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1. 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., Rayner, Julian C., Price, Ric N., and Auburn, Sarah

Published
2024
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2. Identification of complex Plasmodium falciparum genetic backgrounds circulating in Africa: a multicountry genomic epidemiology analysis

Author

Miotto, Olivo, Amambua-Ngwa, Alfred, Amenga-Etego, Lucas N, Abdel Hamid, Muzamil M, Adam, Ishag, Aninagyei, Enoch, Apinjoh, Tobias, Awandare, Gordon A, Bejon, Philip, Bertin, Gwladys I, Bouyou-Akotet, Marielle, Claessens, Antoine, Conway, David J, D'Alessandro, Umberto, Diakite, Mahamadou, Djimdé, Abdoulaye, Dondorp, Arjen M, Duffy, Patrick, Fairhurst, Rick M, Fanello, Caterina I, Ghansah, Anita, Ishengoma, Deus S, Lawniczak, Mara, Maïga-Ascofaré, Oumou, Auburn, Sarah, Rosanas-Urgell, Anna, Wasakul, Varanya, White, Nina F D, Harrott, Alexandria, Almagro-Garcia, Jacob, Pearson, Richard D, Goncalves, Sonia, Ariani, Cristina, Bozdech, Zbynek, Hamilton, William L, Simpson, Victoria, and Kwiatkowski, Dominic P

Published
2024
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3. Drug resistance and vaccine target surveillance of Plasmodium falciparum using nanopore sequencing in Ghana

Author

Girgis, Sophia T., Adika, Edem, Nenyewodey, Felix E., Senoo Jnr, Dodzi K., Ngoi, Joyce M., Bandoh, Kukua, Lorenz, Oliver, van de Steeg, Guus, Harrott, Alexandria J. R., Nsoh, Sebastian, Judge, Kim, Pearson, Richard D., Almagro-Garcia, Jacob, Saiid, Samirah, Atampah, Solomon, Amoako, Enock K., Morang’a, Collins M., Asoala, Victor, Adjei, Elrmion S., Burden, William, Roberts-Sengier, William, Drury, Eleanor, Pierce, Megan L., Gonçalves, Sónia, Awandare, Gordon A., Kwiatkowski, Dominic P., Amenga-Etego, Lucas N., and Hamilton, William L.

Published
2023
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4. Chloroquine resistance evolution in Plasmodium falciparum is mediated by the putative amino acid transporter AAT1

Author

Amambua-Ngwa, Alfred, Button-Simons, Katrina A., Li, Xue, Kumar, Sudhir, Brenneman, Katelyn Vendrely, Ferrari, Marco, Checkley, Lisa A., Haile, Meseret T., Shoue, Douglas A., McDew-White, Marina, Tindall, Sarah M., Reyes, Ann, Delgado, Elizabeth, Dalhoff, Haley, Larbalestier, James K., Amato, Roberto, Pearson, Richard D., Taylor, Alexander B., Nosten, François H., D’Alessandro, Umberto, Kwiatkowski, Dominic, Cheeseman, Ian H., Kappe, Stefan H. I., Avery, Simon V., Conway, David J., Vaughan, Ashley M., Ferdig, Michael T., and Anderson, Timothy J. C.

Published
2023
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5. Genomic reconstruction of the SARS-CoV-2 epidemic in England

Author

Robson, Samuel C, Connor, Thomas R, Loman, Nicholas J, Golubchik, Tanya, Martinez Nunez, Rocio T, Bonsall, David, Rambaut, Andrew, Snell, Luke B, Ludden, Catherine, Corden, Sally, Nastouli, Eleni, Nebbia, Gaia, Lythgoe, Katrina, Torok, M Estee, Goodfellow, Ian G, Prieto, Jacqui A, Saeed, Kordo, Houlihan, Catherine, Frampton, Dan, Hamilton, William L, Witney, Adam A, Bucca, Giselda, Pope, Cassie F, Moore, Catherine, Thomson, Emma C, Harrison, Ewan M, Smith, Colin P, Rogan, Fiona, Beckwith, Shaun M, Murray, Abigail, Singleton, Dawn, Eastick, Kirstine, Sheridan, Liz A, Randell, Paul, Jackson, Leigh M, Gonçalves, Sónia, Fairley, Derek J, Loose, Matthew W, Watkins, Joanne, Moses, Samuel, Nicholls, Sam, Bull, Matthew, Smith, Darren L, Aanensen, David M, Aggarwal, Dinesh, Shepherd, James G, Curran, Martin D, Parmar, Surendra, Parker, Matthew D, Williams, Catryn, Glaysher, Sharon, Underwood, Anthony P, Bashton, Matthew, Pacchiarini, Nicole, Loveson, Katie F, Byott, Matthew, Carabelli, Alessandro M, Templeton, Kate E, de Silva, Thushan I, Wang, Dennis, Langford, Cordelia F, Gunson, Rory N, Cottrell, Simon, O’Grady, Justin, Kwiatkowski, Dominic, Lillie, Patrick J, Cortes, Nicholas, Moore, Nathan, Thomas, Claire, Burns, Phillipa J, Mahungu, Tabitha W, Liggett, Steven, Beckett, Angela H, Holden, Matthew TG, Levett, Lisa J, Osman, Husam, Hassan-Ibrahim, Mohammed O, Simpson, David A, Chand, Meera, Gupta, Ravi K, Darby, Alistair C, Paterson, Steve, Pybus, Oliver G, Volz, Erik, de Angelis, Daniela, Robertson, David L, Page, Andrew J, Bassett, Andrew R, Wong, Nick, Taha, Yusri, Erkiert, Michelle J, Spencer Chapman, Michael H, Dewar, Rebecca, McHugh, Martin P, Mookerjee, Siddharth, Aplin, Stephen, Harvey, Matthew, Sass, Thea, Umpleby, Helen, and Wheeler, Helen

Subjects
Genetics, Prevention, Emerging Infectious Diseases, Infectious Diseases, Lung, Good Health and Well Being, Amino Acid Substitution, COVID-19, England, Epidemiological Monitoring, Genome, Viral, Genomics, Humans, Molecular Epidemiology, Mutation, Quarantine, SARS-CoV-2, Spatio-Temporal Analysis, Spike Glycoprotein, Coronavirus, Wellcome Sanger Institute COVID-19 Surveillance Team, COVID-19 Genomics UK (COG-UK) Consortium*, General Science & Technology
Abstract

The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use the dense genomic surveillance data generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of subepidemics that peaked in early autumn 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. The Alpha variant grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed the Alpha variant and eliminated nearly all other lineages in early 2021. Yet a series of variants (most of which contained the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. However, by accounting for sustained introductions, we found that the transmissibility of these variants is unlikely to have exceeded the transmissibility of the Alpha variant. Finally, B.1.617.2/Delta was repeatedly introduced in England and grew rapidly in early summer 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on 26 June 2021.

Published
2021

6. Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination.

Author

Jacob, Christopher G, Thuy-Nhien, Nguyen, Mayxay, Mayfong, Maude, Richard J, Quang, Huynh Hong, Hongvanthong, Bouasy, Vanisaveth, Viengxay, Ngo Duc, Thang, Rekol, Huy, van der Pluijm, Rob, von Seidlein, Lorenz, Fairhurst, Rick, Nosten, François, Hossain, Md Amir, Park, Naomi, Goodwin, Scott, Ringwald, Pascal, Chindavongsa, Keobouphaphone, Newton, Paul, Ashley, Elizabeth, Phalivong, Sonexay, Maude, Rapeephan, Leang, Rithea, Huch, Cheah, Dong, Le Thanh, Nguyen, Kim-Tuyen, Nhat, Tran Minh, Hien, Tran Tinh, Nguyen, Hoa, Zdrojewski, Nicole, Canavati, Sara, Sayeed, Abdullah Abu, Uddin, Didar, Buckee, Caroline, Fanello, Caterina I, Onyamboko, Marie, Peto, Thomas, Tripura, Rupam, Amaratunga, Chanaki, Myint Thu, Aung, Delmas, Gilles, Landier, Jordi, Parker, Daniel M, Chau, Nguyen Hoang, Lek, Dysoley, Suon, Seila, Callery, James, Jittamala, Podjanee, Hanboonkunupakarn, Borimas, Pukrittayakamee, Sasithon, Phyo, Aung Pyae, Smithuis, Frank, Lin, Khin, Thant, Myo, Hlaing, Tin Maung, Satpathi, Parthasarathi, Satpathi, Sanghamitra, Behera, Prativa K, Tripura, Amar, Baidya, Subrata, Valecha, Neena, Anvikar, Anupkumar R, Ul Islam, Akhter, Faiz, Abul, Kunasol, Chanon, Drury, Eleanor, Kekre, Mihir, Ali, Mozam, Love, Katie, Rajatileka, Shavanthi, Jeffreys, Anna E, Rowlands, Kate, Hubbart, Christina S, Dhorda, Mehul, Vongpromek, Ranitha, Kotanan, Namfon, Wongnak, Phrutsamon, Almagro Garcia, Jacob, Pearson, Richard D, Ariani, Cristina V, Chookajorn, Thanat, Malangone, Cinzia, Nguyen, T, Stalker, Jim, Jeffery, Ben, Keatley, Jonathan, Johnson, Kimberly J, Muddyman, Dawn, Chan, Xin Hui S, Sillitoe, John, Amato, Roberto, Simpson, Victoria, Gonçalves, Sonia, Rockett, Kirk, Day, Nicholas P, Dondorp, Arjen M, Kwiatkowski, Dominic P, and Miotto, Olivo

Subjects
asia, drug resistance, epidemiology, genetic surveillance, global health, infectious disease, malaria, microbiology, Biochemistry and Cell Biology
Abstract

BackgroundNational Malaria Control Programmes (NMCPs) currently make limited use of parasite genetic data. We have developed GenRe-Mekong, a platform for genetic surveillance of malaria in the Greater Mekong Subregion (GMS) that enables NMCPs to implement large-scale surveillance projects by integrating simple sample collection procedures in routine public health procedures.MethodsSamples from symptomatic patients are processed by SpotMalaria, a high-throughput system that produces a comprehensive set of genotypes comprising several drug resistance markers, species markers and a genomic barcode. GenRe-Mekong delivers Genetic Report Cards, a compendium of genotypes and phenotype predictions used to map prevalence of resistance to multiple drugs.ResultsGenRe-Mekong has worked with NMCPs and research projects in eight countries, processing 9623 samples from clinical cases. Monitoring resistance markers has been valuable for tracking the rapid spread of parasites resistant to the dihydroartemisinin-piperaquine combination therapy. In Vietnam and Laos, GenRe-Mekong data have provided novel knowledge about the spread of these resistant strains into previously unaffected provinces, informing decision-making by NMCPs.ConclusionsGenRe-Mekong provides detailed knowledge about drug resistance at a local level, and facilitates data sharing at a regional level, enabling cross-border resistance monitoring and providing the public health community with valuable insights. The project provides a rich open data resource to benefit the entire malaria community.FundingThe GenRe-Mekong project is funded by the Bill and Melinda Gates Foundation (OPP11188166, OPP1204268). Genotyping and sequencing were funded by the Wellcome Trust (098051, 206194, 203141, 090770, 204911, 106698/B/14/Z) and Medical Research Council (G0600718). A proportion of samples were collected with the support of the UK Department for International Development (201900, M006212), and Intramural Research Program of the National Institute of Allergy and Infectious Diseases.

Published
2021

7. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

Author

Meng, Bo, Kemp, Steven A, Papa, Guido, Datir, Rawlings, Ferreira, Isabella ATM, Marelli, Sara, Harvey, William T, Lytras, Spyros, Mohamed, Ahmed, Gallo, Giulia, Thakur, Nazia, Collier, Dami A, Mlcochova, Petra, Consortium, The COVID-19 Genomics UK, Robson, Samuel C, Loman, Nicholas J, Connor, Thomas R, Golubchik, Tanya, Nunez, Rocio T Martinez, Ludden, Catherine, Corden, Sally, Johnston, Ian, Bonsall, David, Smith, Colin P, Awan, Ali R, Bucca, Giselda, Torok, M Estee, Saeed, Kordo, Prieto, Jacqui A, Jackson, David K, Hamilton, William L, Snell, Luke B, Moore, Catherine, Harrison, Ewan M, Goncalves, Sonia, Fairley, Derek J, Loose, Matthew W, Watkins, Joanne, Livett, Rich, Moses, Samuel, Amato, Roberto, Nicholls, Sam, Bull, Matthew, Smith, Darren L, Barrett, Jeff, Aanensen, David M, Curran, Martin D, Parmar, Surendra, Aggarwal, Dinesh, Shepherd, James G, Parker, Matthew D, Glaysher, Sharon, Bashton, Matthew, Underwood, Anthony P, Pacchiarini, Nicole, Loveson, Katie F, Templeton, Kate E, Langford, Cordelia F, Sillitoe, John, de Silva, Thushan I, Wang, Dennis, Kwiatkowski, Dominic, Rambaut, Andrew, O’Grady, Justin, Cottrell, Simon, Holden, Matthew TG, Thomson, Emma C, Osman, Husam, Andersson, Monique, Chauhan, Anoop J, Hassan-Ibrahim, Mohammed O, Lawniczak, Mara, Alderton, Alex, Chand, Meera, Constantinidou, Chrystala, Unnikrishnan, Meera, Darby, Alistair C, Hiscox, Julian A, Paterson, Steve, Martincorena, Inigo, Volz, Erik M, Page, Andrew J, Pybus, Oliver G, Bassett, Andrew R, Ariani, Cristina V, Chapman, Michael H Spencer, Li, Kathy K, Shah, Rajiv N, Jesudason, Natasha G, Taha, Yusri, McHugh, Martin P, Dewar, Rebecca, Jahun, Aminu S, McMurray, Claire, Pandey, Sarojini, McKenna, James P, Nelson, Andrew, Young, Gregory R, McCann, Clare M, and Elliott, Scott

Subjects
Emerging Infectious Diseases, Infectious Diseases, Lung, Pneumonia, Good Health and Well Being, Animals, Antibodies, Neutralizing, Antibodies, Viral, COVID-19, Cell Line, Chlorocebus aethiops, HEK293 Cells, Humans, Immune Evasion, Mutation, Pandemics, Phylogeny, Protein Binding, Recurrence, SARS-CoV-2, Spike Glycoprotein, Coronavirus, Vero Cells, COVID-19 Genomics UK (COG-UK) Consortium, Alpha variant, B.1.1.7, antibody escape, deletion, infectivity, neutralizing antibodies, resistance, spike mutation, Biochemistry and Cell Biology, Medical Physiology
Abstract

We report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike ΔH69/V70 in multiple independent lineages, often occurring after acquisition of receptor binding motif replacements such as N439K and Y453F, known to increase binding affinity to the ACE2 receptor and confer antibody escape. In vitro, we show that, although ΔH69/V70 itself is not an antibody evasion mechanism, it increases infectivity associated with enhanced incorporation of cleaved spike into virions. ΔH69/V70 is able to partially rescue infectivity of spike proteins that have acquired N439K and Y453F escape mutations by increased spike incorporation. In addition, replacement of the H69 and V70 residues in the Alpha variant B.1.1.7 spike (where ΔH69/V70 occurs naturally) impairs spike incorporation and entry efficiency of the B.1.1.7 spike pseudotyped virus. Alpha variant B.1.1.7 spike mediates faster kinetics of cell-cell fusion than wild-type Wuhan-1 D614G, dependent on ΔH69/V70. Therefore, as ΔH69/V70 compensates for immune escape mutations that impair infectivity, continued surveillance for deletions with functional effects is warranted.

Published
2021

8. Malaria is a cause of iron deficiency in African children

Author

Muriuki, John Muthii, Mentzer, Alexander J, Mitchell, Ruth, Webb, Emily L, Etyang, Anthony O, Kyobutungi, Catherine, Morovat, Alireza, Kimita, Wandia, Ndungu, Francis M, Macharia, Alex W, Ngetsa, Caroline J, Makale, Johnstone, Lule, Swaib A, Musani, Solomon K, Raffield, Laura M, Cutland, Clare L, Sirima, Sodiomon B, Diarra, Amidou, Tiono, Alfred B, Fried, Michal, Gwamaka, Moses, Adu-Afarwuah, Seth, Wirth, James P, Wegmüller, Rita, Madhi, Shabir A, Snow, Robert W, Hill, Adrian VS, Rockett, Kirk A, Sandhu, Manjinder S, Kwiatkowski, Dominic P, Prentice, Andrew M, Byrd, Kendra A, Ndjebayi, Alex, Stewart, Christine P, Engle-Stone, Reina, Green, Tim J, Karakochuk, Crystal D, Suchdev, Parminder S, Bejon, Philip, Duffy, Patrick E, Davey Smith, George, Elliott, Alison M, Williams, Thomas N, and Atkinson, Sarah H

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Clinical Sciences, Infectious Diseases, Clinical Research, Sickle Cell Disease, Malaria, Rare Diseases, Genetics, Vector-Borne Diseases, Hematology, Pediatric, 2.4 Surveillance and distribution, 6.1 Pharmaceuticals, Infection, Good Health and Well Being, Absorption, Physiological, Adolescent, Africa, Child, Child, Preschool, Female, Geography, Hepcidins, Humans, Infant, Iron Deficiencies, Male, Mendelian Randomization Analysis, Sickle Cell Trait, Medical and Health Sciences, Immunology, Biomedical and clinical sciences, Health sciences
Abstract

Malaria and iron deficiency (ID) are common and interrelated public health problems in African children. Observational data suggest that interrupting malaria transmission reduces the prevalence of ID1. To test the hypothesis that malaria might cause ID, we used sickle cell trait (HbAS, rs334 ), a genetic variant that confers specific protection against malaria2, as an instrumental variable in Mendelian randomization analyses. HbAS was associated with a 30% reduction in ID among children living in malaria-endemic countries in Africa (n = 7,453), but not among individuals living in malaria-free areas (n = 3,818). Genetically predicted malaria risk was associated with an odds ratio of 2.65 for ID per unit increase in the log incidence rate of malaria. This suggests that an intervention that halves the risk of malaria episodes would reduce the prevalence of ID in African children by 49%.

Published
2021

9. Genomic analysis of Plasmodium vivax describes patterns of connectivity and putative drivers of adaptation in Ethiopia

Author

Kebede, Alebachew Messele, Sutanto, Edwin, Trimarsanto, Hidayat, Benavente, Ernest Diez, Barnes, Mariana, Pearson, Richard D., Siegel, Sasha V., Erko, Berhanu, Assefa, Ashenafi, Getachew, Sisay, Aseffa, Abraham, Petros, Beyene, Lo, Eugenia, Mohammed, Rezika, Yilma, Daniel, Rumaseb, Angela, Nosten, Francois, Noviyanti, Rintis, Rayner, Julian C., Kwiatkowski, Dominic P., Price, Ric N., Golassa, Lemu, and Auburn, Sarah

Published
2023
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10. 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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11. Genome-wide association studies reveal novel loci associated with pyrethroid and organophosphate resistance in Anopheles gambiae and Anopheles coluzzii

Author

Lucas, Eric R., Nagi, Sanjay C., Egyir-Yawson, Alexander, Essandoh, John, Dadzie, Samuel, Chabi, Joseph, Djogbénou, Luc S., Medjigbodo, Adandé A., Edi, Constant V., Kétoh, Guillaume K., Koudou, Benjamin G., Van’t Hof, Arjen E., Rippon, Emily J., Pipini, Dimitra, Harding, Nicholas J., Dyer, Naomi A., Cerdeira, Louise T., Clarkson, Chris S., Kwiatkowski, Dominic P., Miles, Alistair, Donnelly, Martin J., and Weetman, David

Published
2023
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12. Malaria outbreak in Laos driven by a selective sweep for Plasmodium falciparum kelch13 R539T mutants: a genetic epidemiology analysis

Author

Wasakul, Varanya, Disratthakit, Areeya, Mayxay, Mayfong, Chindavongsa, Keobouphaphone, Sengsavath, Viengphone, Thuy-Nhien, Nguyen, Pearson, Richard D, Phalivong, Sonexay, Xayvanghang, Saiamphone, Maude, Richard J, Gonçalves, Sónia, Day, Nicholas P, Newton, Paul N, Ashley, Elizabeth A, Kwiatkowski, Dominic P, Dondorp, Arjen M, and Miotto, Olivo

Published
2023
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13. Malaria protection due to sickle haemoglobin depends on parasite genotype

Author

Band, Gavin, Leffler, Ellen M., Jallow, Muminatou, Sisay-Joof, Fatoumatta, Ndila, Carolyne M., Macharia, Alexander W., Hubbart, Christina, Jeffreys, Anna E., Rowlands, Kate, Nguyen, Thuy, Gonçalves, Sónia, Ariani, Cristina V., Stalker, Jim, Pearson, Richard D., Amato, Roberto, Drury, Eleanor, Sirugo, Giorgio, d’Alessandro, Umberto, Bojang, Kalifa A., Marsh, Kevin, Peshu, Norbert, Saelens, Joseph W., Diakité, Mahamadou, Taylor, Steve M., Conway, David J., Williams, Thomas N., Rockett, Kirk A., and Kwiatkowski, Dominic P.

Published
2022
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15. 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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16. Genomic reconstruction of the SARS-CoV-2 epidemic in England

Author

Vöhringer, Harald S., Sanderson, Theo, Sinnott, Matthew, De Maio, Nicola, Nguyen, Thuy, Goater, Richard, Schwach, Frank, Harrison, Ian, Hellewell, Joel, Ariani, Cristina V., Gonçalves, Sonia, Jackson, David K., Johnston, Ian, Jung, Alexander W., Saint, Callum, Sillitoe, John, Suciu, Maria, Goldman, Nick, Panovska-Griffiths, Jasmina, Birney, Ewan, Volz, Erik, Funk, Sebastian, Kwiatkowski, Dominic, Chand, Meera, Martincorena, Inigo, Barrett, Jeffrey C., and Gerstung, Moritz

Published
2021
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17. Molecular epidemiology of resistance to antimalarial drugs in the Greater Mekong subregion: an observational study

Author

Imwong, Mallika, Dhorda, Mehul, Myo Tun, Kyaw, Thu, Aung Myint, Phyo, Aung Pyae, Proux, Stephane, Suwannasin, Kanokon, Kunasol, Chanon, Srisutham, Suttipat, Duanguppama, Jureeporn, Vongpromek, Ranitha, Promnarate, Cholrawee, Saejeng, Aungkana, Khantikul, Nardlada, Sugaram, Rungniran, Thanapongpichat, Supinya, Sawangjaroen, Nongyao, Sutawong, Kreepol, Han, Kay Thwe, Htut, Ye, Linn, Khin, Win, Aye Aye, Hlaing, Tin M, van der Pluijm, Rob W, Mayxay, Mayfong, Pongvongsa, Tiengkham, Phommasone, Koukeo, Tripura, Rupam, Peto, Thomas J, von Seidlein, Lorenz, Nguon, Chea, Lek, Dysoley, Chan, Xin Hui S, Rekol, Huy, Leang, Rithea, Huch, Cheah, Kwiatkowski, Dominic P, Miotto, Olivo, Ashley, Elizabeth A, Kyaw, Myat Phone, Pukrittayakamee, Sasithon, Day, Nicholas P J, Dondorp, Arjen M, Smithuis, Frank M, Nosten, Francois H, and White, Nicholas J

Published
2020
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18. Triple artemisinin-based combination therapies versus artemisinin-based combination therapies for uncomplicated Plasmodium falciparum malaria: a multicentre, open-label, randomised clinical trial

Author

van der Pluijm, Rob W, Tripura, Rupam, Hoglund, Richard M, Phyo, Aung Pyae, Lek, Dysoley, ul Islam, Akhter, Anvikar, Anupkumar R, Satpathi, Parthasarathi, Satpathi, Sanghamitra, Behera, Prativa Kumari, Tripura, Amar, Baidya, Subrata, Onyamboko, Marie, Chau, Nguyen Hoang, Sovann, Yok, Suon, Seila, Sreng, Sokunthea, Mao, Sivanna, Oun, Savuth, Yen, Sovannary, Amaratunga, Chanaki, Chutasmit, Kitipumi, Saelow, Chalermpon, Runcharern, Ratchadaporn, Kaewmok, Weerayuth, Hoa, Nhu Thi, Thanh, Ngo Viet, Hanboonkunupakarn, Borimas, Callery, James J, Mohanty, Akshaya Kumar, Heaton, James, Thant, Myo, Gantait, Kripasindhu, Ghosh, Tarapada, Amato, Roberto, Pearson, Richard D, Jacob, Christopher G, Gonçalves, Sónia, Mukaka, Mavuto, Waithira, Naomi, Woodrow, Charles J, Grobusch, Martin P, van Vugt, Michele, Fairhurst, Rick M, Cheah, Phaik Yeong, Peto, Thomas J, von Seidlein, Lorenz, Dhorda, Mehul, Maude, Richard J, Winterberg, Markus, Thuy-Nhien, Nguyen T, Kwiatkowski, Dominic P, Imwong, Mallika, Jittamala, Podjanee, Lin, Khin, Hlaing, Tin Maung, Chotivanich, Kesinee, Huy, Rekol, Fanello, Caterina, Ashley, Elizabeth, Mayxay, Mayfong, Newton, Paul N, Hien, Tran Tinh, Valeche, Neena, Smithuis, Frank, Pukrittayakamee, Sasithon, Faiz, Abul, Miotto, Olivo, Tarning, Joel, Day, Nicholas PJ, White, Nicholas J, Dondorp, Arjen M, Pyae Phyo, Aung, Thuy-Nhien, Nguyen Thanh, Valecha, Neena, and Day, Nicholas P J

Published
2020
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19. THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites.

Author

Chang, Hsiao-Han, Worby, Colin J, Yeka, Adoke, Nankabirwa, Joaniter, Kamya, Moses R, Staedke, Sarah G, Dorsey, Grant, Murphy, Maxwell, Neafsey, Daniel E, Jeffreys, Anna E, Hubbart, Christina, Rockett, Kirk A, Amato, Roberto, Kwiatkowski, Dominic P, Buckee, Caroline O, and Greenhouse, Bryan

Subjects
Humans, Plasmodium falciparum, Malaria, Falciparum, Population Surveillance, Risk Assessment, Risk Factors, Gene Frequency, Polymorphism, Single Nucleotide, Uganda, Malaria, Falciparum, Polymorphism, Single Nucleotide, Mathematical Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics
Abstract

As many malaria-endemic countries move towards elimination of Plasmodium falciparum, the most virulent human malaria parasite, effective tools for monitoring malaria epidemiology are urgent priorities. P. falciparum population genetic approaches offer promising tools for understanding transmission and spread of the disease, but a high prevalence of multi-clone or polygenomic infections can render estimation of even the most basic parameters, such as allele frequencies, challenging. A previous method, COIL, was developed to estimate complexity of infection (COI) from single nucleotide polymorphism (SNP) data, but relies on monogenomic infections to estimate allele frequencies or requires external allele frequency data which may not available. Estimates limited to monogenomic infections may not be representative, however, and when the average COI is high, they can be difficult or impossible to obtain. Therefore, we developed THE REAL McCOIL, Turning HEterozygous SNP data into Robust Estimates of ALelle frequency, via Markov chain Monte Carlo, and Complexity Of Infection using Likelihood, to incorporate polygenomic samples and simultaneously estimate allele frequency and COI. This approach was tested via simulations then applied to SNP data from cross-sectional surveys performed in three Ugandan sites with varying malaria transmission. We show that THE REAL McCOIL consistently outperforms COIL on simulated data, particularly when most infections are polygenomic. Using field data we show that, unlike with COIL, we can distinguish epidemiologically relevant differences in COI between and within these sites. Surprisingly, for example, we estimated high average COI in a peri-urban subregion with lower transmission intensity, suggesting that many of these cases were imported from surrounding regions with higher transmission intensity. THE REAL McCOIL therefore provides a robust tool for understanding the molecular epidemiology of malaria across transmission settings.

Published
2017

21. Genomic Analysis of Plasmodium vivax in Southern Ethiopia Reveals Selective Pressures in Multiple Parasite Mechanisms

Author

Auburn, Sarah, Getachew, Sisay, Pearson, Richard D., Amato, Roberto, Miotto, Olivo, Trimarsanto, Hidayat, Zhu, Sha Joe, Rumaseb, Angela, Marfurt, Jutta, Noviyanti, Rintis, Grigg, Matthew J., Barber, Bridget, William, Timothy, Goncalves, Sonia Morgado, Drury, Eleanor, Sriprawat, Kanlaya, Anstey, Nicholas M., Nosten, Francois, Petros, Beyene, Aseffa, Abraham, McVean, Gil, Kwiatkowski, Dominic P., and Price, Ric N.

Published
2019

23. Evolution and expansion of multidrug-resistant malaria in southeast Asia: a genomic epidemiology study

Author

Hamilton, William L, Amato, Roberto, van der Pluijm, Rob W, Jacob, Christopher G, Quang, Huynh Hong, Thuy-Nhien, Nguyen Thanh, Hien, Tran Tinh, Hongvanthong, Bouasy, Chindavongsa, Keobouphaphone, Mayxay, Mayfong, Huy, Rekol, Leang, Rithea, Huch, Cheah, Dysoley, Lek, Amaratunga, Chanaki, Suon, Seila, Fairhurst, Rick M, Tripura, Rupam, Peto, Thomas J, Sovann, Yok, Jittamala, Podjanee, Hanboonkunupakarn, Borimas, Pukrittayakamee, Sasithon, Chau, Nguyen Hoang, Imwong, Mallika, Dhorda, Mehul, Vongpromek, Ranitha, Chan, Xin Hui S, Maude, Richard J, Pearson, Richard D, Nguyen, T, Rockett, Kirk, Drury, Eleanor, Gonçalves, Sónia, White, Nicholas J, Day, Nicholas P, Kwiatkowski, Dominic P, Dondorp, Arjen M, and Miotto, Olivo

Published
2019
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24. Determinants of dihydroartemisinin-piperaquine treatment failure in Plasmodium falciparum malaria in Cambodia, Thailand, and Vietnam: a prospective clinical, pharmacological, and genetic study

Author

van der Pluijm, Rob W, Imwong, Mallika, Chau, Nguyen Hoang, Hoa, Nhu Thi, Thuy-Nhien, Nguyen Thanh, Thanh, Ngo Viet, Jittamala, Podjanee, Hanboonkunupakarn, Borimas, Chutasmit, Kitipumi, Saelow, Chalermpon, Runjarern, Ratchadaporn, Kaewmok, Weerayuth, Tripura, Rupam, Peto, Thomas J, Yok, Sovann, Suon, Seila, Sreng, Sokunthea, Mao, Sivanna, Oun, Savuth, Yen, Sovannary, Amaratunga, Chanaki, Lek, Dysoley, Huy, Rekol, Dhorda, Mehul, Chotivanich, Kesinee, Ashley, Elizabeth A, Mukaka, Mavuto, Waithira, Naomi, Cheah, Phaik Yeong, Maude, Richard J, Amato, Roberto, Pearson, Richard D, Gonçalves, Sónia, Jacob, Christopher G, Hamilton, William L, Fairhurst, Rick M, Tarning, Joel, Winterberg, Markus, Kwiatkowski, Dominic P, Pukrittayakamee, Sasithon, Hien, Tran Tinh, Day, Nicholas PJ, Miotto, Olivo, White, Nicholas J, and Dondorp, Arjen M

Published
2019
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26. A complexPlasmodium falciparumcryptotype circulating at low frequency across the African continent

Author

Miotto, Olivo, primary, Amambua-Ngwa, Alfred, additional, Amenga-Etego, Lucas, additional, Abdel Hamid, Muzamil M, additional, Adam, Ishag, additional, Aninagyei, Enoch, additional, Apinjoh, Tobias, additional, Awandare, Gordon A, additional, Bejon, Philip, additional, Bertin, Gwladys I, additional, Bouyou-Akotet, Marielle, additional, Claessens, Antoine, additional, Conway, David J, additional, D’Alessandro, Umberto, additional, Diakite, Mahamadou, additional, Djimdé, Abdoulaye, additional, Dondorp, Arjen M, additional, Duffy, Patrick, additional, Fairhurst, Rick M, additional, Fanello, Caterina I, additional, Ghansah, Anita, additional, Ishengoma, Deus, additional, Lawniczak, Mara, additional, Maïga-Ascofaré, Oumou, additional, Auburn, Sarah, additional, Rosanas-Urgell, Anna, additional, Wasakul, Varanya, additional, White, Nina FD, additional, Almagro-Garcia, Jacob, additional, Pearson, Richard D, additional, Goncalves, Sonia, additional, Ariani, Cristina, additional, Bozdech, Zbynek, additional, Hamilton, William, additional, Simpson, Victoria, additional, and Kwiatkowski, Dominic P, additional

Published
2024
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28. Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study

Author

Abathina, Amadou, Abubakar, Ismaela, Achidi, Eric, Agbenyega, Tsiri, Aiyegbo, Mohammed, Akoto, Alex, Allen, Angela, Allen, Stephen, Amenga-Etego, Lucas, Amodu, Folakemi, Amodu, Olukemi, Anchang-Kimbi, Judith, Ansah, Nana, Ansah, Patrick, Ansong, Daniel, Antwi, Sampson, Anyorigiya, Thomas, Apinjoh, Tobias, Asafo-Agyei, Emmanuel, Asoala, Victor, Atuguba, Frank, Auburn, Sarah, Bah, Abdou, Bamba, Kariatou, Bancone, Germana, Band, Gavin, Barnwell, David, Barry, Abdoulaye, Bauni, Evasius, Besingi, Richard, Bojang, Kalifa, Bougouma, Edith, Bull, Susan, Busby, George, Camara, Abdoulie, Camara, Landing, Campino, Susana, Carter, Richard, Carucci, Dan, Casals-Pascual, Climent, Ceesay, Ndey, Ceesay, Pa, Chau, Tran, Chuong, Ly, Clark, Taane, Clarke, Geraldine, Cole-Ceesay, Ramou, Conway, David, Cook, Katharine, Cook, Olivia, Cornelius, Victoria, Corran, Patrick, Correa, Simon, Cox, Sharon, Craik, Rachel, Danso, Bakary, Davis, Timothy, Day, Nicholas, Deloukas, Panos, Dembele, Awa, deVries, Jantina, Dewasurendra, Rajika, Diakite, Mahamadou, Diarra, Elizabeth, Dibba, Yaya, Diss, Andrea, Djimdé, Abdoulaye, Dolo, Amagana, Doumbo, Ogobara, Doyle, Alan, Drakeley, Chris, Drury, Eleanor, Duffy, Patrick, Dunstan, Sarah, Ebonyi, Augustine, Elhassan, Ahmed, Elhassan, Ibrahim, Elzein, Abier, Enimil, Anthony, Esangbedo, Pamela, Evans, Jennifer, Evans, Julie, Farrar, Jeremy, Fernando, Deepika, Fitzpatrick, Kathryn, Fullah, Janet, Garcia, Jacob, Ghansah, Anita, Gottleib, Michael, Green, Angie, Hart, Lee, Hennsman, Meike, Hien, Tran, Hieu, Nguyen, Hilton, Eliza, Hodgson, Abraham, Horstmann, Rolf, Hubbart, Christina, Hughes, Catherine, Hussein, Ayman, Hutton, Robert, Ibrahim, Muntaser, Ishengoma, Deus, Jaiteh, Jula, Jallow, Mariatou, Jallow, Muminatou, Jammeh, Kebba, Jasseh, Momodou, Jeffreys, Anna, Jobarteh, Amie, Johnson, Kimberly, Joseph, Sarah, Jyothi, Dushyanth, Kachala, David, Kamuya, Dorcas, Kanyi, Haddy, Karunajeewa, Harin, Karunaweera, Nadira, Keita, Momodou, Kerasidou, Angeliki, Khan, Aja, Kivinen, Katja, Kokwaro, Gilbert, Konate, Amadou, Konate, Salimata, Koram, Kwadwo, Kwiatkowski, Dominic, Laman, Moses, Le, Si, Leffler, Ellen, Lemnge, Martha, Lin, Enmoore, Ly, Alioune, Macharia, Alexander, MacInnis, Bronwyn, Mai, Nguyen, Makani, Julie, Malangone, Cinzia, Mangano, Valentina, Manjurano, Alphaxard, Manneh, Lamin, Manning, Laurens, Manske, Magnus, Marsh, Kevin, Marsh, Vicki, Maslen, Gareth, Maxwell, Caroline, Mbunwe, Eric, McCreight, Marilyn, Mead, Daniel, Mendy, Alieu, Mendy, Anthony, Mensah, Nathan, Michon, Pascal, Miles, Alistair, Miotto, Olivo, Modiano, David, Mohamed, Hiba, Molloy, Sile, Molyneux, Malcolm, Molyneux, Sassy, Moore, Mike, Moyes, Catherine, Mtei, Frank, Mtove, George, Mueller, Ivo, Mugri, Regina, Munthali, Annie, Mutabingwa, Theonest, Nadjm, Behzad, Ndi, Andre, Ndila, Carolyne, Newton, Charles, Niangaly, Amadou, Njie, Haddy, Njie, Jalimory, Njie, Madi, Njie, Malick, Njie, Sophie, Njiragoma, Labes, Nkrumah, Francis, Ntunthama, Neema, Nyika, Aceme, Nyirongo, Vysaul, O'Brien, John, Obu, Herbert, Oduro, Abraham, Ofori, Alex, Olaniyan, Subulade, Olaosebikan, Rasaq, Oluoch, Tom, Omotade, Olayemi, Oni, Olajumoke, Onykwelu, Emmanuel, Opi, Daniel, Orimadegun, Adebola, O'Riordan, Sean, Ouedraogo, Issa, Oyola, Samuel, Parker, Michael, Pearson, Richard, Pensulo, Paul, Peshu, Norbert, Phiri, Ajib, Phu, Nguyen, Pinder, Margaret, Pirinen, Matti, Plowe, Chris, Potter, Claire, Poudiougou, Belco, Puijalon, Odile, Quyen, Nguyen, Ragoussis, Ioannis, Ragoussis, Jiannis, Rasheed, Oba, Reeder, John, Reyburn, Hugh, Riley, Eleanor, Risley, Paul, Rockett, Kirk, Rodford, Joanne, Rogers, Jane, Rogers, William, Rowlands, Kate, Ruano-Rubio, Valentín, Sabally-Ceesay, Kumba, Sadiq, Abubacar, Saidy-Khan, Momodou, Saine, Horeja, Sakuntabhai, Anavaj, Sall, Abdourahmane, Sambian, David, Sambou, Idrissa, SanJoaquin, Miguel, Sepúlveda, Nuno, Shah, Shivang, Shelton, Jennifer, Siba, Peter, Silva, Nilupa, Simmons, Cameron, Simpore, Jaques, Singhasivanon, Pratap, Sinh, Dinh, Sirima, Sodiomon, Sirugo, Giorgio, Sisay-Joof, Fatoumatta, Sissoko, Sibiry, Small, Kerrin, Somaskantharajah, Elilan, Spencer, Chris, Stalker, Jim, Stevens, Marryat, Suriyaphol, Prapat, Sylverken, Justice, Taal, Bintou, Tall, Adama, Taylor, Terrie, Teo, Yik, Thai, Cao, Thera, Mahamadou, Titanji, Vincent, Toure, Ousmane, Troye-Blomberg, Marita, Usen, Stanley, Uyoga, Sophie, Vanderwal, Aaron, Wangai, Hannah, Watson, Renee, Williams, Thomas, Wilson, Michael, Wrigley, Rebecca, Yafi, Clarisse, Yamoah, Lawrence, Ndila, Carolyne M, Macharia, Alexander W, Nyutu, Gideon, Ojal, John, Shebe, Mohammed, Awuondo, Kennedy O, Mturi, Neema, Tsofa, Benjamin, Clark, Taane G, Kariuki, Silvia, Mackinnon, Margaret, Maitland, Kathryn, Kwiatkowski, Dominic P, Rockett, Kirk A, and Williams, Thomas N

Published
2018
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30. Publisher Correction: Genomic reconstruction of the SARS CoV-2 epidemic in England

Author

Vöhringer, Harald S., Sanderson, Theo, Sinnott, Matthew, De Maio, Nicola, Nguyen, Thuy, Goater, Richard, Schwach, Frank, Harrison, Ian, Hellewell, Joel, Ariani, Cristina V., Gonçalves, Sonia, Jackson, David K., Johnston, Ian, Jung, Alexander W., Saint, Callum, Sillitoe, John, Suciu, Maria, Goldman, Nick, Panovska-Griffiths, Jasmina, Birney, Ewan, Volz, Erik, Funk, Sebastian, Kwiatkowski, Dominic, Chand, Meera, Martincorena, Inigo, Barrett, Jeffrey C., and Gerstung, Moritz

Published
2022
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31. Resistance to malaria through structural variation of red blood cell invasion receptors

Author

Malaria Genomic Epidemiology Network, Leffler, Ellen M., Band, Gavin, Busby, George B. J., Kivinen, Katja, Le, Quang Si, Clarke, Geraldine M., Bojang, Kalifa A., Conway, David J., Jallow, Muminatou, Sisay-Joof, Fatoumatta, Bougouma, Edith C., Mangano, Valentina D., Modiano, David, Sirima, Sodiomon B., Achidi, Eric, Apinjoh, Tobias O., Marsh, Kevin, Ndila, Carolyne M., Peshu, Norbert, Williams, Thomas N., Drakeley, Chris, Manjurano, Alphaxard, Reyburn, Hugh, Riley, Eleanor, Kachala, David, Molyneux, Malcolm, Nyirongo, Vysaul, Taylor, Terrie, Thornton, Nicole, Tilley, Louise, Grimsley, Shane, Drury, Eleanor, Stalker, Jim, Cornelius, Victoria, Hubbart, Christina, Jeffreys, Anna E., Rowlands, Kate, Rockett, Kirk A., Spencer, Chris C. A., and Kwiatkowski, Dominic P.

Published
2017

37. Non-O ABO blood group genotypes differ in their associations with Plasmodium falciparum rosetting and severe malaria

Author

Opi, D. Herbert, primary, Ndila, Carolyne M., additional, Uyoga, Sophie, additional, Macharia, Alex W., additional, Fennell, Clare, additional, Ochola, Lucy B., additional, Nyutu, Gideon, additional, Siddondo, Bethseba R., additional, Ojal, John, additional, Shebe, Mohammed, additional, Awuondo, Kennedy O., additional, Mturi, Neema, additional, Peshu, Norbert, additional, Tsofa, Benjamin, additional, Band, Gavin, additional, Maitland, Kathryn, additional, Kwiatkowski, Dominic P., additional, Rockett, Kirk A., additional, Williams, Thomas N., additional, and Rowe, J. Alexandra, additional

Published
2023
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39. Binding of Plasmodium falciparum Merozoite Surface Proteins DBLMSP and DBLMSP2 to Human Immunoglobulin M Is Conserved among Broadly Diverged Sequence Variants

Author

Crosnier, Cécile, Iqbal, Zamin, Knuepfer, Ellen, Maciuca, Sorina, Perrin, Abigail J., Kamuyu, Gathoni, Goulding, David, Bustamante, Leyla Y., Miles, Alistair, Moore, Shona C., Dougan, Gordon, Holder, Anthony A., Kwiatkowski, Dominic P., Rayner, Julian C., Pleass, Richard J., and Wright, Gavin J.

Published
2016
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40. A Method to Exploit the Structure of Genetic Ancestry Space to Enhance Case-Control Studies

Author

Barclay, Murray, Peyrin-Biroulet, Laurent, Chamaillard, Mathias, Colombel, Jean-Frederick, Cottone, Mario, Croft, Anthony, D’Incà, Renata, Halfvarson, Jonas, Hanigan, Katherine, Henderson, Paul, Hugot, Jean-Pierre, Karban, Amir, Kennedy, Nicholas A., Khan, Mohammed Azam, Lémann, Marc, Levine, Arie, Massey, Dunecan, Milla, Monica, Montgomery, Grant W., Ng, Sok Meng Evelyn, Oikonomou, Ioannis, Peeters, Harald, Proctor, Deborah D., Rahier, Jean-Francois, Roberts, Rebecca, Rutgeerts, Paul, Seibold, Frank, Stronati, Laura, Taylor, Kirstin M., Törkvist, Leif, Ublick, Kullak, Van Limbergen, Johan, Van Gossum, Andre, Vatn, Morten H., Zhang, Hu, Zhang, Wei, Andrews, Jane M., Bampton, Peter A., Florin, Timothy H., Gearry, Richard, Krishnaprasad, Krupa, Lawrance, Ian C., Mahy, Gillian, Radford-Smith, Graham, Roberts, Rebecca L., Simms, Lisa A., Amininijad, Leila, Cleynen, Isabelle, Dewit, Olivier, Franchimont, Denis, Georges, Michel, Laukens, Debby, Theatre, Emilie, Van Gossum, André, Vermeire, Severine, Aumais, Guy, Baidoo, Leonard, Barrie, Arthur M., III, Beck, Karen, Bernard, Edmond-Jean, Binion, David G., Bitton, Alain, Brant, Steve R., Cho, Judy H., Cohen, Albert, Croitoru, Kenneth, Daly, Mark J., Datta, Lisa W., Deslandres, Colette, Duerr, Richard H., Dutridge, Debra, Ferguson, John, Fultz, Joann, Goyette, Philippe, Greenberg, Gordon R., Haritunians, Talin, Jobin, Gilles, Katz, Seymour, Lahaie, Raymond G., McGovern, Dermot P., Nelson, Linda, Ng, Sok Meng, Ning, Kaida, Paré, Pierre, Regueiro, Miguel D., Rioux, John D., Ruggiero, Elizabeth, Schumm, L. Philip, Schwartz, Marc, Scott, Regan, Sharma, Yashoda, Silverberg, Mark S., Spears, Denise, Steinhart, A. Hillary, Stempak, Joanne M., Swoger, Jason M., Tsagarelis, Constantina, Zhang, Clarence, Zhao, Hongyu, Aerts, Jan, Ahmad, Tariq, Arbury, Hazel, Attwood, Anthony, Auton, Adam, Ball, Stephen G., Balmforth, Anthony J., Barnes, Chris, Barrett, Jeffrey C., Barroso, Inês, Barton, Anne, Bennett, Amanda J., Bhaskar, Sanjeev, Blaszczyk, Katarzyna, Bowes, John, Brand, Oliver J., Braund, Peter S., Bredin, Francesca, Breen, Gerome, Brown, Morris J., Bruce, Ian N., Bull, Jaswinder, Burren, Oliver S., Burton, John, Byrnes, Jake, Caesar, Sian, Cardin, Niall, Clee, Chris M., Coffey, Alison J., Connell, John M.C., Conrad, Donald F., Cooper, Jason D., Dominiczak, Anna F., Downes, Kate, Drummond, Hazel E., Dudakia, Darshna, Dunham, Andrew, Ebbs, Bernadette, Eccles, Diana, Edkins, Sarah, Edwards, Cathryn, Elliot, Anna, Emery, Paul, Evans, David M., Evans, Gareth, Eyre, Steve, Farmer, Anne, I, Ferrier, Nicol, Flynn, Edward, Forbes, Alistair, Forty, Liz, Franklyn, Jayne A., Frayling, Timothy M., Freathy, Rachel M., Giannoulatou, Eleni, Gibbs, Polly, Gilbert, Paul, Gordon-Smith, Katherine, Gray, Emma, Green, Elaine, Groves, Chris J., Grozeva, Detelina, Gwilliam, Rhian, Hall, Anita, Hammond, Naomi, Hardy, Matt, Harrison, Pile, Hassanali, Neelam, Hebaishi, Husam, Hines, Sarah, Hinks, Anne, Hitman, Graham A., Hocking, Lynne, Holmes, Chris, Howard, Eleanor, Howard, Philip, Howson, Joanna M.M., Hughes, Debbie, Hunt, Sarah, Isaacs, John D., Jain, Mahim, Jewell, Derek P., Johnson, Toby, Jolley, Jennifer D., Jones, Ian R., Jones, Lisa A., Kirov, George, Langford, Cordelia F., Lango-Allen, Hana, Lathrop, G. Mark, Lee, James, Lee, Kate L., Lees, Charlie, Lewis, Kevin, Lindgren, Cecilia M., Maisuria-Armer, Meeta, Maller, Julian, Mansfield, John, Marchini, Jonathan L., Martin, Paul, Massey, Dunecan C.O., McArdle, Wendy L., McGuffin, Peter, McLay, Kirsten E., McVean, Gil, Mentzer, Alex, Mimmack, Michael L., Morgan, Ann E., Morris, Andrew P., Mowat, Craig, Munroe, Patricia B., Myers, Simon, Newman, William, Nimmo, Elaine R., O’Donovan, Michael C., Onipinla, Abiodun, Ovington, Nigel R., Owen, Michael J., Palin, Kimmo, Palotie, Aarno, Parnell, Kirstie, Pearson, Richard, Pernet, David, Perry, John R.B., Phillips, Anne, Plagnol, Vincent, Prescott, Natalie J., Prokopenko, Inga, Quail, Michael A., Rafelt, Suzanne, Rayner, Nigel W., Reid, David M., Renwick, Anthony, Ring, Susan M., Robertson, Neil, Robson, Samuel, Russell, Ellie, St Clair, David, Sambrook, Jennifer G., Sanderson, Jeremy D., Sawcer, Stephen J., Schuilenburg, Helen, Scott, Carol E., Scott, Richard, Seal, Sheila, Shaw-Hawkins, Sue, Shields, Beverley M., Simmonds, Matthew J., Smyth, Debbie J., Somaskantharajah, Elilan, Spanova, Katarina, Steer, Sophia, Stephens, Jonathan, Stevens, Helen E., Stirrups, Kathy, Stone, Millicent A., Strachan, David P., Su, Zhan, Symmons, Deborah P.M., Thompson, John R., Thomson, Wendy, Tobin, Martin D., Travers, Mary E., Turnbull, Clare, Vukcevic, Damjan, Wain, Louise V., Walker, Mark, Walker, Neil M., Wallace, Chris, Warren-Perry, Margaret, Watkins, Nicholas A., Webster, John, Weedon, Michael N., Wilson, Anthony G., Woodburn, Matthew, Wordsworth, B. Paul, Yau, Chris, Young, Allan H., Zeggini, Eleftheria, Brown, Matthew A., Burton, Paul R., Caulfield, Mark J., Compston, Alastair, Farrall, Martin, Gough, Stephen C.L., Hall, Alistair S., Hattersley, Andrew T., Hill, Adrian V.S., Mathew, Christopher G., Pembrey, Marcus, Satsangi, Jack, Stratton, Michael R., Worthington, Jane, Hurles, Matthew E., Duncanson, Audrey, Ouwehand, Willem H., Parkes, Miles, Rahman, Nazneen, Todd, John A., Samani, Nilesh J., Kwiatkowski, Dominic P., McCarthy, Mark I., Craddock, Nick, Deloukas, Panos, Donnelly, Peter, Blackwell, Jenefer M., Bramon, Elvira, Casas, Juan P., Corvin, Aiden, Jankowski, Janusz, Markus, Hugh S., Palmer, Colin N.A., Plomin, Robert, Rautanen, Anna, Trembath, Richard C., Viswanathan, Ananth C., Wood, Nicholas W., Spencer, Chris C.A., Band, Gavin, Bellenguez, Céline, Freeman, Colin, Hellenthal, Garrett, Pirinen, Matti, Strange, Amy, Blackburn, Hannah, Bumpstead, Suzannah J., Dronov, Serge, Gillman, Matthew, Jayakumar, Alagurevathi, McCann, Owen T., Liddle, Jennifer, Potter, Simon C., Ravindrarajah, Radhi, Ricketts, Michelle, Waller, Matthew, Weston, Paul, Widaa, Sara, Whittaker, Pamela, Bodea, Corneliu A., Neale, Benjamin M., Ripke, Stephan, Devlin, Bernie, and Roeder, Kathryn

Published
2016
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41. 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

43. Mapping the travel patterns of people with malaria in Bangladesh

Author

Sinha, Ipsita, Sayeed, Abdullah Abu, Uddin, Didar, Wesolowski, Amy, Zaman, Sazid Ibna, Faiz, M. Abul, Ghose, Aniruddha, Rahman, M. Ridwanur, Islam, Akramul, Karim, Mohammad Jahirul, Saha, Anjan, Rezwan, M. Kamar, Shamsuzzaman, Abul Khair Mohammad, Jhora, Sanya Tahmina, Aktaruzzaman, M. M., Chang, Hsiao-Han, Miotto, Olivo, Kwiatkowski, Dominic, Dondorp, Arjen M., Day, Nicholas P. J., Hossain, M. Amir, Buckee, Caroline, and Maude, Richard J.

Published
2020
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47. Genomic analysis of Plasmodium vivax describes patterns of connectivity and putative drivers of adaptation in Ethiopia

Author

Experimental Cardiology Laboratory, Experimentele Afd. Cardiologie 1, Kebede, Alebachew Messele, Sutanto, Edwin, Trimarsanto, Hidayat, Benavente, Ernest Diez, Barnes, Mariana, Pearson, Richard D., Siegel, Sasha V., Erko, Berhanu, Assefa, Ashenafi, Getachew, Sisay, Aseffa, Abraham, Petros, Beyene, Lo, Eugenia, Mohammed, Rezika, Yilma, Daniel, Rumaseb, Angela, Nosten, Francois, Noviyanti, Rintis, Rayner, Julian C., Kwiatkowski, Dominic P., Price, Ric N., Golassa, Lemu, Auburn, Sarah, Experimental Cardiology Laboratory, Experimentele Afd. Cardiologie 1, Kebede, Alebachew Messele, Sutanto, Edwin, Trimarsanto, Hidayat, Benavente, Ernest Diez, Barnes, Mariana, Pearson, Richard D., Siegel, Sasha V., Erko, Berhanu, Assefa, Ashenafi, Getachew, Sisay, Aseffa, Abraham, Petros, Beyene, Lo, Eugenia, Mohammed, Rezika, Yilma, Daniel, Rumaseb, Angela, Nosten, Francois, Noviyanti, Rintis, Rayner, Julian C., Kwiatkowski, Dominic P., Price, Ric N., Golassa, Lemu, and Auburn, Sarah

Published
2023

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

Author

Experimental Cardiology Laboratory, Experimentele Afd. Cardiologie 1, 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., Auburn, Sarah, Experimental Cardiology Laboratory, Experimentele Afd. Cardiologie 1, 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

50. 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
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