to deltamethrin (0.05%) within 24 h post exposure, with mortalities ranging from 86.3 ± 1.9 (mean ± SD) to 96.8 ± 0.9 (mean ± SD). The lowest and highest susceptibilities were recorded in Mikocheni and Sinza wards, respectively. Similarly, all sites demonstrated reduced susceptibility permethrin (0.75%) ranging from 83.1 ± 2.1% (mean ± SD) to 96.2 ± 0.9% (mean ± SD), in Kipawa and Sinza, respectively. Relatively low mortality rates were observed in relation to lambda-cyhalothrin (0.05%) at all sites, ranging from 83.1 ± 0.7 (mean ± SD) to 86.3 ± 1.4 (mean ± SD). The median KDT
50
for deltamethrin, permethrin and lambda-cyhalothrin were 24.9-30.3 min, 24.3-34.4 min and 26.7-32.8 min, respectively. The KDT
95
were 55.2-90.9 min for deltamethrin, 54.3-94.6 min for permethrin and 64.5-69.2 min for lambda-cyhalothrin.
Conclusions
The productive habitats for A. aegypti mosquitoes found in Dar es Salaam were water storage containers, discarded tins and tyres. There was a reduced susceptibility of A. aegypti to and emergence of resistance against pyrethroid-based insecticides. The documented differences in the resistance profiles of A. aegypti mosquitoes warrants regular monitoring the pattern concerning resistance against pyrethroid-based insecticides and define dengue vector control strategies.
Artemether-lumefantrine (AL) and artesunate-amodiaquine (AS-AQ) are the most commonly used artemisinin-based combination therapies (ACT) for treatment of
Plasmodium falciparum
in Africa. Both treatments remain efficacious, but single nucleotide polymorphisms (SNPs) in the
Plasmodium falciparum
multidrug resistance 1 (
Pfmdr1
) gene may compromise sensitivity. AL and AS-AQ exert opposing selective pressures: parasites with genotype 86Y, Y184 and 1246Y are partially resistant to AS-AQ treatment, while N86, 184 F and D1246 are favoured by AL treatment. Through a systematic review, we identified 397 surveys measuring the prevalence of
Pfmdr1
polymorphisms at positions 86 184 or 1246 in 30 countries in Africa. Temporal trends in SNP frequencies after introduction of AL or AS-AQ as first-line treatment were analysed in 32 locations, and selection coefficients estimated. We examined associations between antimalarial policies, consumption, transmission intensity and rate of SNP selection. 1246Y frequency decreased on average more rapidly in locations where national policy recommended AL (median selection coefficient(
s
) of -0.083), compared with policies of AS-AQ or both AL and AS-AQ (median
s
=-0.035 and 0.021, p<0.001 respectively). 86Y frequency declined markedly after ACT policy introduction, with a borderline significant trend for a more rapid decline in countries with AL policies (p=0.055). However, these trends could also be explained by a difference in initial SNP frequencies at the time of ACT introduction. There were non-significant trends for faster selection of N86 and D1246 in areas with higher AL consumption and no trend with transmission intensity. Recorded consumption of AS-AQ was low in the locations and times
Pfmdr1
data were collected. SNP trends in countries with AL policies suggest a broad increase in sensitivity of parasites to AS-AQ, by 7-10 years after AL introduction. Observed rates of selection have implications for planning strategies to cycle drugs or use multiple first-line therapies to maintain drug efficacy.
Despite increased malaria control efforts, school-aged children (5-14 years) have higher a malaria prevalence compared to children under-five. In high-transmission settings, up to 70% of school-aged children harbour malaria parasitaemia and therefore contribute significantly to the reservoir for transmission. A systematic review was performed to explore the correlation between the malaria parasite carriage in pregnant women and school-aged children living in similar endemic settings of sub Saharan Africa to inform strategies to improve targeted malaria control. In order to obtain data on malaria prevalence in pregnant women and school-aged children living in the same endemic setting, we searched the Malaria in Pregnancy Library, PubMed, Cochrane library and Web of Science in December 2018. We fit a fixed effect model to obtain a pooled risk ratio (PRR) of malaria in school-aged children versus pregnant women and used Poisson regression to estimate risk ratios in school-aged children for every increase in prevalence in pregnant women. We used data from six (out of 1096) sources that included 10 data points. There was a strong linear relation between the prevalence of malaria infection in pregnant women and school-aged children (
r
= 0·93,
p
< 0·0001). School-aged children were nearly twice at risk to carry parasites compared to pregnant women (RR = 1.95, 95% CI: 1·69-2.25,
p
< 0.01). Poisson regression showed that a 1% increase in prevalence of malaria infection in pregnant women was significantly associated with increase in risk in school-aged children by 4%. Malaria infection prevalence in school-aged children is strongly correlated with the prevalence in pregnant women living in the same community, and may be considered as alternative indicators to track temporal and spatial trends in malaria transmission intensity. Chemoprevention strategies targeting school-aged children should be explored to reduce malaria burden and transmission in school-aged children and its potential impact on communities.
MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000
Plasmodium falciparum
samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed. Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.
The emergence of resistance against artemisinin combination treatment is a major concern for malaria control. ACTs are recommended as the rescue treatment, however, there is limited evidence as to whether treatment and re-treatment with ACTs select for drug-resistant P. falciparum parasites. Thus, the purpose of the present study is to investigate the impact of (re-)treatment using artesunate-amodiaquine (ASAQ) and artemether-lumefantrine (AL) on the selection of P. falciparum multidrug resistance-1 (Pfmdr1) alleles in clinical settings.P. falciparum positive samples were collected from children aged 12-59 months in a clinical trial in DR Congo and Uganda. Pfmdr1 single nucleotide polymorphisms (SNPs) analysis at codons N86Y, Y184F, and D1246Y were performed at baseline and post-treatment with either AL or ASAQ as a rescue treatment using nested PCR followed by restriction fragment length polymorphism (RFLP) assays.The pre-treatment prevalence of Pfmdr1 N86 and D1246Y varied significantly between the sites, (p>0.001) and (p = 0.013), respectively. There was borderline significant directional selection for Pfmdr1 184F in recurrent malaria infections after treatment with AL in Uganda site (p = 0.05). Pfmdr1 NFD haplotype did not significantly change in post-treatment infections after re-treatment with either AL or ASAQ. Comparison between pre-treatment and post-treatment recurrences did not indicate directional selection of Pfmdr1 N86, D1246 alleles in the pre-RCT, RCT and post-RCT phases in both AL and ASAQ treatment arms. Pfmdr1 86Y was significantly associated with reduced risk of AL treatment failure (RR = 0.34, 95% CI:0.11-1.05, p = 0.04) while no evidence for D1246 allele (RR = 1.02; 95% CI: 0.42-2.47, p = 1.0). Survival estimates showed that the Pfmdr1 alleles had comparable mean-time to PCR-corrected recrudescence and new infections in both AL and ASAQ treatment arms.We found limited impact of (re-)treatment with AL or ASAQ on selection for Pfmdr1 variants and haplotypes associated with resistance to partner drugs. These findings further supplement the evidence use of same or alternative ACTs as a rescue therapy for recurrent P.falciparum infections. Continued monitoring of genetic signatures of resistance is warranted to timely inform malaria (re-)treatment policies and guidelines.
Background
Quinine or alternative artemisinin-based combination treatment (ACT) is the recommended rescue treatment for uncomplicated malaria. However, patients are often re-treated with the same ACT though it is unclear whether this is the most suitable approach. We assessed the efficacy and safety of re-treating malaria patients with uncomplicated failures with the same ACT used for the primary episode, compared with other rescue treatments.
Methods
This was a bicentre, open-label, randomised, three-arm phase 3 trial done in Lisungi health centre in DR Congo, and Kazo health centre in Uganda in 2012-14. Children aged 12-60 months with recurrent malaria infection after treatment with the first-line ACT were randomly assigned to either re-treatment with the same first-line ACT, an alternative ACT, which were given for 3 days, or quinine-clindamycin (QnC), which was given for 5-7 days, following a 2:2:1 ratio. Randomisation was done by computer-generated randomisation list in a block design by country. The three treatment groups were assumed to have equivalent efficacy above 90%. Both the research team and parents or guardians were aware of treatment allocation. The primary outcome was the proportion of patients with an adequate clinical and parasitological response (ACPR) at day 28, in the per-protocol population. This trial was registered under the numbers NCT01374581 in ClinicalTrials.gov and PACTR201203000351114 in the Pan African Clinical Trials Registry.
Findings
From May 22, 2012, to Jan 31, 2014, 571 children were included in the trial. 240 children were randomly assigned to the re-treatment ACT group, 233 to the alternative ACT group, and 98 to the QnC group. 500 children were assessed for the primary outcome. 71 others were not included because they did not complete the follow-up or PCR genotyping result was not conclusive. The ACPR response was similar in the three groups: 91·4% (95% CI 87·5-95·2) for the re-treatment ACT, 91·3% (95% CI 87·4-95·1) for the alternative ACT, and 89·5% (95% CI 83·0-96·0) for QnC. The estimates for rates of malaria recrudescence in the three treatment groups were similar (log-rank test: χ
2
=0·22, p=0·894). Artemether-lumefantrine was better tolerated than QnC (p=0·0005) and artesunate-amodiaquine (p<0·0001) in the modified intention-to-treat analysis. No serious adverse events were observed. The most common adverse events reported in the re-treatment ACT group were anorexia (31 [13%] of 240 patients), asthenia (20 [8%]), coughing (16 [7%]), abnormal behaviour (13 [5%]), and diarrhoea (12 [5%]). Anorexia (13 [6%] of 233 patients) was the most frequently reported adverse event in the alternative ACT group. The most commonly reported adverse events in the QnC group were anorexia (12 [12%] of 98 patients), abnormal behaviour (6 [6%]), asthenia (6 [6%]), and pruritus (5 [5%]).
Interpretation
Re-treatment with the same ACT shows similar efficacy as recommended rescue treatments and could be considered for rescue treatment for Plasmodium falciparum malaria. However, the effect of this approach on the selection of resistant strains should be monitored to ensure that re-treatment with the same ACT does not contribute to P falciparum resistance.
Funding
Fonds Wetenschappelijk Onderzoek, Vlaamse Interuniversitaire Raad-Universitaire Ontwikkelings Samenwerking, European and Developing Countries Clinical Trials Partnership, and the Belgian Technical Cooperation-Programme d'Etudes et d'Expertises-in the Democratic Republic of Congo.
Background:In high transmission settings, up to 70% of school-aged children harbour malaria parasites without showing any clinical symptoms. Thus, epidemiologically, school aged children act as a substantial reservoir for malaria transmission. Asymptomatic Plasmodium infections induce inflammation leading to iron deficiency anaemia. Consequently, anaemia retards child growth, predisposes children to other diseases and reduces cognitive potential that could lead to poor academic performance. School aged children become increasingly more vulnerable as compared to those aged less than five years due to delayed acquisition of protective immunity. None of the existing Intermittent Preventive Treatment (IPT) strategies is targeting school-aged children. Here, we describe the study protocol of a clinical trial conducted in north-eastern Tanzania to expand the IPT by assessing the effectiveness and safety of two antimalarial drugs, Dihydroartemisinin-Piperaquine (DP) and Artesunate-Amodiaquine (ASAQ) in preventing malaria related morbidities in school-aged children (IPTsc) living in a high endemic area. Methods/design:The trial is a phase IIIb, individual randomized, open label, controlled trial enrolling school children aged 5-15 years, who receive either DP or ASAQ or control (no drug), using a "balanced block design" with the "standard of care" arm as reference. The interventional treatments are given three times a year for the first year. A second non-interventional year will assess possible rebound effects. Sample size was estimated to 1602 school children (534 per group) from selected primary schools in an area with high malaria endemicity. Thick and thin blood smears (to measure malaria parasitaemia using microscope) were obtained prior to treatment at baseline, and will be obtained again at month 12 and 20 from all participants. Haemoglobin concentration using a haemoglobinometer (HemoCue AB, Sweden) will be measured four monthly. Finger-prick blood (dried bloodspot-DBS) prepared on Whatman 3 M filter paper, will be used for sub-microscopic malaria parasite detection usingPCR, detect markers of drug resistance (using next generation sequencing (NGS) technology), and malaria serological assays (using enzyme-linked immunosorbent assay, ELISA). To determine the benefit of IPTsc on cognitive and psychomotor ability test of everyday attention for children (TEA-Ch) and a '20 m Shuttle run' respectively, will be conducted at baseline, month 12 and 20. The primary endpoints are change in mean haemoglobin from baseline concentration and reduction in clinical malaria incidence at month 12 and 20 of follow up. Mixed design methods are used to assess the acceptability, cost-effectiveness and feasibility of IPTsc as part of a more comprehensive school children health package. Statistical analysis will be in the form of multilevel modelling, owing to repeated measurements and clustering effect of participants. Discussion:Malaria intervention using IPTsc strategy may be integrated in the existing national school health programme. However, there is limited systematic evidence to assess the effectiveness and operational feasibility of this approach. School-aged children are easily accessible in most endemic malaria settings. The evidence from this study will guide the implementation of the strategy to provide complementary approach to reduce malaria related morbidity, anaemia and contribute to the overall burden reduction. Trial registration:Clinicaltrials.gov: NCT03640403, registered on Aug 21, 2018, prospectively registered.Url https://www.clinicaltrials.gov/ct2/show/NCT03640403?term=NCT03640403&rank=1.
Project Title
Genetic profiling of drug resistance and population structure of plasmodium falciparum using high-throughput next generation sequencing
EDCTP Project
TMA2018CDF-2398
EDCTP Program
EDCTP2
EDCTP Project Call
Career Development Fellowship (CDF)
Host Organisation
| Department | Institution | Country |
|---|---|---|
| National Institute for Medical Research - Tanzania (NIMR) | TZ |
Project Objectives
Broad Objective. To leverage the use of next generation sequencing to monitor the spread of genetic signatures of resistance and track the evolutionary origin of Plasmodium falciparum infections Specific Objectives 1. To establish and assess ex vivo sensitivity of clinical P. falciparum isolates to lumefantrine, amodiaquine, chloroquine, piperaquine, and dihydroartemisinin. 2. To characterize the allele frequencies and prevalence of P. falciparum background mutation associated with the emergence of artemisinin resistance (multidrug resistance protein 2 (mdr2), ferredoxin (fd) and apicoplast ribosomal protein S10 (arps10)) 3. To investigate the proportion of the P. falciparum plasmepsin 2-3 (Pfpm2-3) copy number variation 4. To determine the temporal prevalence and distribution of Pfkelch 13 mutations associated with artemisinin resistance and partner drugs (pfcrt, pfmdr1, Pfdhfr, Pfdhps, adaptor protein complex 2 mu subunit (pfap2mu) and ubiquitin specific protease 1 (pfubp1)) using high throughput next generation sequencing technology. 5. To characterize genetic structure of P. falciparum populations and elucidate geographic origin of infections using molecular barcodes 6. To strengthen capacity in next generation sequencing technologies and bioinformatics in the context of molecular surveillance of antimalarial drug resistance
Study Design
Observational
Project Summary
Dr. Vito Baraka of the National Institute for Medical Research (NIMR), Tanzania in collaboration with researchers at the University of Kinshasa, and Ministry of Health DR Congo and Institut de Recherche en Sciences de la Santé (IRSS), Burkina Faso and University of Strasbourg, France aim to use high-throughput next generation sequencing to determine genetic profiles of drug resistance and population structure of Plasmodium falciparum. The emergence and spread of Plasmodium falciparum resistance present major threat for malaria control and elimination efforts. Recently, report suggest de novo emergence of drug resistance in the region (Rwanda and Uganda). Thus, molecular monitoring of drug resistance is considered important for the detection and tracking of drug-resistant parasites. The recent advancement in next generation sequencing (NGS) facilitates cost-effective high-throughput detection of resistance and the origin of parasite populations with different genetic backgrounds. This is relevant for monitoring antimalarial drug resistance and tracking the geographic spread of parasite populations. We are leveraging the use NGS-based approaches to determine molecular markers of resistance to both artemisinin and partner drugs, parasite genetic diversity, and population structure in African settings. Retrospective and prospective dried blood spot samples from study sites in Tanzania, Burkina Faso, the Democratic Republic of the Congo (DRC) will be used for the study. The detection of molecular markers of drug resistance will be carried out using a “TSARA” technique, a high-throughput NGS platform based on Miseq (Illumina®-based technology) sequencing for determination of the SNPs associated with drug resistance to artemisinin combination therapies (ACTs). Following pooled PCR amplification of the targeted parasite gene sequences and indexing PCR, pooled gene fragments will be sequenced using the Illumina Miseq® platform. We have demonstrated in DRC the occurrence of mutations in PfKelch13 (R561H and P441L) known to be associated with the partial artemisinin resistance, manifested as delayed parasite clearance. Our data suggests that PfKelch13 mutations is spreading in the regions bordering Rwanda where the first report in Africa were documented. At present, PfKelch13 mutations have been confirmed in East African countries, Tanzania, Eritrea and Uganda. These are first report of occurrence of Pf kelch 13 mutations in DR Congo, one of the countries with the highest malaria burden in the region. The mutations are validated and have been shown to be associated with delayed clearance in clinical trials and therefore these findings are likely to have significance in the parasite clearance rate and hence clinical treatment outcomes. Decreased parasite clearance due to PfKelch13 mutations will impact malaria case management and control in the region. The finding highlights the need to urgently implement resistance mitigation strategies to deter the spread of artemisinin partial resistance in the region. https://www.nimr.or.tz/bio/?smid=2588