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1. Genomics of Plasmodium vivax in Colombia reveals evidence of local bottle-necking and inter-country connectivity in the Americas

Author

Sutanto, Edwin, Pava, Zuleima, Echeverry, Diego F., Lopera-Mesa, Tatiana M., Montenegro, Lidia Madeline, Yasnot-Acosta, Maria F., Benavente, Ernest Diez, Pearson, Richard D., Herrera, Sócrates, Arévalo-Herrera, Myriam, Trimarsanto, Hidayat, Rumaseb, Angela, Noviyanti, Rintis, Kwiatkowski, Dominic P., Price, Ric N., and Auburn, Sarah

Published
2023
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2. A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria

Author

Trimarsanto, Hidayat, Amato, Roberto, Pearson, Richard D., Sutanto, Edwin, Noviyanti, Rintis, Trianty, Leily, Marfurt, Jutta, Pava, Zuleima, Echeverry, Diego F., Lopera-Mesa, Tatiana M., Montenegro, Lidia M., Tobón-Castaño, Alberto, Grigg, Matthew J., Barber, Bridget, William, Timothy, Anstey, Nicholas M., Getachew, Sisay, Petros, Beyene, Aseffa, Abraham, Assefa, Ashenafi, Rahim, Awab G., Chau, Nguyen H., Hien, Tran T., Alam, Mohammad S., Khan, Wasif A., Ley, Benedikt, Thriemer, Kamala, Wangchuck, Sonam, Hamedi, Yaghoob, Adam, Ishag, Liu, Yaobao, Gao, Qi, Sriprawat, Kanlaya, Ferreira, Marcelo U., Laman, Moses, Barry, Alyssa, Mueller, Ivo, Lacerda, Marcus V. G., Llanos-Cuentas, Alejandro, Krudsood, Srivicha, Lon, Chanthap, Mohammed, Rezika, Yilma, Daniel, Pereira, Dhelio B., Espino, Fe E. J., Chu, Cindy S., Vélez, Iván D., Namaik-larp, Chayadol, Villegas, Maria F., Green, Justin A., Koh, Gavin, Rayner, Julian C., Drury, Eleanor, Gonçalves, Sónia, Simpson, Victoria, Miotto, Olivo, Miles, Alistair, White, Nicholas J., Nosten, Francois, Kwiatkowski, Dominic P., Price, Ric N., and Auburn, Sarah

Published
2022
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5. Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples

Author

MalariaGEN, Abdel Hamid, Muzamil Mahdi, Abdelraheem, Mohamed Hassan, Acheampong, Desmond Omane, Ahouidi, Ambroise, Ali, Mozam, Almagro-Garcia, Jacob, Amambua-Ngwa, Alfred, Amaratunga, Chanaki, Amenga-Etego, Lucas, Andagalu, Ben, Anderson, Tim, Andrianaranjaka, Voahangy, Aniebo, Ifeyinwa, Aninagyei, Enoch, Ansah, Felix, Ansah, Patrick O, Apinjoh, Tobias, Arnaldo, Paulo, Ashley, Elizabeth, Auburn, Sarah, Awandare, Gordon A, Ba, Hampate, Baraka, Vito, Barry, Alyssa, Bejon, Philip, Bertin, Gwladys I, Boni, Maciej F, Borrmann, Steffen, Bousema, Teun, Bouyou-Akotet, Marielle, Branch, Oralee, Bull, Peter C, Cheah, Huch, Chindavongsa, Keobouphaphone, Chookajorn, Thanat, Chotivanich, Kesinee, Claessens, Antoine, Conway, David J, Corredor, Vladimir, Courtier, Erin, Craig, Alister, D'Alessandro, Umberto, Dama, Souleymane, Day, Nicholas, Denis, Brigitte, Dhorda, Mehul, Diakite, Mahamadou, Djimde, Abdoulaye, Dolecek, Christiane, Dondorp, Arjen, Doumbia, Seydou, Drakeley, Chris, Drury, Eleanor, Duffy, Patrick, Echeverry, Diego F, Egwang, Thomas G, Enosse, Sonia Maria Mauricio, Erko, Berhanu, Fairhurst, Rick M, Faiz, Abdul, Fanello, Caterina A, Fleharty, Mark, Forbes, Matthew, Fukuda, Mark, Gamboa, Dionicia, Ghansah, Anita, Golassa, Lemu, Goncalves, Sonia, Harrison, GL Abby, Healy, Sara Anne, Hendry, Jason A, Hernandez-Koutoucheva, Anastasia, Hien, Tran Tinh, Hill, Catherine A, Hombhanje, Francis, Hott, Amanda, Htut, Ye, Hussein, Mazza, Imwong, Mallika, Ishengoma, Deus, Jackson, Scott A, Jacob, Chris G, Jeans, Julia, Johnson, Kimberly J, Kamaliddin, Claire, Kamau, Edwin, Keatley, Jon, Kochakarn, Theerarat, Konate, Drissa S, Konaté, Abibatou, Kone, Aminatou, Kwiatkowski, Dominic P, Kyaw, Myat P, Kyle, Dennis, Lawniczak, Mara, Lee, Samuel K, Lemnge, Martha, Lim, Pharath, Lon, Chanthap, Loua, Kovana M, Mandara, Celine I, Marfurt, Jutta, Marsh, Kevin, Maude, Richard James, Mayxay, Mayfong, Maïga-Ascofaré, Oumou, Miotto, Olivo, Mita, Toshihiro, Mobegi, Victor, Mohamed, Abdelrahim Osman, Mokuolu, Olugbenga A, Montgomery, Jaqui, Morang'a, Collins Misita, Mueller, Ivo, Murie, Kathryn, Newton, Paul N, Ngo Duc, Thang, Nguyen, Thuy, Nguyen, Thuy-Nhien, Nguyen Thi Kim, Tuyen, Nguyen Van, Hong, Noedl, Harald, Nosten, Francois, Noviyanti, Rintis, Ntui, Vincent Ntui-Njock, Nzila, Alexis, Ochola-Oyier, Lynette Isabella, Ocholla, Harold, Oduro, Abraham, Omedo, Irene, Onyamboko, Marie A, Ouedraogo, Jean-Bosco, Oyebola, Kolapo, Oyibo, Wellington Aghoghovwia, Pearson, Richard, Peshu, Norbert, Phyo, Aung P, Plowe, Christopher V, Price, Ric N, Pukrittayakamee, Sasithon, Quang, Huynh Hong, Randrianarivelojosia, Milijaona, Rayner, Julian C, Ringwald, Pascal, Rosanas-Urgell, Anna, Rovira-Vallbona, Eduard, Ruano-Rubio, Valentin, Ruiz, Lastenia, Saunders, David, Shayo, Alex, Siba, Peter, Simpson, Victoria J, Sissoko, Mahamadou S, Smith, Christen, Su, Xin-Zhuan, Sutherland, Colin, Takala-Harrison, Shannon, Talman, Arthur, Tavul, Livingstone, Thanh, Ngo Viet, Thathy, Vandana, Thu, Aung Myint, Toure, Mahamoudou, Tshefu, Antoinette, Verra, Federica, Vinetz, Joseph, Wellems, Thomas E, Wendler, Jason, White, Nicholas J, Whitton, Georgia, Yavo, William, Van Der Pluijm, Rob W, Amenga-Etego, Lucas [0000-0003-4468-0506], Anderson, Tim [0000-0002-0191-0204], Ansah, Patrick O [0000-0002-3214-5621], Ashley, Elizabeth [0000-0002-7620-4822], Ba, Hampate [0000-0002-9299-5775], Baraka, Vito [0000-0001-9694-9293], Bejon, Philip [0000-0002-2135-7549], Bertin, Gwladys I [0000-0002-2218-9591], Boni, Maciej F [0000-0002-0830-9630], Bousema, Teun [0000-0003-2666-094X], Chookajorn, Thanat [0000-0003-2876-6203], Claessens, Antoine [0000-0002-4277-0914], Conway, David J [0000-0002-8711-3037], Craig, Alister [0000-0003-0914-6164], D'Alessandro, Umberto [0000-0001-6341-5009], Day, Nicholas [0000-0003-2309-1171], Diakite, Mahamadou [0000-0002-4268-8857], Djimde, Abdoulaye [0000-0003-0062-2283], Dondorp, Arjen [0000-0001-5190-2395], Drakeley, Chris [0000-0003-4863-075X], Echeverry, Diego F [0000-0003-0301-4478], Erko, Berhanu [0000-0003-1685-752X], Faiz, Abdul [0000-0002-3460-7535], Fanello, Caterina A [0000-0003-1932-9562], Gamboa, Dionicia [0000-0002-1420-7729], Golassa, Lemu [0000-0002-1216-8711], Healy, Sara Anne [0000-0003-3078-6094], Ishengoma, Deus [0000-0003-2040-3416], Jackson, Scott A [0000-0002-3172-1607], Kamaliddin, Claire [0000-0001-8198-6235], Kamau, Edwin [0000-0002-5761-7883], Konate, Drissa S [0000-0002-4177-9642], Kwiatkowski, Dominic P [0000-0002-5023-0176], Kyle, Dennis [0000-0002-0238-965X], Lawniczak, Mara [0000-0002-3006-2080], Loua, Kovana M [0000-0003-0571-0944], Marsh, Kevin [0000-0001-8377-5466], Mayxay, Mayfong [0000-0002-6056-4516], Miotto, Olivo [0000-0001-8060-6771], Mita, Toshihiro [0000-0001-8180-2344], Mobegi, Victor [0000-0002-1962-5583], Morang'a, Collins Misita [0000-0002-6988-150X], Nguyen, Thuy-Nhien [0000-0002-4101-5706], Nosten, Francois [0000-0002-7951-0745], Ntui, Vincent Ntui-Njock [0000-0002-7532-9930], Oduro, Abraham [0000-0002-4191-7419], Onyamboko, Marie A [0000-0002-7501-5931], Ouedraogo, Jean-Bosco [0000-0003-0412-8733], Oyebola, Kolapo [0000-0002-1003-2570], Pearson, Richard [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], Rosanas-Urgell, Anna [0000-0002-0432-5203], Shayo, Alex [0000-0002-7099-8537], Su, Xin-Zhuan [0000-0003-3246-3248], Vinetz, Joseph [0000-0001-8344-2004], Wellems, Thomas E [0000-0003-3899-8454], and Apollo - University of Cambridge Repository

Subjects
data resource, plasmodium falciparum, genomics, malaria, genomic epidemiology
Abstract

We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network. It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented. For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations. We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent. We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines. Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website.

Published
2023

6. Resolving drug selection and migration in an inbred South American Plasmodium falciparum population with identity-by-descent analysis

Author

Carrasquilla, Manuela, primary, Early, Angela M., additional, Taylor, Aimee R., additional, Knudson Ospina, Angélica, additional, Echeverry, Diego F., additional, Anderson, Timothy J. C., additional, Mancilla, Elvira, additional, Aponte, Samanda, additional, Cárdenas, Pablo, additional, Buckee, Caroline O., additional, Rayner, Julian C., additional, Sáenz, Fabián E., additional, Neafsey, Daniel E., additional, and Corredor, Vladimir, additional

Published
2022
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7. From contigs towards chromosomes: automatic Improvement of Long Read Assemblies (ILRA)

Author

Ruiz, José L., Reimering, Susanne, Sanders, Mandy, Escobar-Prieto, Juan David, Brancucci, Nicolas M. B., Echeverry, Diego F., Abdirahman I. Abdi, Marti, Matthias, Gómez-Díaz, Elena, and Otto, Thomas D.

Subjects
PacBio, de novo, polishing, Plasmodium, genome assembly, ONT, long reads sequencing
Abstract

Recent advances in long read technologies not only enable large consortia to aim to sequence all eukaryotes on Earth, but they also allow individual laboratories to sequence their species of interest with relatively low investment. There is a promise to obtain “perfect genomes” with long read technologies, but the number of contigs often exceeds the number of chromosomes by far, containing many insertion and deletion errors around homopolymer tracks. To overcome these issues, we implemented the ILRA pipeline to correct long read-based assemblies, so contigs are reordered, renamed, merged, circularized, or filtered if erroneous or contaminated, and Illumina reads are used to correct homopolymer errors. We successfully tested our approach to assemble the genomes of four novel Plasmodium falciparum field samples, and on existing assemblies of the human data, Trypanosoma brucei and Leptosphaeria spp. We found that correcting homopolymer tracks reduced the number of genes incorrectly annotated as pseudogenes, but an iterative correction seemed to be required to correct larger numbers of homopolymer errors. In summary, we described and compared the performance of a new software, which improved the quality of novel long read assemblies, and that can be used to correct small- and medium-sized genomes up to 1Gbp.

Published
2023
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8. 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

10. 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

18. Identity-by-descent relatedness estimates with uncertainty characterise departure from isolation-by-distance betweenPlasmodium falciparumpopulations on the Colombian-Pacific coast

Author

Taylor, Aimee R., Echeverry, Diego F., Anderson, Timothy J. C., Neafsey, Daniel E., and Buckee, Caroline O.

Subjects
0303 health sciences, education.field_of_study, biology, 030231 tropical medicine, Population, Plasmodium falciparum, Sample (statistics), biology.organism_classification, medicine.disease, Mating system, Identity by descent, 3. Good health, law.invention, 03 medical and health sciences, 0302 clinical medicine, Transmission (mechanics), Evolutionary biology, law, medicine, education, Malaria, 030304 developmental biology, Isolation by distance
Abstract

Characterising connectivity between geographically separated biological populations is a common goal in many fields. Recent approaches to understanding connectivity between malaria parasite populations, with implications for disease control efforts, have used estimates of relatedness based on identity-by-descent (IBD). However, uncertainty around estimated relatedness has not been accounted for to date. IBD-based relatedness estimates with uncertainty were computed for pairs of monoclonalPlasmodium falciparumsamples collected from five cities on the Colombian-Pacific coast where long-term clonal propagation ofP. falciparumis frequent. The cities include two official ports, Buenaventura and Tumaco, that are separated geographically but connected by frequent marine traffic. The fraction of highly-related sample pairs (whose classification accounts for uncertainty) was greater within cities versus between. However, based on both the fraction of highly-related sample pairs and on a threshold-free approach (Wasserstein distances between parasite populations) connectivity between Buenaventura and Tumaco was disproportionally high. Buenaventura-Tumaco connectivity was consistent with three separate transmission events involving parasites from five different clonal components (groups of statistically indistinguishable parasites identified under a graph theoretic framework). To conclude,P. falciparumpopulation connectivity on the Colombian-Pacific coast abides by accessibility not isolation-by-distance, potentially implicating marine traffic in malaria transmission with opportunities for targeted intervention. Further investigations are required to test this and alternative hypotheses. For the first time in malaria epidemiology, we account for uncertainty around estimated relatedness (an important consideration for future studies that plan to use genotype versus whole genome sequence data to estimate IBD-based relatedness); we also use a threshold-free approach to compare parasite populations, and identify clonal components in a statistically principled manner. The approaches we employ could be adapted to other recombining organisms with mixed mating systems, thus have broad relevance.

Published
2020

22. 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
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23. Long term persistence of clonal malaria parasite Plasmodium falciparum lineages in the Colombian Pacific region

Author

Echeverry Diego F, Nair Shalini, Osorio Lyda, Menon Sanjay, Murillo Claribel, and Anderson Tim JC

Subjects
Plasmodium falciparum, Colombia, Clonality, Relatedness, Persistence, Genotypic richness, Population structure, SNPs, Linkage disequilibrium, Association studies, Genetics, QH426-470
Abstract

Abstract Background Resistance to chloroquine and antifolate drugs has evolved independently in South America, suggesting that genotype - phenotype studies aimed at understanding the genetic basis of resistance to these and other drugs should be conducted in this continent. This research was conducted to better understand the population structure of Colombian Plasmodium falciparum in preparation for such studies. Results A set of 384 SNPs were genotyped in blood spot DNA samples from 447 P. falciparum infected subjects collected over a ten year period from four provinces of the Colombian Pacific coast to evaluate clonality, population structure and linkage disequilibrium (LD). Most infections (81%) contained a single predominant clone. These clustered into 136 multilocus genotypes (MLGs), with 32% of MLGs recovered from multiple (2 – 28) independent subjects. We observed extremely low genotypic richness (R = 0.42) and long persistence of MLGs through time (median = 537 days, range = 1 – 2,997 days). There was a high probability (>5%) of sampling parasites from the same MLG in different subjects within 28 days, suggesting caution is needed when using genotyping methods to assess treatment success in clinical drug trials. Panmixia was rejected as four well differentiated subpopulations (FST = 0.084 - 0.279) were identified. These occurred sympatrically but varied in frequency within the four provinces. Linkage disequilibrium (LD) decayed more rapidly (r2 = 0.17 for markers Conclusions We conclude that Colombian populations have several advantages for association studies, because multiple clone infections are uncommon and LD decays over the scale of one or a few genes. However, the extensive population structure and low genotype richness will need to be accounted for when designing and analyzing association studies.

Published
2013
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24. ¿Pueden las imágenes Doppler Color y Espectral diferenciar entre un derrame pleural o pericárdico‚ engrosamiento pleural y el ventrículo derecho en perros? reporte de caso.

Author

Espinosa Arango, Juliana, Echeverry, Diego F., and Buriticá, Edwin F.

Abstract

Antecedentes: la ultrasonografía pulmonar ha ganado importancia dentro de la evaluación de diversas patologías pulmonares en medicina veterinaria. Sin embargo‚ se ha descrito que en determinadas circunstancias es posible confundir un derrame pleural con un engrosamiento pleural o con el ventrículo derecho. La utilidad del Doppler Color para diferenciar estas condiciones ha sido reportada previamente. Objetivo: describir la utilidad del Doppler Color y Espectral en la diferenciación entre: derrame pleural‚ o pericárdico‚ engrosamiento pleural y el ventrículo derecho en un perro. Métodos: paciente bulldog ingles‚ macho no castrado‚ de 21 kg de peso y 7 años que fue referido a nuestro hospital por presentar disnea severa. Se realizaron pruebas de diagnóstico por imagen‚ bioquímicas y hematológicas. Resultados: la analítica sanguínea estuvo en rango normal. Las imágenes radiográficas mostraron signos compatibles con efusión pleural bilateral severa. La ecocardiografía evidenció efusión pleural tabicada bilateral y pericárdica severas‚ con función cardiaca conservada. Con fines diagnósticos y terapéuticos se realizó pericardiocentesis y toracocentesis. Debido a las limitaciones propias de las ventanas acústicas de tórax‚ en algún momento de la insonación no se tenía claridad si lo observado se trataba de engrosamiento pleural‚ derrame pleural‚ de una tabicación pleural o del ventrículo derecho. El Doppler Color mostro el ¨signo de color líquido¨ indicando la presencia de fluido en ambos lugares y descartando engrosamiento pleural. El Doppler Espectral mostro una señal de baja intensidad en lo que se sospechaba pudiera ser el ventrículo derecho‚ con lo que se confirmó de esta manera que se trataba del derrame pericárdico y no de la cámara cardiaca. El derrame pericárdico y pleural fueron drenados y el paciente se recuperó sin complicaciones. Conclusiones: la utilización del Doppler color y Espectral permitió la identificación y diferenciación de las estructuras anatómicas y fluidos presentes en el tórax del paciente‚ lo que permitió realizar una toracocentesis y drenaje de ambas cavidades disminuyendo el riesgo de una punción cardiaca no deseada. [ABSTRACT FROM AUTHOR]

Published
2024

26. Global sequence variation in the histidine-rich proteins 2 and 3 of Plasmodium falciparum: implications for the performance of malaria rapid diagnostic tests

Author

Gamboa Dionicia, Echeverry Diego F, Djalle Djibrine, Cunningham Jane, Bell David, Barnwell John, Ariey Frederic, Albertini Audrey, Abdullah Salim, Chen Nanhua, Gatton Michelle, Pelecanos Anita, Ho Mei-Fong, Baker Joanne, Hii Jeffery, Kyaw Myat, Luchavez Jennifer, Membi Christopher, Menard Didier, Murillo Claribel, Nhem Sina, Ogutu Bernhards, Onyor Pamela, Oyibo Wellington, Wang Shan, McCarthy James, and Cheng Qin

Subjects
Arctic medicine. Tropical medicine, RC955-962, Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background Accurate diagnosis is essential for prompt and appropriate treatment of malaria. While rapid diagnostic tests (RDTs) offer great potential to improve malaria diagnosis, the sensitivity of RDTs has been reported to be highly variable. One possible factor contributing to variable test performance is the diversity of parasite antigens. This is of particular concern for Plasmodium falciparum histidine-rich protein 2 (PfHRP2)-detecting RDTs since PfHRP2 has been reported to be highly variable in isolates of the Asia-Pacific region. Methods The pfhrp2 exon 2 fragment from 458 isolates of P. falciparum collected from 38 countries was amplified and sequenced. For a subset of 80 isolates, the exon 2 fragment of histidine-rich protein 3 (pfhrp3) was also amplified and sequenced. DNA sequence and statistical analysis of the variation observed in these genes was conducted. The potential impact of the pfhrp2 variation on RDT detection rates was examined by analysing the relationship between sequence characteristics of this gene and the results of the WHO product testing of malaria RDTs: Round 1 (2008), for 34 PfHRP2-detecting RDTs. Results Sequence analysis revealed extensive variations in the number and arrangement of various repeats encoded by the genes in parasite populations world-wide. However, no statistically robust correlation between gene structure and RDT detection rate for P. falciparum parasites at 200 parasites per microlitre was identified. Conclusions The results suggest that despite extreme sequence variation, diversity of PfHRP2 does not appear to be a major cause of RDT sensitivity variation.

Published
2010
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27. Genomic epidemiology of artemisinin resistant malaria

Author

Amato, Roberto, Miotto, Olivo, Woodrow, Charles J, Almagro-Garcia, Jacob, Sinha, Ipsita, Campino, Susana, Mead, Daniel, Drury, Eleanor, Kekre, Mihir, Sanders, Mandy, Amambua-Ngwa, Alfred, Amaratunga, Chanaki, Amenga-Etego, Lucas, Andrianaranjaka, Voahangy, Apinjoh, Tobias, Ashley, Elizabeth, Auburn, Sarah, Awandare, Gordon, Baraka, Vito, Barry, Alyssa, Boni, Maciej, Borrmann, Steffen, Bousema, Teun, Branch, Oralee, Bull, Peter, Chotivanich, Kesinee, Conway, David, Craig, Alister, Day, Nicholas, Djimde, Abdoulaye, Dolecek, Christiane, Dondorp, Arjen M, Drakeley, Chris, Duffy, Patrick, Echeverry, Diego F, Egwang, Thomas, Fairhurst, Rick, Faiz, Abul, Fanello, Caterina, Hien, Tran Tinh, Hodgson, Abraham, Imwong, Mallika, Ishengoma, Deus, Lim, Pharath, Lon, Chanthap, Marfurt, Jutta, Marsh, Kevin, Mayxay, Mayfong, Michon, Pascal, Mobegi, Victor, Mokuolu, Olugbenga, Montgomery, Jacqui, Mueller, Ivo, Kyaw, Myat Phone, Newton, Paul N, Nosten, François, Noviyanti, Rintis, Nzila, Alexis, Ocholla, Harold, Oduro, Abraham, Onyamboko, Marie, Ouédraogo, Jean-Bosco, Phyo, Aung, Plowe, Christopher, Price, Ric, Pukrittayakamee, Sasithon, Randrianarivelojosia, Milijaona, Ringwald, Pascal, Ruiz, Lastenia, Saunders, David, Shayo, Alex, Siba, Peter, Takala-Harrison, Shannon, Thanh, Thuy-Nhien, Thathy, Vandana, Verra, Federica, Wendler, Jason, White, Nicholas, Ye, Htut, Cornelius, Victoria, Giacomantonio, Rachel, Muddyman, Dawn, Henrichs, Christa, Malangone, Cinzia, Jyothi, Dushyanth, Pearson, Richard, Rayner, Julian, McVean, Gilean, Rockett, Kirk, Miles, Alistair, Vauterin, Paul, Jeffery, Ben, Manske, Magnus, Stalker, Jim, MacInnis, Bronwyn, Kwiatkowski, Dominic, The Wellcome Trust Sanger Institute [Cambridge], Mahidol Oxford Tropical Medicine Research Unit, University of Oxford [Oxford]-Mahidol University [Bangkok], The Wellcome Trust Centre for Human Genetics [Oxford], University of Oxford [Oxford], Medical Research Council Unit The Gambia (MRC), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Navrongo Health Research Centre [Navrongo, Ghana] (NHRC), G4 malaria group [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), University of Buéa, Global and Tropical Health Division [Rocklands, Australia], Menzies School of Health Research [Australia], Charles Darwin University-Charles Darwin University, West African Centre for Cell Biology of Infectious Pathogens [Legon, Ghana] (WACCBIP), University of Ghana, National Institute for Medical Research [Tanzania] (NIMR), The Walter and Eliza Hall Institute of Medical Research (WEHI), Oxford University Clinical Research Unit [Ho Chi Minh City] (OUCRU), KEMRI-Wellcome Trust Research Programme (KWTRP), London School of Hygiene and Tropical Medicine (LSHTM), New York University School of Medicine, NYU System (NYU), Faculty of Tropical Medicine [Bangkok, Thailand], Mahidol University [Bangkok], Liverpool School of Tropical Medicine (LSTM), Faculté de Médecine, de pharmacie et d’Odonto-Stomatologie [Bamako, Mali] (FMPOS), Université de Bamako, Department of Entomology [West Lafayette], Purdue University [West Lafayette], Med Biotech Laboratories [Kampala, Ouganda] (MBL), Armed Forces Research Institute of Medical Sciences [Bangkok] (AFRIMS), Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Mahidol University [Bangkok]-Mahosot Hospital, Faculty of Medicine and Health Sciences [Madang, Papouasie-Nouvelle-Guinée], Divine Word University [Papouasie-Nouvelle-Guinée] (DWU), University of Ilorin, Department of Entomology [University Park], Pennsylvania State University (Penn State), Penn State System-Penn State System, University of Melbourne, Ministry of health and sport [Yangon, Myanmar] (MoHS), Eijkman Institute for Molecular Biology [Jakarta], King Fahd University of Petroleum and Minerals (KFUPM), Malawi Liverpool Wellcome Trust Clinical Research Programme (MLW), Liverpool School of Tropical Medicine (LSTM)-University of Liverpool-Wellcome Trust-University of Malawi, University of Kinshasa (UNIKIN), Institut de Recherche en Sciences de la Santé (IRSS) / Centre Muraz, Shoklo Malaria Research Unit [Mae Sot, Thailand] (SMRU), Mahidol Oxford Tropical Medicine Research Unit (MORU), Wellcome Trust-Mahidol University [Bangkok]-University of Oxford [Oxford]-Wellcome Trust-Mahidol University [Bangkok]-University of Oxford [Oxford], University of Maryland School of Medicine, University of Maryland System, Centre for Tropical Medicine and Global Health [Oxford, UK], Nuffield Department of Medicine [Oxford, UK] (Big Data Institute), University of Oxford [Oxford]-University of Oxford [Oxford], Department of Clinical Tropical Medicine [Bangkok, Thailand] (Faculty of Tropical Medicine), Global Malaria Programme, Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Universidad Nacional de la Amazonía Peruana [Loreto, Perou] (UNAP), University of Dodoma [Tanzanie] (UDOM), Papua New Guinea Institute of Medical Research (PNG-IMR), Wellcome Trust-Mahidol University [Bangkok]-University of Oxford [Oxford], The sequencing, analysis, informatics and management of the Community Project are supported by the Wellcome Trust through Sanger Institute core funding (098051) and a Strategic Award (090770/Z/09/Z) and by the MRC Centre for Genomics and Global Health which is jointly funded by the Medical Research Council and the Department for International Development (DFID) (G0600718, M006212). AEB and IM acknowledge the Victorian State Government Operational Infrastructure Support and Australian Government NHMRC IRIISS., This study was conducted by the MalariaGEN Plasmodium falciparum Community Project, and was made possible by clinical parasite samples contributed by partner studies, whose investigators are represented in the author list. RA and OM contributed equally. In addition, the authors would like to thank the following individuals, who contributed to partner studies or to the MalariaGEN Resource Centre, making this study possible: James Abugri, Nicholas Amoako, Steven M Kiara, John Okombo, Rogelin Raherinjafy, Seheno Razanatsiorimalala, Hongying Jiang, Xin-zhuan Su., and MalariaGEN Plasmodium Falciparum C

Subjects
0301 basic medicine, Drug resistance, Pharmacology, MESH: Asia, Southeastern/epidemiology, MESH: Malaria, Falciparum/epidemiology, Malaria, Falciparum, Artemisinin, Biology (General), GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), Asia, Southeastern, Genetics, Molecular Epidemiology, Microbiology and Infectious Disease, education.field_of_study, MESH: Plasmodium falciparum/genetics, General Neuroscience, General Medicine, MESH: Artemisinins/pharmacology, Artemisinins, 3. Good health, Genomics and Evolutionary Biology, kelch13, Medicine, MESH: Plasmodium falciparum/drug effects, Research Article, medicine.drug, Combination therapy, plasmodium falciparum, QH301-705.5, infectious disease, MESH: Antimalarials/pharmacology, Science, 030106 microbiology, Population, malaria, MESH: Plasmodium falciparum/classification, MESH: Malaria, Falciparum/parasitology, Biology, General Biochemistry, Genetics and Molecular Biology, Antimalarials, 03 medical and health sciences, parasitic diseases, medicine, genomics, MESH: Molecular Epidemiology, education, MESH: Drug Resistance, [SDV.GEN]Life Sciences [q-bio]/Genetics, drug resistance, General Immunology and Microbiology, Molecular epidemiology, evolutionary biology, microbiology, Plasmodium falciparum, medicine.disease, biology.organism_classification, MESH: Africa/epidemiology, lnfectious Diseases and Global Health Radboud Institute for Health Sciences [Radboudumc 4], 030104 developmental biology, artemisinin, Infectious disease (medical specialty), Africa, Other, Human medicine, MESH: Plasmodium falciparum/isolation & purification, Malaria
Abstract

The current epidemic of artemisinin resistant Plasmodium falciparum in Southeast Asia is the result of a soft selective sweep involving at least 20 independent kelch13 mutations. In a large global survey, we find that kelch13 mutations which cause resistance in Southeast Asia are present at low frequency in Africa. We show that African kelch13 mutations have originated locally, and that kelch13 shows a normal variation pattern relative to other genes in Africa, whereas in Southeast Asia there is a great excess of non-synonymous mutations, many of which cause radical amino-acid changes. Thus, kelch13 is not currently undergoing strong selection in Africa, despite a deep reservoir of variations that could potentially allow resistance to emerge rapidly. The practical implications are that public health surveillance for artemisinin resistance should not rely on kelch13 data alone, and interventions to prevent resistance must account for local evolutionary conditions, shown by genomic epidemiology to differ greatly between geographical regions. DOI: http://dx.doi.org/10.7554/eLife.08714.001, eLife digest Malaria is an infectious disease caused by a microscopic parasite called Plasmodium, which is transferred between humans by mosquitos. One species of malaria parasite called Plasmodium falciparum can cause particularly severe and life-threatening forms of the disease. Currently, the most widely used treatment for P. falciparum infections is artemisinin combination therapy, a treatment that combines the drug artemisinin (or a closely related molecule) with another antimalarial drug. However, resistance to artemisinin has started to spread throughout Southeast Asia. Artemisinin resistance is caused by mutations in a parasite gene called kelch13, and researchers have identified over 20 different mutations in P. falciparum that confer artemisinin resistance. The diversity of mutations involved, and the fact that the same mutation can arise independently in different locations, make it difficult to track the spread of resistance using conventional molecular marker approaches. Here, Amato, Miotto et al. sequenced the entire genomes of more than 3,000 clinical samples of P. falciparum from Southeast Asia and Africa, collected as part of a global network of research groups called the MalariaGEN Plasmodium falciparum Community Project. Amato, Miotto et al. found that African parasites had independently acquired many of the same kelch13 mutations that are known to cause resistance to artemisinin in Southeast Asia. However the kelch13 mutations seen in Africa remained at low levels in the parasite population, and appeared to be under much less pressure for evolutionary selection than those found in Southeast Asia. These findings demonstrate that the emergence and spread of resistance to antimalarial drugs does not depend solely on the mutational process, but also on other factors that influence whether the mutations will spread in the population. Understanding how this is affected by different patterns of drug treatments and other environmental conditions will be important in developing more effective strategies for combating malaria. DOI: http://dx.doi.org/10.7554/eLife.08714.002

Published
2016

28. Fast and robust single PCR for Plasmodium sporozoite detection in mosquitoes using the cytochrome oxidase I gene

Author

Echeverry, Diego F., primary, Deason, Nicholas A., additional, Makuru, Victoria, additional, Davidson, Jenna, additional, Xiao, Honglin, additional, Niedbalski, Julie, additional, Yu, Xiaoyu, additional, Stevenson, Jennifer C., additional, Bugoro, Hugo, additional, Aparaimo, Allan, additional, Reuben, Hedrick, additional, Cooper, Robert, additional, Burkot, Thomas R., additional, Russell, Tanya L., additional, Collins, Frank H., additional, and Lobo, Neil F., additional

Published
2017
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29. Índice de Salud para Transformadores de Potencia Inmersos en Aceite Mineral con Voltajes entre 69kV y 230kV usando Lógica Difusa

Author

Cerón, Andrés F, Echeverry, Diego F, Aponte, Guillermo, and Romero, Andrés A

Abstract

Este artículo proporciona una metodología para calcular el índice de salud para el sistema de aislamiento papel-aceite en transformadores de potencia con tensión nominal entre 69kV y 230kV, utilizando lógica difusa. Se presenta una revisión detallada de los límites de aceptación existentes, según la normativa vigente, para cada uno de las variables de entrada: contenido de humedad, acidez, rigidez dieléctrica, factor de disipación del aceite, gases disueltos y el contenido de furanos. Con lo anterior se obtienen las funciones de membresía y se relacionan los seis valores de entrada con el valor de salida, que representa el índice de salud del transformador. Usando datos proporcionados por una empresa del sector eléctrico colombiano para una muestra de 18 transformadores de potencia, se calcula el índice de salud y se presenta un análisis de los resultados. El índice de salud puede ser usado para establecer un ranking de los transformadores de potencia para priorizar por ejemplo la asignación de recursos y definir en mejor forma las actividades de mantenimiento. This article provides a methodology for calculating the health index for oil-paper insulation system in power transformers with rated voltage between 69kV and 230kV, using fuzzy logic. The article also provides a detailed review of the existing limits of acceptance, according to the present standards and for each of the six input variables: moisture content, acidity, dielectric strength, dissipation factor oil, dissolved gas and furan content. With this information, the membership functions are obtained and the six input values are related to the output value, which represents the health index of the transformer. Using data provided by a company of the Colombian electricity sector for 18 power transformers the health index is calculated and the results are analyzed. The health index could be useful for establishing a ranking of the state of power transformers with the aim of better assigning resources and maintenance activities.

Published
2015

31. Compensación Paralelo de Reactivos Durante la Prueba de Aptitud al Cortocircuito en Transformadores de Distribución

Author

Orduña, Iván F, Aponte, Guillermo, and Echeverry, Diego F

Subjects
reactive compensation, capacitors, compensación de reactivos, transformadores, transformers, short-circuit, testing laboratory, capacitores, cortocircuito, laboratorio de ensayos
Abstract

En este artículo se plantea una estrategia de compensación de reactivos paralelo con capacitores, para aumentar la capacidad del campo de prueba de cortocircuito de la Universidad del Valle. Los transformadores son elementos esenciales para mantener el suministro de energía eléctrica. Por esta razón deben tener una capacidad adecuada para soportar las exigencias mecánicas, térmicas y eléctricas que se presentan durante un cortocircuito. En el laboratorio de ensayos de Alta Tensión de la Universidad del Valle (Cali. Colombia), se cuenta con un campo de prueba de cortocircuito para transformadores de distribución, el cual tiene capacidad de probar transformadores monofásicos hasta 100kVA y trifásicos hasta 300kVA. Este campo está limitado por la capacidad de corriente en la red y la prueba sólo se puede hacer a un voltaje fijo, definido por el circuito de alimentación. Los resultados muestran que la compensación paralela es una alternativa viable para reducir los requerimientos de capacidad de corriente de un campo de pruebas de cortocircuito. This article presents a strategy for using parallel reactive compensation with capacitors to increase the capacity of the short circuit test field at the Universidad del Valle. Transformers are key elements to maintain the electrical supply service. For that reason they must have an adequate capacity to withstand the mechanical, thermal and electrical stresses that occur during a short circuit. The High Voltage testing laboratory of the Universidad del Valle ( Cali, Colombia) , carries out short circuit tests for single phase distribution transformers up to 100kVA and for three phase transformers up to 300kVA . The short circuit withstand test at the laboratory is limited by the distribution network current capacity and the test can only be done at a fixed voltage , defined by the electrical network. The results show that parallel reactive compensation is a good alternative to reduce capacity requirements in short circuit tests.

Published
2012

32. A barcode of organellar genome polymorphisms identifies the geographic origin of Plasmodium falciparum strains

Author

Preston, Mark D., primary, Campino, Susana, additional, Assefa, Samuel A., additional, Echeverry, Diego F., additional, Ocholla, Harold, additional, Amambua-Ngwa, Alfred, additional, Stewart, Lindsay B., additional, Conway, David J., additional, Borrmann, Steffen, additional, Michon, Pascal, additional, Zongo, Issaka, additional, Ouédraogo, Jean-Bosco, additional, Djimde, Abdoulaye A., additional, Doumbo, Ogobara K., additional, Nosten, Francois, additional, Pain, Arnab, additional, Bousema, Teun, additional, Drakeley, Chris J., additional, Fairhurst, Rick M., additional, Sutherland, Colin J., additional, Roper, Cally, additional, and Clark, Taane G., additional

Published
2014
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33. Estructura genética y dinámica de la transmisión de malaria por Plasmodium falciparum en la Costa Pacífica colombiana.

Author

Carrasquilla, Manuela, Early, Ángela M., Taylor, Aimee R., Knudson, Angélica, Echeverry, Diego F., Anderson, Timothy J. C., Mancilla, Elvira, Aponte, Samanda, Cárdenas, Pablo, Buckee, Caroline O., Rayner, Julian C., Sáenz, Fabián E., Neafsey, Daniel E., and Corredor, Vladimir

Abstract

Copyright of Biomédica: Revista del Instituto Nacional de Salud is the property of Instituto Nacional de Salud of Colombia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2022

35. Sentinel network for monitoring in vitro susceptibility of Plasmodium falciparum to antimalarial drugs in Colombia: a proof of concept

Author

Aponte, Samanda L, primary, Díaz, Gustavo, additional, Pava, Zuleima, additional, Echeverry, Diego F, additional, Ibarguen, Darío, additional, Rios, Melissa, additional, Murcia, Luz M, additional, Quelal, Claudia, additional, Murillo, Claribel, additional, Gil, Pedro, additional, Björkman, Anders, additional, and Osorio, Lyda, additional

Published
2011
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38. Global sequence variation in the histidine-rich proteins 2 and 3 of Plasmodium falciparum: implications for the performance of malaria rapid diagnostic tests

Author

Baker, Joanne, primary, Ho, Mei-Fong, additional, Pelecanos, Anita, additional, Gatton, Michelle, additional, Chen, Nanhua, additional, Abdullah, Salim, additional, Albertini, Audrey, additional, Ariey, Frederic, additional, Barnwell, John, additional, Bell, David, additional, Cunningham, Jane, additional, Djalle, Djibrine, additional, Echeverry, Diego F, additional, Gamboa, Dionicia, additional, Hii, Jeffery, additional, Kyaw, Myat Phone, additional, Luchavez, Jennifer, additional, Membi, Christopher, additional, Menard, Didier, additional, Murillo, Claribel, additional, Nhem, Sina, additional, Ogutu, Bernhards, additional, Onyor, Pamela, additional, Oyibo, Wellington, additional, Wang, Shan Qing, additional, McCarthy, James, additional, and Cheng, Qin, additional

Published
2010
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42. A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria

Author

Hidayat Trimarsanto, Roberto Amato, Richard D. Pearson, Edwin Sutanto, Rintis Noviyanti, Leily Trianty, Jutta Marfurt, Zuleima Pava, Diego F. Echeverry, Tatiana M. Lopera-Mesa, Lidia M. Montenegro, Alberto Tobón-Castaño, Matthew J. Grigg, Bridget Barber, Timothy William, Nicholas M. Anstey, Sisay Getachew, Beyene Petros, Abraham Aseffa, Ashenafi Assefa, Awab G. Rahim, Nguyen H. Chau, Tran T. Hien, Mohammad S. Alam, Wasif A. Khan, Benedikt Ley, Kamala Thriemer, Sonam Wangchuck, Yaghoob Hamedi, Ishag Adam, Yaobao Liu, Qi Gao, Kanlaya Sriprawat, Marcelo U. Ferreira, Moses Laman, Alyssa Barry, Ivo Mueller, Marcus V. G. Lacerda, Alejandro Llanos-Cuentas, Srivicha Krudsood, Chanthap Lon, Rezika Mohammed, Daniel Yilma, Dhelio B. Pereira, Fe E. J. Espino, Cindy S. Chu, Iván D. Vélez, Chayadol Namaik-larp, Maria F. Villegas, Justin A. Green, Gavin Koh, Julian C. Rayner, Eleanor Drury, Sónia Gonçalves, Victoria Simpson, Olivo Miotto, Alistair Miles, Nicholas J. White, Francois Nosten, Dominic P. Kwiatkowski, Ric N. Price, Sarah Auburn, Pearson, Richard D [0000-0002-7386-3566], Sutanto, Edwin [0000-0002-2997-4648], Marfurt, Jutta [0000-0002-3846-0825], Echeverry, Diego F [0000-0003-0301-4478], Tobón-Castaño, Alberto [0000-0002-1671-2649], Grigg, Matthew J [0000-0001-9914-8352], Alam, Mohammad S [0000-0001-8330-5499], Khan, Wasif A [0000-0002-7650-8068], Ley, Benedikt [0000-0002-5734-0845], Mueller, Ivo [0000-0001-6554-6889], Lacerda, Marcus VG [0000-0003-3374-9985], Pereira, Dhelio B [0000-0002-7761-5498], Espino, Fe EJ [0000-0003-1690-1711], Koh, Gavin [0000-0002-7336-1566], Rayner, Julian C [0000-0002-9835-1014], Drury, Eleanor [0000-0002-9887-6961], Miotto, Olivo [0000-0001-8060-6771], Nosten, Francois [0000-0002-7951-0745], Kwiatkowski, Dominic P [0000-0002-5023-0176], Price, Ric N [0000-0003-2000-2874], Auburn, Sarah [0000-0002-4638-536X], and Apollo - University of Cambridge Repository

Subjects
Likelihood Functions, Internet, Molecular medicine, 45, Epidemiology, 692/308/2056, article, Medicine (miscellaneous), 631/114/1305, General Biochemistry, Genetics and Molecular Biology, 692/4017, Malaria, Genetics research, Machine learning, Malaria, Vivax, 692/699/255/1629, Humans, PLASMODIUM, 692/308/174, Plasmodium vivax, General Agricultural and Biological Sciences
Abstract

Funder: HT was supported by a Charles Darwin University International PhD Scholarship (CDIPS), Funder: Malaysian Ministry of Health (BP00500420), Traditionally, patient travel history has been used to distinguish imported from autochthonous malaria cases, but the dormant liver stages of Plasmodium vivax confound this approach. Molecular tools offer an alternative method to identify, and map imported cases. Using machine learning approaches incorporating hierarchical fixation index and decision tree analyses applied to 799 P. vivax genomes from 21 countries, we identified 33-SNP, 50-SNP and 55-SNP barcodes (GEO33, GEO50 and GEO55), with high capacity to predict the infection's country of origin. The Matthews correlation coefficient (MCC) for an existing, commonly applied 38-SNP barcode (BR38) exceeded 0.80 in 62% countries. The GEO panels outperformed BR38, with median MCCs > 0.80 in 90% countries at GEO33, and 95% at GEO50 and GEO55. An online, open-access, likelihood-based classifier framework was established to support data analysis (vivaxGEN-geo). The SNP selection and classifier methods can be readily amended for other use cases to support malaria control programs.

Published
2022

43. Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples.

Author

Abdel Hamid MM, Abdelraheem MH, Acheampong DO, Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amenga-Etego L, Andagalu B, Anderson T, Andrianaranjaka V, Aniebo I, Aninagyei E, Ansah F, Ansah PO, Apinjoh T, Arnaldo P, Ashley E, Auburn S, Awandare GA, Ba H, Baraka V, Barry A, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Bouyou-Akotet M, Branch O, Bull PC, Cheah H, Chindavongsa K, Chookajorn T, Chotivanich K, Claessens A, Conway DJ, Corredor V, Courtier E, Craig A, D'Alessandro U, Dama S, Day N, Denis B, Dhorda M, Diakite M, Djimde A, Dolecek C, Dondorp A, Doumbia S, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Enosse SMM, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fleharty M, Forbes M, Fukuda M, Gamboa D, Ghansah A, Golassa L, Goncalves S, Harrison GLA, Healy SA, Hendry JA, Hernandez-Koutoucheva A, Hien TT, Hill CA, Hombhanje F, Hott A, Htut Y, Hussein M, Imwong M, Ishengoma D, Jackson SA, Jacob CG, Jeans J, Johnson KJ, Kamaliddin C, Kamau E, Keatley J, Kochakarn T, Konate DS, Konaté A, Kone A, Kwiatkowski DP, Kyaw MP, Kyle D, Lawniczak M, Lee SK, Lemnge M, Lim P, Lon C, Loua KM, Mandara CI, Marfurt J, Marsh K, Maude RJ, Mayxay M, Maïga-Ascofaré O, Miotto O, Mita T, Mobegi V, Mohamed AO, Mokuolu OA, Montgomery J, Morang'a CM, Mueller I, Murie K, Newton PN, Ngo Duc T, Nguyen T, Nguyen TN, Nguyen Thi Kim T, Nguyen Van H, Noedl H, Nosten F, Noviyanti R, Ntui VN, Nzila A, Ochola-Oyier LI, Ocholla H, Oduro A, Omedo I, Onyamboko MA, Ouedraogo JB, Oyebola K, Oyibo WA, Pearson R, Peshu N, Phyo AP, Plowe CV, Price RN, Pukrittayakamee S, Quang HH, Randrianarivelojosia M, Rayner JC, Ringwald P, Rosanas-Urgell A, Rovira-Vallbona E, Ruano-Rubio V, Ruiz L, Saunders D, Shayo A, Siba P, Simpson VJ, Sissoko MS, Smith C, Su XZ, Sutherland C, Takala-Harrison S, Talman A, Tavul L, Thanh NV, Thathy V, Thu AM, Toure M, Tshefu A, Verra F, Vinetz J, Wellems TE, Wendler J, White NJ, Whitton G, Yavo W, and van der Pluijm RW

Abstract

We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network.  It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented.  For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations.  We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent.  We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines.  Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website., Competing Interests: No competing interests were disclosed., (Copyright: © 2023 MalariaGEN et al.)

Published
2023
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44. 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
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45. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples.

Author

Ahouidi A, Ali M, Almagro-Garcia J, Amambua-Ngwa A, Amaratunga C, Amato R, Amenga-Etego L, Andagalu B, Anderson TJC, Andrianaranjaka V, Apinjoh T, Ariani C, Ashley EA, Auburn S, Awandare GA, Ba H, Baraka V, Barry AE, Bejon P, Bertin GI, Boni MF, Borrmann S, Bousema T, Branch O, Bull PC, Busby GBJ, Chookajorn T, Chotivanich K, Claessens A, Conway D, Craig A, D'Alessandro U, Dama S, Day NP, Denis B, Diakite M, Djimdé A, Dolecek C, Dondorp AM, Drakeley C, Drury E, Duffy P, Echeverry DF, Egwang TG, Erko B, Fairhurst RM, Faiz A, Fanello CA, Fukuda MM, Gamboa D, Ghansah A, Golassa L, Goncalves S, Hamilton WL, Harrison GLA, Hart L, Henrichs C, Hien TT, Hill CA, Hodgson A, Hubbart C, Imwong M, Ishengoma DS, Jackson SA, Jacob CG, Jeffery B, Jeffreys AE, Johnson KJ, Jyothi D, Kamaliddin C, Kamau E, Kekre M, Kluczynski K, Kochakarn T, Konaté A, Kwiatkowski DP, Kyaw MP, Lim P, Lon C, Loua KM, Maïga-Ascofaré O, Malangone C, Manske M, Marfurt J, Marsh K, Mayxay M, Miles A, Miotto O, Mobegi V, Mokuolu OA, Montgomery J, Mueller I, Newton PN, Nguyen T, Nguyen TN, Noedl H, Nosten F, Noviyanti R, Nzila A, Ochola-Oyier LI, Ocholla H, Oduro A, Omedo I, Onyamboko MA, Ouedraogo JB, Oyebola K, Pearson RD, Peshu N, Phyo AP, Plowe CV, Price RN, Pukrittayakamee S, Randrianarivelojosia M, Rayner JC, Ringwald P, Rockett KA, Rowlands K, Ruiz L, Saunders D, Shayo A, Siba P, Simpson VJ, Stalker J, Su XZ, Sutherland C, Takala-Harrison S, Tavul L, Thathy V, Tshefu A, Verra F, Vinetz J, Wellems TE, Wendler J, White NJ, Wright I, Yavo W, and Ye H

Abstract

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., Competing Interests: No competing interests were disclosed., (Copyright: © 2021 MalariaGEN et al.)

Published
2021
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46. Short report: polymorphisms in the pfcrt and pfmdr1 genes of Plasmodium falciparum and in vitro susceptibility to amodiaquine and desethylamodiaquine.

Author

Echeverry DF, Holmgren G, Murillo C, Higuita JC, Björkman A, Gil JP, and Osorio L

Subjects
Amino Acid Sequence, Amodiaquine analogs & derivatives, Amodiaquine pharmacology, Animals, Base Sequence, Colombia, Inhibitory Concentration 50, Molecular Sequence Data, Parasitic Sensitivity Tests, Plasmodium falciparum drug effects, Antimalarials pharmacology, Drug Resistance genetics, Membrane Transport Proteins genetics, Multidrug Resistance-Associated Proteins genetics, Plasmodium falciparum genetics, Polymorphism, Single Nucleotide, Protozoan Proteins genetics
Abstract

The potential role of polymorphisms in the pfcrt and pfmdr1 genes and in vitro susceptibility to amodiaquine and desethylamodiaquine were explored in 15 chloroquine-resistant Colombian Plasmodium falciparum isolates. Single nucleotide polymorphisms in the pfcrt gene, including a newly reported mutation (S334N), were seen in isolates with decreased susceptibility to amodiaquine and desethylamodiaquine. The lowest susceptibility found to amodiaquine was observed in an isolate carrying a pfcrt and pfmdr1 Dd2-like haplotype, whereas a pfcrt haplotype related to the 7G8 Brazilian strain was found in a Colombian isolate with the lowest susceptibility to desethylamodiaquine. This exploratory study suggests that polymorphisms in the pfcrt and pfmdr1 genes play a role in amodiaquine and desethylamodiaquine resistance and warrants further study.

Published
2007

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