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1. Additional file 1 of Quantification of parasite clearance in Plasmodium knowlesi infections

Author

T. Thurai Rathnam, Jeyamalar, Grigg, Matthew J., Dini, Saber, William, Timothy, Sakam, Sitti Saimah, Cooper, Daniel J., Rajahram, Giri S., Barber, Bridget E., Anstey, Nicholas M., Haghiri, Ali, Rajasekhar, Megha, and Simpson, Julie A.

Abstract

Additional file1: Figure S1. Example of the traceplot before and after thinning for the population mean parasite clearance rate, $$\gamma$$ γ . Figure S2. Example of the traceplot before and after thinning for the probability of lag and tail phases, $${\pi }^{\ell}$$ π ℓ and $${\pi }^{\tau }$$ π τ . Table S1. Summary statistics for parasite clearance rates (/hour) using WWARN PCE and Bayesian hierarchical modelling methods. Table S2. Estimated parasite clearance rates by antimalarial treatment administered using WWARN PCE and Bayesian hierarchical modelling.

Published
2023
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2. An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples

Author

Adam, Ishag, Alam, Mohammad Shafiul, Alemu, Sisay, Amaratunga, Chanaki, Amato, Roberto, Andrianaranjaka, Voahangy, Anstey, Nicholas M, Aseffa, Abraham, Ashley, Elizabeth, Assefa, Ashenafi, Auburn, Sarah, Barber, Bridget E, Barry, Alyssa, Batista Pereira, Dhelio, Cao, Jun, Chau, Nguyen Hoang, Chotivanich, Kesinee, Chu, Cindy, Dondorp, Arjen M, Drury, Eleanor, Echeverry, Diego F, Erko, Berhanu, Espino, Fe, Fairhurst, Rick, Faiz, Abdul, Fernanda Villegas, María, Gao, Qi, Golassa, Lemu, Goncalves, Sonia, Grigg, Matthew J, Hamedi, Yaghoob, Hien, Tran Tinh, Htut, Ye, Johnson, Kimberly J, Karunaweera, Nadira, Khan, Wasif, Krudsood, Srivicha, Kwiatkowski, Dominic P, Lacerda, Marcus, Ley, Benedikt, Lim, Pharath, Liu, Yaobao, Llanos-Cuentas, Alejandro, Lon, Chanthap, Lopera-Mesa, Tatiana, Marfurt, Jutta, Michon, Pascal, Miotto, Olivo, Mohammed, Rezika, Mueller, Ivo, Namaik-Larp, Chayadol, Newton, Paul N, Nguyen, Thuy-Nhien, Nosten, Francois, Noviyanti, Rintis, Pava, Zuleima, Pearson, Richard D, Petros, Beyene, Phyo, Aung P, Price, Ric N, Pukrittayakamee, Sasithon, Rahim, Awab Ghulam, Randrianarivelojosia, Milijaona, Rayner, Julian C, Rumaseb, Angela, Siegel, Sasha V, Simpson, Victoria J, Thriemer, Kamala, Tobon-Castano, Alberto, Trimarsanto, Hidayat, Urbano Ferreira, Marcelo, Vélez, Ivan D, Wangchuk, Sonam, Wellems, Thomas E, White, Nicholas J, William, Timothy, Yasnot, Maria F, Yilma, Daniel, Alam, Mohammad Shafiul [0000-0001-8330-5499], Ashley, Elizabeth [0000-0002-7620-4822], Barber, Bridget E [0000-0003-1066-7960], Batista Pereira, Dhelio [0000-0002-7761-5498], Chu, Cindy [0000-0001-9465-8214], Dondorp, Arjen M [0000-0001-5190-2395], Echeverry, Diego F [0000-0003-0301-4478], Espino, Fe [0000-0003-1690-1711], Faiz, Abdul [0000-0002-3460-7535], Golassa, Lemu [0000-0002-1216-8711], Grigg, Matthew J [0000-0001-9914-8352], Karunaweera, Nadira [0000-0003-3985-1817], Kwiatkowski, Dominic P [0000-0002-5023-0176], Ley, Benedikt [0000-0002-5734-0845], Miotto, Olivo [0000-0001-8060-6771], Nguyen, Thuy-Nhien [0000-0002-4101-5706], Nosten, Francois [0000-0002-7951-0745], Pearson, Richard D [0000-0002-7386-3566], Phyo, Aung P [0000-0002-0383-9624], Price, Ric N [0000-0003-2000-2874], Rayner, Julian C [0000-0002-9835-1014], Urbano Ferreira, Marcelo [0000-0002-5293-9090], Wellems, Thomas E [0000-0003-3899-8454], Yasnot, Maria F [0000-0001-8081-4212], Yilma, Daniel [0000-0001-6058-2696], and Apollo - University of Cambridge Repository

Subjects
parasitic diseases, Genomics, Genomic Epidemiology, Plasmodium vivax, Malaria, Data Resource
Abstract

This report describes the MalariaGEN Pv4 dataset, a new release of curated genome variation data on 1,895 samples of Plasmodium vivax collected at 88 worldwide locations between 2001 and 2017. It includes 1,370 new samples contributed by MalariaGEN and VivaxGEN partner studies in addition to previously published samples from these and other sources. We provide genotype calls at over 4.5 million variable positions including over 3 million single nucleotide polymorphisms (SNPs), as well as short indels and tandem duplications. This enlarged dataset highlights major compartments of parasite population structure, with clear differentiation between Africa, Latin America, Oceania, Western Asia and different parts of Southeast Asia. Each sample has been classified for drug resistance to sulfadoxine, pyrimethamine and mefloquine based on known markers at the dhfr, dhps and mdr1 loci. The prevalence of all of these resistance markers was much higher in Southeast Asia and Oceania than elsewhere. This open resource of analysis-ready genome variation data from the MalariaGEN and VivaxGEN networks is driven by our collective goal to advance research into the complex biology of P. vivax and to accelerate genomic surveillance for malaria control and elimination.

Published
2022

3. Additional file 1 of Reduced circulating dendritic cells in acute Plasmodium knowlesi and Plasmodium falciparum malaria despite elevated plasma Flt3 ligand levels

Author

Loughland, Jessica R., Woodberry, Tonia, Oyong, Damian, Piera, Kim A., Amante, Fiona H., Barber, Bridget E., Grigg, Matthew J., William, Timothy, Engwerda, Christian R., Anstey, Nicholas M., McCarthy, James S., Boyle, Michelle J., and Minigo, Gabriela

Subjects
parasitic diseases
Abstract

Additional file 1: Figure S1. No significant correlation between plasma Flt3L and peripheral blood pDC or CD1c+ DC in induced blood-stage malaria. Correlations of DC subset numbers and Flt3L concentration on day 0 (left plot), correlation of DC subset numbers and Flt3L concentration at peak infection (middle plot) and correlation of DC subset numbers at peak infection and Flt3L concentration at day 0 (right plot) for A. pDC (red) and B. CD1c+ DCs (green) in volunteer infection studies. Spearman correlation was used and tests were two-tailed and considered significant if p-values

Published
2021
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4. Additional file 2 of Safety, infectivity and immunogenicity of a genetically attenuated blood-stage malaria vaccine

Author

Webster, Rebecca, Sekuloski, Silvana, Odedra, Anand, Woolley, Stephen, Jennings, Helen, Amante, Fiona, Trenholme, Katharine R., Healer, Julie, Cowman, Alan F., Eriksson, Emily M., Sathe, Priyanka, Penington, Jocelyn, Blanch, Adam J., Dixon, Matthew W. A., Tilley, Leann, Duffy, Michael F., Craig, Alister, Storm, Janet, Chan, Jo-Anne, Evans, Krystal, Papenfuss, Anthony T., Schofield, Louis, Griffin, Paul, Barber, Bridget E., Andrew, Dean, Boyle, Michelle J., de Labastida Rivera, Fabian, Engwerda, Christian, and McCarthy, James S.

Abstract

Additional File 2. Supplementary methods and results for immunogenicity assessments of GAP vaccine. Text S1. Methodology for determining antibody mediated immune response to GAP vaccine. Text S2. Methodology for determining cell mediated immune response to GAP vaccine. Table S1. Antibodies used for flow cytometry. Figure S1. The gating strategy used to identify CD4+ T cells and subsets, as well as the expression of T cell activation markers. Figure S2. The anti-MSP2 IgM response over the course of the study in each subject. Figure S3. The IgG and IgM response to whole parasite lysate over the course of the study in each subject. Figure S4. The frequency of CD4+ T cells, Treg cells, Th1 cells and Tfh cells in peripheral blood mononuclear cells over the course of the study in each subject.

Published
2021
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6. Additional file 3 of Safety, infectivity and immunogenicity of a genetically attenuated blood-stage malaria vaccine

Author

Webster, Rebecca, Sekuloski, Silvana, Odedra, Anand, Woolley, Stephen, Jennings, Helen, Amante, Fiona, Trenholme, Katharine R., Healer, Julie, Cowman, Alan F., Eriksson, Emily M., Sathe, Priyanka, Penington, Jocelyn, Blanch, Adam J., Dixon, Matthew W. A., Tilley, Leann, Duffy, Michael F., Craig, Alister, Storm, Janet, Chan, Jo-Anne, Evans, Krystal, Papenfuss, Anthony T., Schofield, Louis, Griffin, Paul, Barber, Bridget E., Andrew, Dean, Boyle, Michelle J., de Labastida Rivera, Fabian, Engwerda, Christian, and McCarthy, James S.

Abstract

Additional File 3. Supplementary methods and results for in vitro assessments of GAP vaccine. Text S1. Methodology for parasite genotyping. Text S2. Methodology for cytoadherence assays. Text S3. Methodology for scanning electron microscopy. Text S4. Methodology for var gene expression analysis. Table S1. Duration of in vitro culture of P. falciparum prior to harvest for RNA extraction for var gene transcription analysis. Text S5. Results of parasite genotyping. Text S6. Results of scanning electron microscopy analysis of parasite-infected erythrocytes. Text S7. Results of cytoadherence assays. Text S8. Results of var gene expression analysis. Table S2. Most abundantly expressed var genes.

Published
2021
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7. Additional file 1 of Development and evaluation of a new Plasmodium falciparum 3D7 blood stage malaria cell bank for use in malaria volunteer infection studies

Author

Woolley, Stephen D., Fernandez, Melissa, Rebelo, Maria, Llewellyn, Stacey A., Marquart, Louise, Amante, Fiona H., Jennings, Helen E., Webster, Rebecca, Trenholme, Katharine, Chalon, Stephan, Joerg J. Moehrle, McCarthy, James S., and Barber, Bridget E.

Abstract

Additional file 1: Table S1. Schedule of events for both studies. Table S2. Growth parameters of the 3D7-MBE-008 pilot bank (n = 2) compared to 3D7 bank using historical data (n = 177). Table S3. Growth parameters of the 3D7-V1 pilot bank (n = 2) compared to 3D7-V2 bank using historical data (n = 177). Table S4. Overall clinical score recorded for each participant during 3D7-MBE-008 study. Table S5. Overall clinical score recorded for each participant during 3D7-V1 study.

Published
2021
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8. Additional file 1 of Safety, infectivity and immunogenicity of a genetically attenuated blood-stage malaria vaccine

Author

Webster, Rebecca, Sekuloski, Silvana, Odedra, Anand, Woolley, Stephen, Jennings, Helen, Amante, Fiona, Trenholme, Katharine R., Healer, Julie, Cowman, Alan F., Eriksson, Emily M., Sathe, Priyanka, Penington, Jocelyn, Blanch, Adam J., Dixon, Matthew W. A., Tilley, Leann, Duffy, Michael F., Craig, Alister, Storm, Janet, Chan, Jo-Anne, Evans, Krystal, Papenfuss, Anthony T., Schofield, Louis, Griffin, Paul, Barber, Bridget E., Andrew, Dean, Boyle, Michelle J., de Labastida Rivera, Fabian, Engwerda, Christian, and McCarthy, James S.

Abstract

Additional File 1. Supplementary methods and results for subject eligibility and safety assessments. Text S1: Subject eligibility criteria. Table S1: Incidence of adverse events by subject. Table S2: Red blood cell alloantibody test results for Cohort 4 and phenotype of donor red blood cells used for GAP master cell bank manufacture.

Published
2021
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