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131 results for “P. falciparum”
(Fastq Files) Amplicon sequencing of ama1 and mdr1 to track within-host P. falciparum diversity in Kilifi, KENYA
<p>These data were generated from amplicon sequencing of <em>Plasmodium falciparum</em> <em>ama1 </em>and<em> </em><em>mdr1</em> genes in samples collected from Kilifi, at the coast of Kenya.</p> <p>The two papers that reference these data will soon be included here:</p> <ol> <li> The Journal of Infectious Diseases - https://doi.org/10.1093/infdis/jiac144</li> <li>Wellcome Open Research - https://wellcomeopenresearch.org/articles/7-95</li> </ol> <p>Two objectives were explored:</p> <ol> <li>To determine temporal changes in the genetic diversity of malaria parasites in asymptomatic and febrile infections.</li> <li>To track within-host parasite diversity, throughout treatment in a clinical drug trial.</li> </ol>
Detection of novel P. falciparum haplotypes under treatment pressure in pediatric severe malaria
<p>The dataset contains Amplicon sequencing data targeting three <em>Plasmodium falciparum</em> polymorphic markers—<em>cpmp</em>, <em>cpp</em>, and <em>ama1</em>. These markers were analyzed to investigate the association between parasite clearance rate and the multiplicity of infection in Beninese children undergoing treatment for severe malaria.</p>
(Extended Data) Amplicon deep sequencing of ama1 and mdr1 to track within-host P. falciparum diversity throughout treatment in a clinical drug trial
<p>These extended data accompany the manuscript: Targeted Amplicon deep sequencing of ama1 and mdr1 to track within-host <em>P. falciparum</em> diversity throughout treatment in a clinical drug trial</p> <p><strong>Table S1: Concentration ratios and resulting parasitemia in artificial dna mixtures of P. falciparum Lab Isolates 3D7 and Dd2.</strong> This table presents the parasitemia for the artificial mixtures of P. falciparum lab isolates 3D7 and Dd2. Each mixture was prepared at varying ratios of 3D7 to Dd2, starting from equal proportions to a complete presence of only 3D7. The original concentration of each isolate was approximately 50,000 parasites per microliter (pf/μl), and the table displays the proportion of each strain in the mixture and the resulting total parasitemia concentration.</p> <p><strong>Table S2. List of PCR and deep sequencing primers.</strong> This table shows the list of forward and reverse primers used for deep sequencing. In boldface are the MID tags, while in the regular face are the forward primers</p> <p><strong>Table S3. The relative frequencies of each ama1 variant and the number of samples with each variant.</strong> The relative frequencies (%) of the 33 AMA1 variants in pre-and post-treatment samples (n = 330) are shown as a 33 amino acid sequence. The frequencies were calculated by dividing the number of reads of each microhaplotype by the total number of reads obtained per sample (116,187,131).</p> <p><strong>Table S4. Distribution of microhaplotypes among samples.</strong> This table shows the occurrence of microhaplotypes across all participants, both with monoclonal and multiclonal ama1 infections. It presents the ama1 clonality – monoclonal or multiclonal (column 1) - participant IDs (column 2), microhaplotype IDs (column 3), and the relative frequencies of these microhaplotypes across timepoints from 0 to 1008 hours (day 42) (column 3). Dashes represent time points where microhaplotypes were missing or were not detected.</p> <p><strong>Table S5. Distribution of rare microhaplotypes among samples.</strong> This table shows the occurrence of rare microhaplotypes in various samples. It presents participant IDs (column 1), microhaplotype IDs (column 2), and the relative frequencies of these microhaplotypes across time points from 0 to 1008 hours (day 42) (column 3). Samples containing rare microhaplotypes - specifically from PID10, PID32, PID38, PID40, PID49, PID60, PID63, and PID65 - are shown in orange, along with the corresponding rare microhaplotypes and their time points of occurrence. Furthermore, participants are categorised by shared microhaplotypes to indicate instances of rarity and commonality. Except for one microhaplotype unique to PID30, rare microhaplotypes were detected in several samples, frequently exceeding a 5% relative frequency. Dashes represent time points where microhaplotypes were missing or were not detected.</p> <p><strong>Table S6. The parasitemia levels associated with each ama1 microhaplotype per timepoint.</strong> This table shows the parasitemia for each ama1 microhaplotype per timepoint and each participant. “Patient ID” represents the patient ID, “AMA1 COI at 0h” represents the complexity of infection (COI) for each participant at baseline, based on ama1 while subsequent columns represent the parasitemia for each ama1 microhaplotype from timepoint 0h to 1008h. Parasitemia was back-calculated using the COI and total parasitemia for each time point. For time points with a COI > 1, parasitemia for the respective ama1 microhaplotypes are separated by commas, cells in red indicate timepoints without sequencing data (ND = not determined). In contrast, cells in grey indicate time points where microhaplotypes were detected below 10 parasites/μl, hence at risk of falling below the sampling limit.</p> <p><strong>Figure S1. Performance of AmpSeq in the sequencing controls.</strong> Six aliquots were prepared for each control set to ensure sufficient control data in case of PCR or sequencing failure. The median read depth in the lab controls was 5,658 (range 4,310 – 12,603) and 704 (291 – 1,676). The x-axis represents the aliquot identifier across the five mixtures, starting from 1 to 6, while the y-axis represents the proportions of each variant across all aliquots. For ama1 (A), two variants (3D7 and Dd2) were detected, whereas in mdr1 (B), two variants were detected YY, FY and NY following amplification of Dd2 Copy I, Dd2 Copy II and 3D7, respectively. For ama1, sequencing failed for aliquot 6 of control set 1, while for mdr1, sequencing failed for aliquot 2 and 6 of control set 3, aliquots 1 and 6 of control set 4 and aliquots 1 and 5 of control set 5. Under the mdr1 control set 4, the Dd2 copy II (86F, 184Y) was not identified, possibly due to having very low concentrations that were not picked up in this aliquot. Based on our control mixtures, the minimum variant frequency we could detect was 5%.</p> <p><strong>Figure S2. Heatmaps of the successfully PCR amplified and sequenced samples for ama1 (A) and mdr1 (B).</strong> The rows represent the study participants, while the columns represent time in hours. Successfully sequenced samples are shown in blue, those that failed PCR are shown in red and those that failed sequencing are in black. The timepoint “ Rec” represents unscheduled visits where a recurrent sample was collected. The unshaded areas with "-" are time points where samples were not collected. For each time point, the number of samples successfully sequenced (n Successful) is indicated in the last row of each panel. The table in panel C shows the groupings of samples based on parasitemia, high (> 5,000), moderate (100-5,000) and low (< 100 parasites per microlitre). Many samples collected between 0h-12h had high parasitemia, samples collected between 18h–30h had moderate parasitemia, while samples collected after 30h were primarily of low parasitemia.</p> <p><strong>Figure S3. The mean complexity of infection (COI) by AMA1 throughout treatment.</strong> The mean COI (red diamonds) appeared to be stable (between 1.5 - 2) from baseline (0h) up to 72h and thereafter fluctuated due to the small sample sizes (<5) in the post-treatment samples. The black dots represent the COI per sample.</p> <p> </p>
Two mosquito salivary antigens demonstrate promise as biomarkers of recent exposure to P. falciparum-infected mosquito bites
<p>Measuring malaria transmission intensity using the traditional entomological inoculation rate is difficult. Antibody responses to mosquito salivary proteins such as SG6 have previously been used as biomarkers of exposure to <em>Anopheles</em> mosquito bites. Here, we investigate four mosquito salivary proteins as potential biomarkers of human exposure to mosquitoes infected with <em>P. falciparum</em>: mosGILT, SAMPSP1, AgSAP, and AgTRIO. We tested population-level human immune responses in longitudinal and cross-sectional plasma samples from subjects with known <em>P. falciparum</em> infection from low and moderate transmission areas in Senegal using a multiplexed magnetic bead-based assay. AgSAP and AgTRIO were the best indicators of recent exposure to infected mosquitoes, with antibody responses to AgSAP in a moderate endemic area, and to AgTRIO in both low and moderate endemic areas, significantly higher than healthy non-endemic control cohort (p-values = 0.0245, 0.0064, and <0.0001 respectively). No antibody responses significantly differed between the low and moderate transmission area, or between equivalent groups during and outside the malaria transmission seasons. For AgSAP and AgTRIO, reactivity peaked 2-4 weeks after clinical <em>P. falciparum</em> infection and declined 3 months after infection. Reactivity to both AgSAP and AgTRIO peaked after infection and did not differ seasonally nor between areas of low and moderate transmission, suggesting reactivity is due to exposure to infectious mosquitos or recent biting rather than general mosquito exposure. Kinetics suggest reactivity is relatively short-lived. AgSAP and AgTRIO are promising candidates to incorporate into multiplexed assays for serosurveillance of population-level changes in <em>P. falciparum</em>-infected mosquito exposure.</p>
PfRH5-induced human monoclonal antibodies show broadly neutralizing activity in P. falciparum clinical isolates
<p>Vaccines to the <em>Plasmodium falciparum </em>reticulocyte binding-like protein homolog 5 (PfRH5) target the blood stage of the parasite's life cycle. PfRH5 has the potential to trigger the production of strain-transcendent antibodies and has proven its efficacy both in pre-clinical and early clinical studies. Vaccine-induced monoclonal antibodies (mAbs) to PfRH5 showed promising outcomes in cultured <em>P. falciparum </em>strains from distinct geographic areas. Here, we assessed the functional impact of vaccine-induced mAbs to PfRH5 on the genetically more complex <em>P. falciparum </em>clinical isolates. We used mAbs isolated from single-cell sorted B-cells of volunteers enrolled in the phase 1a (NCT02181088) clinical trial of the viral-vectored PfRH5 vaccine and used ex-vivo growth inhibition assays (GIA) to assess their efficacy in <em>P. falciparum </em>clinical isolates. Next-generation sequencing (NGS) was used to assess the breadth of genetic diversity in <em>P. falciparum </em>clinical isolates and to infer the genotype/phenotype relationship involved in antibody susceptibility. We showed a dose-dependent inhibition of clinical isolates with three main GIA groups, high, medium, and low. Except for one isolate, our data shows no significant differences in antibody GIA profile between the <em>P. falciparum </em>clinical isolates and the 3D7 reference strain, which harbours the vaccine allele. We observed an additive relationship, where the combination of GIA-low and GIA-medium antibodies resulted in increased GIA activities, having important implications for the contribution of specific monoclonal antibodies in polyclonal IgG responses. While our NGS analysis showed the occurrence of novel mutations in the <em>pfrh5 </em>gene, these mutations were predicted to have little or no functional impact on the antigen's structure or recognition by known mAbs. Our present findings complement earlier reports on the strain transcendent potential of mAbs to PfRH5 and constitute, to our knowledge, the first report on the susceptibility of <em>P. falciparum </em>clinical isolates from natural infections to vaccine-induced mAbs to PfRH5.</p>
A randomized clinical trial to compare P. falciparum gametocytaemia and infectivity following blood-stage or mosquito bite induced controlled malaria infection
<p>For malaria elimination efforts, it is important to better understand parasite transmission to mosquitoes and to develop models to allow early clinical evaluation of transmission-blocking interventions. We previously described a Controlled Human Malaria Infection protocol for induction of gametocytemia in malaria naïve volunteers by mosquito bite (CHMI-trans) (Reuling et al., 2018). Here, we compared gametocyte production and infectivity in the CHMI-trans model after bites of <em>Plasmodium falciparum (Pf)- </em>infected mosquitoes to that after intravenous administration of <em>Pf-</em>infected-erythrocytes. Volunteers received (sub) curative treatments with gametocyte-permissive piperaquine or sulfadoxine-pyrimethamine. Blood-stage inoculation induced considerably higher gametocyte densities compared to mosquito bitesthat was predicted by <em>Pf</em>AP2-G transcripts indicative of gametocyte commitment, and resulted in <em>Pf</em>-positive mosquito infections in 9/12 volunteers versus 0/12 volunteers after mosquito bite inoculation. Current findings firmly establish the CHMI-trans with intravenous administration of asexual parasites as a model for early clinical evaluation of interventions that aim to interrupt <em>Pf</em>-transmission.</p>
Efficacy of RTS,S/AS01 Vaccine Against Episodes of Malaria Due to P. Falciparum Infection in Children.
ClinicalTrials.gov study NCT00380393. IPD Sharing: YES. Countries: 2. Publications: 7.
A Study to Find the Minimum Inhibitory Concentration of KAE609 in Adult Male Patients With P. Falciparum Monoinfection
ClinicalTrials.gov study NCT01836458. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Reducing the Risk of P. Vivax After Falciparum Infections in Co-endemic Areas
ClinicalTrials.gov study NCT03916003. IPD Sharing: YES. Countries: 3. Publications: 2.
Pyronaridine Artesunate 3:1 Granule Formulation vs. Coartem© Crushed Tablets in P. Falciparum Malaria Pediatric Patients
ClinicalTrials.gov study NCT00541385. IPD Sharing: Not stated. Countries: 8. Publications: 4.
A Community Setting Study of Malaria After Systematic Treatment of Symptomatic Carriers of P. Falciparum With COA566 (Coartem®)
ClinicalTrials.gov study NCT01256658. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Azithromycin Plus Chloroquine Versus Artemether-Lumefantrine For The Treatment Of Uncomplicated P. Falciparum Malaria In Children In Africa
ClinicalTrials.gov study NCT00677833. IPD Sharing: Not stated. Countries: 5. Publications: 1.
MMV390048 POC in Patients With P. Vivax and P. Falciparum Malaria
ClinicalTrials.gov study NCT02880241. IPD Sharing: NO. Countries: 1. Publications: 1.
Pyronaridine Artesunate (3:1) Versus Coartem® in P Falciparum Malaria Patients
ClinicalTrials.gov study NCT00422084. IPD Sharing: Not stated. Countries: 9. Publications: 4.
Phase II Efficacy Study of Artefenomel & Piperaquine in Adults & Children With P. Falciparum Malaria.
ClinicalTrials.gov study NCT02083380. IPD Sharing: NO. Countries: 7. Publications: 2.
PfRH5-induced human monoclonal antibodies show broadly neutralizing activity in P. falciparum clinical isolates
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Two mosquito salivary antigens demonstrate promise as biomarkers of recent exposure to P. falciparum-infected mosquito bites
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Data from: Quantification of sporozoite expelling by Anopheles mosquitoes infected with laboratory and naturally circulating P. falciparum gametocytes
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A randomized clinical trial to compare P. falciparum gametocytaemia and infectivity following blood-stage or mosquito bite induced controlled malaria infection
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Data from: Blood-stage parasitaemia and age determine Plasmodium falciparum and P. vivax gametocytaemia in Papua New Guinea
A better understanding of human-to-mosquito transmission is crucial to control malaria. In order to assess factors associated with gametocyte carriage, 2083 samples were collected in a cross-sectional survey in Papua New Guinea. Plasmodium species were detected by light microscopy and qPCR and gametocytes by detection of pfs25 and pvs25 mRNA transcripts by reverse-transcriptase PCR (qRT-PCR). The parasite prevalence by PCR was 18.5% for Plasmodium falciparum and 13.0% for P. vivax. 52.5% of all infections were submicroscopic. Gametocytes were detected in 60% of P. falciparum-positive and 51% of P. vivax-positive samples. Each 10-fold increase in parasite density led to a 1.8-fold and 3.3-fold increase in the odds of carrying P. falciparum and P. vivax gametocytes. Thus the proportion of gametocyte positive and gametocyte densities was highest in young children carrying high asexual parasite densities and in symptomatic individuals. Dilution series of gametocytes allowed absolute quantification of gametocyte densities by qRT-PCR and showed that pvs25 expression is 10-20 fold lower than pfs25 expression. Between 2006 and 2010 parasite prevalence in the study site has decreased by half. 90% of the remaining infections were asymptomatic and likely constitute an important reservoir of transmission. However, mean gametocyte densities were low (approx. 1-2 gametocyte/μL) and it remains to be determined to what extent low-density gametocyte positive individuals are infective to mosquitos.
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