15 results on '"Rahim, Awab Ghulam"'
Number of results to display per page
Search Results
2. Lineage-informative microhaplotypes for recurrence classification and spatio-temporal surveillance of Plasmodium vivax malaria parasites.
- Author
-
Siegel, Sasha V., Trimarsanto, Hidayat, Amato, Roberto, Murie, Kathryn, Taylor, Aimee R., Sutanto, Edwin, Kleinecke, Mariana, Whitton, Georgia, Watson, James A., Imwong, Mallika, Assefa, Ashenafi, Rahim, Awab Ghulam, Nguyen, Hoang Chau, Tran, Tinh Hien, Green, Justin A., Koh, Gavin C. K. W., White, Nicholas J., Day, Nicholas, Kwiatkowski, Dominic P., and Rayner, Julian C.
- Subjects
WHOLE genome sequencing ,PLASMODIUM vivax ,PLASMODIUM ,DISEASE relapse ,TREATMENT failure ,MALARIA - Abstract
Challenges in classifying recurrent Plasmodium vivax infections constrain surveillance of antimalarial efficacy and transmission. Recurrent infections may arise from activation of dormant liver stages (relapse), blood-stage treatment failure (recrudescence) or reinfection. Molecular inference of familial relatedness (identity-by-descent or IBD) can help resolve the probable origin of recurrences. As whole genome sequencing of P. vivax remains challenging, targeted genotyping methods are needed for scalability. We describe a P. vivax marker discovery framework to identify and select panels of microhaplotypes (multi-allelic markers within small, amplifiable segments of the genome) that can accurately capture IBD. We evaluate panels of 50–250 microhaplotypes discovered in a global set of 615 P. vivax genomes. A candidate global 100-microhaplotype panel exhibits high marker diversity in the Asia-Pacific, Latin America and horn of Africa (median H
E = 0.70–0.81) and identifies 89% of the polyclonal infections detected with genome-wide datasets. Data simulations reveal lower error in estimating pairwise IBD using microhaplotypes relative to traditional biallelic SNP barcodes. The candidate global panel also exhibits high accuracy in predicting geographic origin and captures local infection outbreak and bottlenecking events. Our framework is open-source enabling customised microhaplotype discovery and selection, with potential for porting to other species or data resources. This work describes an informatic framework to identify multi-allelic markers in the genome of the malaria-causing Plasmodium vivax parasite that can inform on familial relatedness between infections. Spatial and temporal transmission patterns are demonstrated with an example marker set. [ABSTRACT FROM AUTHOR]- Published
- 2024
- Full Text
- View/download PDF
3. Weekly primaquine for radical cure of patients with Plasmodium vivax malaria and glucose-6-phosphate dehydrogenase deficiency
- Author
-
Taylor, Walter R. J., primary, Meagher, Niamh, additional, Ley, Benedikt, additional, Thriemer, Kamala, additional, Bancone, Germana, additional, Satyagraha, Ari, additional, Assefa, Ashenafi, additional, Chand, Krisin, additional, Chau, Nguyen Hoang, additional, Dhorda, Mehul, additional, Degaga, Tamiru S., additional, Ekawati, Lenny L., additional, Hailu, Asrat, additional, Hasanzai, Mohammad Anwar, additional, Naddim, Mohammad Nader, additional, Pasaribu, Ayodhia Pitaloka, additional, Rahim, Awab Ghulam, additional, Sutanto, Inge, additional, Thanh, Ngo Viet, additional, Tuyet-Trinh, Nguyen Thi, additional, Waithira, Naomi, additional, Woyessa, Adugna, additional, Dondorp, Arjen, additional, von Seidlein, Lorenz, additional, Simpson, Julie A., additional, White, Nicholas J., additional, Baird, J. Kevin, additional, Day, Nicholas P., additional, and Price, Ric N., additional
- Published
- 2023
- Full Text
- View/download PDF
4. Lineage-informative microhaplotypes for spatio-temporal surveillance of Plasmodium vivax malaria parasites
- Author
-
Siegel, Sasha V, primary, Amato, Roberto, additional, Trimarsanto, Hidayat, additional, Sutanto, Edwin, additional, Kleinecke, Mariana, additional, Murie, Kathryn, additional, Whitton, Georgia, additional, Taylor, Aimee R, additional, Watson, James A, additional, Imwong, Mallika, additional, Assefa, Ashenafi, additional, Rahim, Awab Ghulam, additional, Chao, Nguyen Hoang, additional, Hien, Tran Tinh, additional, Green, Justin A, additional, Koh, Gavin, additional, White, Nicholas J, additional, Kwiatkowski, Dominic P, additional, Rayner, Julian C, additional, Price, Ric N, additional, and Auburn, Sarah, additional
- Published
- 2023
- Full Text
- View/download PDF
5. Leishmaniasis Epidemiology and Psychosocial Aspect
- Author
-
Rahim, Awab, Ghulam
- Abstract
Leishmaniasis is a neglected tropical and the most important vector-borne disease caused by protozoan parasites of the genus Leishmania, transmitted by female sand-fly vector to the vertebrate host including human, highly correlated with poverty, malnutrition, climate and environmental factors such as crowded living conditions and poor sanitation that affect health, wellbeing, and livelihoods of millions of people around the world. Transmission is complex due to relationships between reservoir hosts, parasites, sand fly vectors, and socio-environmental risk factors. There are various clinical manifestations, ranging from spontaneously healing cutaneous lesions to potentially fatal visceral leishmaniasis caused by different Leishmania species. The psychological long-term manifestations leading to stigmatization, social exclusion, discrimination, and psychosocial impacts, advocating the importance of the One Health approach to combat these diseases effectively.
- Published
- 2023
6. Haematological consequences of acute uncomplicated falciparum malaria: a WorldWide Antimalarial Resistance Network pooled analysis of individual patient data
- Author
-
Mansoor, Rashid, Commons, Robert J, Douglas, Nicholas M, Abuaku, Benjamin, Achan, Jane, Adam, Ishag, Adjei, George O, Adjuik, Martin, Alemayehu, Bereket H, Allan, Richard, Allen, Elizabeth N, Anvikar, Anupkumar R, Arinaitwe, Emmanuel, Ashley, Elizabeth A, Ashurst, Hazel, Asih, Puji BS, Bakyaita, Nathan, Barennes, Hubert, Barnes, Karen I, Basco, Leonardo, Bassat, Quique, Baudin, Elisabeth, Bell, David J, Bethell, Delia, Bjorkman, Anders, Boulton, Caroline, Bousema, Teun, Brasseur, Philippe, Bukirwa, Hasifa, Burrow, Rebekah, Carrara, Verena I, Cot, Michel, D'Alessandro, Umberto, Das, Debashish, Das, Sabyasachi, Davis, Timothy ME, Desai, Meghna, Djimde, Abdoulaye A, Dondorp, Arjen M, Dorsey, Grant, Drakeley, Chris J, Duparc, Stephan, Espie, Emmanuelle, Etard, Jean-Francois, Falade, Catherine, Faucher, Jean Francois, Filler, Scott, Fogg, Carole, Fukuda, Mark, Gaye, Oumar, Genton, Blaise, Rahim, Awab Ghulam, Gilayeneh, Julius, Gonzalez, Raquel, Grais, Rebecca F, Grandesso, Francesco, Greenwood, Brian, Grivoyannis, Anastasia, Hatz, Christoph, Hodel, Eva Maria, Humphreys, Georgina S, Hwang, Jimee, Ishengoma, Deus, Juma, Elizabeth, Kachur, S Patrick, Kager, Piet A, Kamugisha, Erasmus, Kamya, Moses R, Karema, Corine, Kayentao, Kassoum, Kazienga, Adama, Kiechel, Jean-Rene, Kofoed, Poul-Erik, Koram, Kwadwo, Kremsner, Peter G, Lalloo, David G, Laman, Moses, Lee, Sue J, Lell, Bertrand, Maiga, Amelia W, Martensson, Andreas, Mayxay, Mayfong, Mbacham, Wilfred, McGready, Rose, Menan, Herve, Menard, Didier, Mockenhaupt, Frank, Moore, Brioni R, Muller, Olaf, Nahum, Alain, Ndiaye, Jean-Louis, Newton, Paul N, Ngasala, Billy E, Nikiema, Frederic, Nji, Akindeh M, Noedl, Harald, Nosten, Francois, Ogutu, Bernhards R, Ojurongbe, Olusola, Osorio, Lyda, Ouedraogo, Jean-Bosco, Owusu-Agyei, Seth, Pareek, Anil, Penali, Louis K, Piola, Patrice, Plucinski, Mateusz, Premji, Zul, Ramharter, Michael, Richmond, Caitlin L, Rombo, Lars, Rosenthal, Philip J, Salman, Sam, Same-Ekobo, Albert, Sibley, Carol, Sirima, Sodiomon B, Smithuis, Frank M, Some, Fabrice A, Staedke, Sarah G, Starzengruber, Peter, Strub-Wourgaft, Nathalie, Sutanto, Inge, Swarthout, Todd D, Syafruddin, Din, Talisuna, Ambrose O, Taylor, Walter R, Temu, Emmanuel A, Thwing, Julie I, Tinto, Halidou, Tjitra, Emiliana, Toure, Offianan A, Tran, T Hien, Ursing, Johan, Valea, Innocent, Valentini, Giovanni, van Vugt, Michele, von Seidlein, Lorenz, Ward, Stephen A, Were, Vincent, White, Nicholas J, Woodrow, Charles J, Yavo, William, Yeka, Adoke, Zongo, Issaka, Simpson, Julie A, Guerin, Philippe J, Stepniewska, Kasia, Price, Ric N, Roper, Cally, Resistance, WorldWide Antimalarial, WorldWide Antimalarial Resistance Network Falciparum Haematology Study Group, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Epidémiologie des Maladies Chroniques en zone tropicale (EpiMaCT), CHU Limoges-Institut d'Epidémiologie Neurologique et de Neurologie Tropicale-Institut National de la Santé et de la Recherche Médicale (INSERM)-OmégaHealth (ΩHealth), Université de Limoges (UNILIM)-Université de Limoges (UNILIM), Group, WorldWide Antimalarial Resistance Network Falciparum Haematology Study, Mansoor, R, Ashley, EA, Ashurst, H, Burrow, R, Carrara, VI, Das, D, Dondorp, AM, Humphreys, GS, Lee, SJ, Mayxay, M, McGready, R, Newton, PN, Nosten, F, Richmond, CL, Sibley, C, Smithuis, FM, Taylor, WR, Tran, TH, von Seidlein, L, White, NJ, Woodrow, CJ, Guerin, PJ, Stepniewska, K, Price, RN, AII - Infectious diseases, Intensive Care Medicine, Infectious diseases, APH - Global Health, and APH - Quality of Care
- Subjects
Infectious Medicine ,Plasmodium falciparum ,wh_120 ,Infektionsmedicin ,Severe anaemia ,Parasitemia ,wa_530 ,Antimalarials ,Non-artemisinin-based therapy ,[SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system ,[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases ,parasitic diseases ,qv_256 ,Humans ,[SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology ,Malaria, Falciparum ,Child ,[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases ,Pooled analysis of individual patient data ,Anemia ,Public Health, Global Health, Social Medicine and Epidemiology ,General Medicine ,Artemisinin-based therapy ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,Malaria ,wc_750 ,Folkhälsovetenskap, global hälsa, socialmedicin och epidemiologi ,lnfectious Diseases and Global Health Radboud Institute for Health Sciences [Radboudumc 4] ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Haemoglobin - Abstract
Background Plasmodium falciparum malaria is associated with anaemia-related morbidity, attributable to host, parasite and drug factors. We quantified the haematological response following treatment of uncomplicated P. falciparum malaria to identify the factors associated with malarial anaemia. Methods Individual patient data from eligible antimalarial efficacy studies of uncomplicated P. falciparum malaria, available through the WorldWide Antimalarial Resistance Network data repository prior to August 2015, were pooled using standardised methodology. The haematological response over time was quantified using a multivariable linear mixed effects model with nonlinear terms for time, and the model was then used to estimate the mean haemoglobin at day of nadir and day 7. Multivariable logistic regression quantified risk factors for moderately severe anaemia (haemoglobin < 7 g/dL) at day 0, day 3 and day 7 as well as a fractional fall ≥ 25% at day 3 and day 7. Results A total of 70,226 patients, recruited into 200 studies between 1991 and 2013, were included in the analysis: 50,859 (72.4%) enrolled in Africa, 18,451 (26.3%) in Asia and 916 (1.3%) in South America. The median haemoglobin concentration at presentation was 9.9 g/dL (range 5.0–19.7 g/dL) in Africa, 11.6 g/dL (range 5.0–20.0 g/dL) in Asia and 12.3 g/dL (range 6.9–17.9 g/dL) in South America. Moderately severe anaemia (Hb < 7g/dl) was present in 8.4% (4284/50,859) of patients from Africa, 3.3% (606/18,451) from Asia and 0.1% (1/916) from South America. The nadir haemoglobin occurred on day 2 post treatment with a mean fall from baseline of 0.57 g/dL in Africa and 1.13 g/dL in Asia. Independent risk factors for moderately severe anaemia on day 7, in both Africa and Asia, included moderately severe anaemia at baseline (adjusted odds ratio (AOR) = 16.10 and AOR = 23.00, respectively), young age (age < 1 compared to ≥ 12 years AOR = 12.81 and AOR = 6.79, respectively), high parasitaemia (AOR = 1.78 and AOR = 1.58, respectively) and delayed parasite clearance (AOR = 2.44 and AOR = 2.59, respectively). In Asia, patients treated with an artemisinin-based regimen were at significantly greater risk of moderately severe anaemia on day 7 compared to those treated with a non-artemisinin-based regimen (AOR = 2.06 [95%CI 1.39–3.05], p < 0.001). Conclusions In patients with uncomplicated P. falciparum malaria, the nadir haemoglobin occurs 2 days after starting treatment. Although artemisinin-based treatments increase the rate of parasite clearance, in Asia they are associated with a greater risk of anaemia during recovery.
- Published
- 2022
7. 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
8. An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples
- Author
-
MalariaGEN, 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, AII - Infectious diseases, Intensive Care Medicine, MalariaGEN, 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], 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
Data resource ,parasitic diseases ,Medicine (miscellaneous) ,Genomics ,Genomic epidemiology ,Plasmodium vivax ,General Biochemistry, Genetics and Molecular Biology ,Malaria - 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
9. A molecular barcode and online tool to identify and map imported infection with Plasmodium vivax
- Author
-
Trimarsanto, Hidayat, primary, Amato, Roberto, additional, Pearson, Richard D, additional, Sutanto, Edwin, additional, Noviyanti, Rintis, additional, Trianty, Leily, additional, Marfurt, Jutta, additional, Pava, Zuleima, additional, Echeverry, Diego F, additional, Lopera-Mesa, Tatiana M, additional, Montenegro, Lidia Madeline, additional, Tobón-Castaño, Alberto, additional, Grigg, Matthew J, additional, Barber, Bridget, additional, William, Timothy, additional, Anstey, Nicholas M, additional, Getachew, Sisay, additional, Petros, Beyene, additional, Aseffa, Abraham, additional, Assefa, Ashenafi, additional, Rahim, Awab Ghulam, additional, Chau, Nguyen Hoang, additional, Hien, Tran Tinh, additional, Alam, Mohammad Shafiul, additional, Khan, Wasif A, additional, Ley, Benedikt, additional, Thriemer, Kamala, additional, Wangchuck, Sonam, additional, Hamedi, Yaghoob, additional, Adam, Ishag, additional, Liu, Yaobao, additional, Gao, Qi, additional, Sriprawat, Kanlaya, additional, Ferreira, Marcelo U, additional, Barry, Alyssa, additional, Mueller, Ivo, additional, Drury, Eleanor, additional, Goncalves, Sonia, additional, Simpson, Victoria, additional, Miotto, Olivo, additional, Miles, Alistair, additional, White, Nicholas J, additional, Nosten, Francois, additional, Kwiatkowski, Dominic P, additional, Price, Ric N, additional, and Auburn, Sarah, additional
- Published
- 2019
- Full Text
- View/download PDF
10. Short-course primaquine for the radical cure of Plasmodium vivax malaria: a multicentre, randomised, placebo-controlled non-inferiority trial
- Author
-
Taylor, Walter R J, primary, Thriemer, Kamala, additional, von Seidlein, Lorenz, additional, Yuentrakul, Prayoon, additional, Assawariyathipat, Thanawat, additional, Assefa, Ashenafi, additional, Auburn, Sarah, additional, Chand, Krisin, additional, Chau, Nguyen Hoang, additional, Cheah, Phaik Yeong, additional, Dong, Le Thanh, additional, Dhorda, Mehul, additional, Degaga, Tamiru Shibru, additional, Devine, Angela, additional, Ekawati, Lenny L, additional, Fahmi, Fahmi, additional, Hailu, Asrat, additional, Hasanzai, Mohammad Anwar, additional, Hien, Tran Tinh, additional, Khu, Htee, additional, Ley, Benedikt, additional, Lubell, Yoel, additional, Marfurt, Jutta, additional, Mohammad, Hussein, additional, Moore, Kerryn A, additional, Naddim, Mohammad Nader, additional, Pasaribu, Ayodhia Pitaloka, additional, Pasaribu, Syahril, additional, Promnarate, Cholrawee, additional, Rahim, Awab Ghulam, additional, Sirithiranont, Pasathron, additional, Solomon, Hiwot, additional, Sudoyo, Herawati, additional, Sutanto, Inge, additional, Thanh, Ngo Viet, additional, Tuyet-Trinh, Nguyen Thi, additional, Waithira, Naomi, additional, Woyessa, Adugna, additional, Yamin, Fazal Yamin, additional, Dondorp, Arjen, additional, Simpson, Julie A, additional, Baird, J Kevin, additional, White, Nicholas J, additional, Day, Nicholas P, additional, and Price, Ric N, additional
- Published
- 2019
- Full Text
- View/download PDF
11. A Worldwide Map ofPlasmodium falciparumK13-Propeller Polymorphisms
- Author
-
Ménard, Didier, primary, Khim, Nimol, additional, Beghain, Johann, additional, Adegnika, Ayola A., additional, Shafiul-Alam, Mohammad, additional, Amodu, Olukemi, additional, Rahim-Awab, Ghulam, additional, Barnadas, Céline, additional, Berry, Antoine, additional, Boum, Yap, additional, Bustos, Maria D., additional, Cao, Jun, additional, Chen, Jun-Hu, additional, Collet, Louis, additional, Cui, Liwang, additional, Thakur, Garib-Das, additional, Dieye, Alioune, additional, Djallé, Djibrine, additional, Dorkenoo, Monique A., additional, Eboumbou-Moukoko, Carole E., additional, Espino, Fe-Esperanza-Caridad J., additional, Fandeur, Thierry, additional, Ferreira-da-Cruz, Maria-Fatima, additional, Fola, Abebe A., additional, Fuehrer, Hans-Peter, additional, Hassan, Abdillahi M., additional, Herrera, Socrates, additional, Hongvanthong, Bouasy, additional, Houzé, Sandrine, additional, Ibrahim, Maman L., additional, Jahirul-Karim, Mohammad, additional, Jiang, Lubin, additional, Kano, Shigeyuki, additional, Ali-Khan, Wasif, additional, Khanthavong, Maniphone, additional, Kremsner, Peter G., additional, Lacerda, Marcus, additional, Leang, Rithea, additional, Leelawong, Mindy, additional, Li, Mei, additional, Lin, Khin, additional, Mazarati, Jean-Baptiste, additional, Ménard, Sandie, additional, Morlais, Isabelle, additional, Muhindo-Mavoko, Hypolite, additional, Musset, Lise, additional, Na-Bangchang, Kesara, additional, Nambozi, Michael, additional, Niaré, Karamoko, additional, Noedl, Harald, additional, Ouédraogo, Jean-Bosco, additional, Pillai, Dylan R., additional, Pradines, Bruno, additional, Quang-Phuc, Bui, additional, Ramharter, Michael, additional, Randrianarivelojosia, Milijaona, additional, Sattabongkot, Jetsumon, additional, Sheikh-Omar, Abdiqani, additional, Silué, Kigbafori D., additional, Sirima, Sodiomon B., additional, Sutherland, Colin, additional, Syafruddin, Din, additional, Tahar, Rachida, additional, Tang, Lin-Hua, additional, Touré, Offianan A., additional, Tshibangu-wa-Tshibangu, Patrick, additional, Vigan-Womas, Inès, additional, Warsame, Marian, additional, Wini, Lyndes, additional, Zakeri, Sedigheh, additional, Kim, Saorin, additional, Eam, Rotha, additional, Berne, Laura, additional, Khean, Chanra, additional, Chy, Sophy, additional, Ken, Malen, additional, Loch, Kaknika, additional, Canier, Lydie, additional, Duru, Valentine, additional, Legrand, Eric, additional, Barale, Jean-Christophe, additional, Stokes, Barbara, additional, Straimer, Judith, additional, Witkowski, Benoit, additional, Fidock, David A., additional, Rogier, Christophe, additional, Ringwald, Pascal, additional, Ariey, Frederic, additional, and Mercereau-Puijalon, Odile, additional
- Published
- 2016
- Full Text
- View/download PDF
12. Short-course primaquine for the radical cure of Plasmodium vivaxmalaria: a multicentre, randomised, placebo-controlled non-inferiority trial
- Author
-
Taylor, Walter R J, Thriemer, Kamala, von Seidlein, Lorenz, Yuentrakul, Prayoon, Assawariyathipat, Thanawat, Assefa, Ashenafi, Auburn, Sarah, Chand, Krisin, Chau, Nguyen Hoang, Cheah, Phaik Yeong, Dong, Le Thanh, Dhorda, Mehul, Degaga, Tamiru Shibru, Devine, Angela, Ekawati, Lenny L, Fahmi, Fahmi, Hailu, Asrat, Hasanzai, Mohammad Anwar, Hien, Tran Tinh, Khu, Htee, Ley, Benedikt, Lubell, Yoel, Marfurt, Jutta, Mohammad, Hussein, Moore, Kerryn A, Naddim, Mohammad Nader, Pasaribu, Ayodhia Pitaloka, Pasaribu, Syahril, Promnarate, Cholrawee, Rahim, Awab Ghulam, Sirithiranont, Pasathron, Solomon, Hiwot, Sudoyo, Herawati, Sutanto, Inge, Thanh, Ngo Viet, Tuyet-Trinh, Nguyen Thi, Waithira, Naomi, Woyessa, Adugna, Yamin, Fazal Yamin, Dondorp, Arjen, Simpson, Julie A, Baird, J Kevin, White, Nicholas J, Day, Nicholas P, and Price, Ric N
- Abstract
Primaquine is the only widely used drug that prevents Plasmodium vivaxmalaria relapses, but adherence to the standard 14-day regimen is poor. We aimed to assess the efficacy of a shorter course (7 days) of primaquine for radical cure of vivax malaria.
- Published
- 2019
- Full Text
- View/download PDF
13. Lineage-informative microhaplotypes for spatio-temporal surveillance of Plasmodium vivax malaria parasites.
- Author
-
Siegel SV, Amato R, Trimarsanto H, Sutanto E, Kleinecke M, Murie K, Whitton G, Taylor AR, Watson JA, Imwong M, Assefa A, Rahim AG, Chau NH, Hien TT, Green JA, Koh G, White NJ, Day N, Kwiatkowski DP, Rayner JC, Price RN, and Auburn S
- Abstract
Challenges in understanding the origin of recurrent Plasmodium vivax infections constrains the surveillance of antimalarial efficacy and transmission of this neglected parasite. Recurrent infections within an individual may arise from activation of dormant liver stages (relapse), blood-stage treatment failure (recrudescence) or new inoculations (reinfection). Molecular inference of familial relatedness (identity-by-descent or IBD) based on whole genome sequence data, together with analysis of the intervals between parasitaemic episodes ("time-to-event" analysis), can help resolve the probable origin of recurrences. Whole genome sequencing of predominantly low-density P. vivax infections is challenging, so an accurate and scalable genotyping method to determine the origins of recurrent parasitaemia would be of significant benefit. We have developed a P. vivax genome-wide informatics pipeline to select specific microhaplotype panels that can capture IBD within small, amplifiable segments of the genome. Using a global set of 615 P. vivax genomes, we derived a panel of 100 microhaplotypes, each comprising 3-10 high frequency SNPs within <200 bp sequence windows. This panel exhibits high diversity in regions of the Asia-Pacific, Latin America and the horn of Africa (median H
E = 0.70-0.81) and it captured 89% (273/307) of the polyclonal infections detected with genome-wide datasets. Using data simulations, we demonstrate lower error in estimating pairwise IBD using microhaplotypes, relative to traditional biallelic SNP barcodes. Our panel exhibited high accuracy in predicting the country of origin (median Matthew's correlation coefficient >0.9 in 90% countries tested) and it also captured local infection outbreak and bottlenecking events. The informatics pipeline is available open-source and yields microhaplotypes that can be readily transferred to high-throughput amplicon sequencing assays for surveillance in malaria-endemic regions.- Published
- 2023
- Full Text
- View/download PDF
14. An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples.
- Author
-
Adam I, Alam MS, Alemu S, Amaratunga C, Amato R, Andrianaranjaka V, Anstey NM, Aseffa A, Ashley E, Assefa A, Auburn S, Barber BE, Barry A, Batista Pereira D, Cao J, Chau NH, Chotivanich K, Chu C, Dondorp AM, Drury E, Echeverry DF, Erko B, Espino F, Fairhurst R, Faiz A, Fernanda Villegas M, Gao Q, Golassa L, Goncalves S, Grigg MJ, Hamedi Y, Hien TT, Htut Y, Johnson KJ, Karunaweera N, Khan W, Krudsood S, Kwiatkowski DP, Lacerda M, Ley B, Lim P, Liu Y, Llanos-Cuentas A, Lon C, Lopera-Mesa T, Marfurt J, Michon P, Miotto O, Mohammed R, Mueller I, Namaik-Larp C, Newton PN, Nguyen TN, Nosten F, Noviyanti R, Pava Z, Pearson RD, Petros B, Phyo AP, Price RN, Pukrittayakamee S, Rahim AG, Randrianarivelojosia M, Rayner JC, Rumaseb A, Siegel SV, Simpson VJ, Thriemer K, Tobon-Castano A, Trimarsanto H, Urbano Ferreira M, Vélez ID, Wangchuk S, Wellems TE, White NJ, William T, Yasnot MF, and Yilma D
- 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., Competing Interests: No competing interests were disclosed., (Copyright: © 2022 MalariaGEN et al.)
- Published
- 2022
- Full Text
- View/download PDF
15. A Worldwide Map of Plasmodium falciparum K13-Propeller Polymorphisms.
- Author
-
Ménard D, Khim N, Beghain J, Adegnika AA, Shafiul-Alam M, Amodu O, Rahim-Awab G, Barnadas C, Berry A, Boum Y, Bustos MD, Cao J, Chen JH, Collet L, Cui L, Thakur GD, Dieye A, Djallé D, Dorkenoo MA, Eboumbou-Moukoko CE, Espino FE, Fandeur T, Ferreira-da-Cruz MF, Fola AA, Fuehrer HP, Hassan AM, Herrera S, Hongvanthong B, Houzé S, Ibrahim ML, Jahirul-Karim M, Jiang L, Kano S, Ali-Khan W, Khanthavong M, Kremsner PG, Lacerda M, Leang R, Leelawong M, Li M, Lin K, Mazarati JB, Ménard S, Morlais I, Muhindo-Mavoko H, Musset L, Na-Bangchang K, Nambozi M, Niaré K, Noedl H, Ouédraogo JB, Pillai DR, Pradines B, Quang-Phuc B, Ramharter M, Randrianarivelojosia M, Sattabongkot J, Sheikh-Omar A, Silué KD, Sirima SB, Sutherland C, Syafruddin D, Tahar R, Tang LH, Touré OA, Tshibangu-wa-Tshibangu P, Vigan-Womas I, Warsame M, Wini L, Zakeri S, Kim S, Eam R, Berne L, Khean C, Chy S, Ken M, Loch K, Canier L, Duru V, Legrand E, Barale JC, Stokes B, Straimer J, Witkowski B, Fidock DA, Rogier C, Ringwald P, Ariey F, and Mercereau-Puijalon O
- Subjects
- Algorithms, Artemisinins therapeutic use, Asia, Southeastern, China, Endemic Diseases, Genotype, Humans, Lactones therapeutic use, Malaria, Falciparum drug therapy, Malaria, Falciparum parasitology, Plasmodium falciparum drug effects, Sequence Analysis, DNA, Artemisinins pharmacology, Drug Resistance genetics, Lactones pharmacology, Mutation, Plasmodium falciparum genetics, Polymorphism, Genetic, Protozoan Proteins genetics
- Abstract
Background: Recent gains in reducing the global burden of malaria are threatened by the emergence of Plasmodium falciparum resistance to artemisinins. The discovery that mutations in portions of a P. falciparum gene encoding kelch (K13)-propeller domains are the major determinant of resistance has provided opportunities for monitoring such resistance on a global scale., Methods: We analyzed the K13-propeller sequence polymorphism in 14,037 samples collected in 59 countries in which malaria is endemic. Most of the samples (84.5%) were obtained from patients who were treated at sentinel sites used for nationwide surveillance of antimalarial resistance. We evaluated the emergence and dissemination of mutations by haplotyping neighboring loci., Results: We identified 108 nonsynonymous K13 mutations, which showed marked geographic disparity in their frequency and distribution. In Asia, 36.5% of the K13 mutations were distributed within two areas--one in Cambodia, Vietnam, and Laos and the other in western Thailand, Myanmar, and China--with no overlap. In Africa, we observed a broad array of rare nonsynonymous mutations that were not associated with delayed parasite clearance. The gene-edited Dd2 transgenic line with the A578S mutation, which expresses the most frequently observed African allele, was found to be susceptible to artemisinin in vitro on a ring-stage survival assay., Conclusions: No evidence of artemisinin resistance was found outside Southeast Asia and China, where resistance-associated K13 mutations were confined. The common African A578S allele was not associated with clinical or in vitro resistance to artemisinin, and many African mutations appear to be neutral. (Funded by Institut Pasteur Paris and others.).
- Published
- 2016
- Full Text
- View/download PDF
Catalog
Books, media, physical & digital resources
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.