469 results on '"Auburn, Sarah"'
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2. Chloroquine has shown high therapeutic efficacy against uncomplicated Plasmodium vivax malaria in southern Ethiopia: seven decades after its introduction
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Mare, Anteneh Kassahun, Mohammed, Hussein, Sime, Heven, Hailgiorgis, Henok, Gubae, Kale, Gidey, Bekuretsion, Haile, Mebrahtom, Assefa, Gudissa, Bekele, Worku, Auburn, Sarah, Price, Rick, Parr, Jonathan B., Juliano, Jonathan J., Tasew, Geremew, Abay, Solomon Mequanente, and Assefa, Ashenafi
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- 2024
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3. Identification of complex Plasmodium falciparum genetic backgrounds circulating in Africa: a multicountry genomic epidemiology analysis
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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
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- 2024
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4. Molecular markers for malaria genetic epidemiology: progress and pitfalls
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Ruybal-Pesántez, Shazia, McCann, Kirsty, Vibin, Jessy, Siegel, Sasha, Auburn, Sarah, and Barry, Alyssa E.
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- 2024
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5. Genomic analysis of Plasmodium vivax describes patterns of connectivity and putative drivers of adaptation in Ethiopia
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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
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- 2023
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6. Genomics of Plasmodium vivax in Colombia reveals evidence of local bottle-necking and inter-country connectivity in the Americas
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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
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- 2023
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7. Analysis of the relapse of imported Plasmodium vivax and Plasmodium ovale in five provinces of China
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Yan, Hui, Wei, Shujiao, Sui, Yuan, Lu, Shenning, Zhang, Weiwei, Feng, Xiangyang, Liu, Ying, Zhang, Tao, Ruan, Wei, Xia, Jing, Lin, Wen, Ley, Benedikt, Auburn, Sarah, Li, Shizhu, Li, Jun, and Wang, Duoquan
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- 2023
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8. Whole genome sequencing of Plasmodium vivax isolates reveals frequent sequence and structural polymorphisms in erythrocyte binding genes.
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Ford, Anthony, Kepple, Daniel, Abagero, Beka Raya, Connors, Jordan, Pearson, Richard, Auburn, Sarah, Getachew, Sisay, Ford, Colby, Gunalan, Karthigayan, Miller, Louis H, Janies, Daniel A, Rayner, Julian C, Yan, Guiyun, Yewhalaw, Delenasaw, and Lo, Eugenia
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Erythrocytes ,Humans ,Plasmodium vivax ,Malaria ,Vivax ,Receptors ,Cell Surface ,Protozoan Proteins ,DNA ,Protozoan ,Antigens ,Protozoan ,Duffy Blood-Group System ,Phylogeny ,Polymorphism ,Single Nucleotide ,Genome ,Protozoan ,Ethiopia ,DNA Copy Number Variations ,Whole Genome Sequencing ,Biological Sciences ,Medical and Health Sciences ,Tropical Medicine - Abstract
Plasmodium vivax malaria is much less common in Africa than the rest of the world because the parasite relies primarily on the Duffy antigen/chemokine receptor (DARC) to invade human erythrocytes, and the majority of Africans are Duffy negative. Recently, there has been a dramatic increase in the reporting of P. vivax cases in Africa, with a high number of them being in Duffy negative individuals, potentially indicating P. vivax has evolved an alternative invasion mechanism that can overcome Duffy negativity. Here, we analyzed single nucleotide polymorphism (SNP) and copy number variation (CNV) in Whole Genome Sequence (WGS) data from 44 P. vivax samples isolated from symptomatic malaria patients in southwestern Ethiopia, where both Duffy positive and Duffy negative individuals are found. A total of 123,711 SNPs were detected, of which 22.7% were nonsynonymous and 77.3% were synonymous mutations. The largest number of SNPs were detected on chromosomes 9 (24,007 SNPs; 19.4% of total) and 10 (16,852 SNPs, 13.6% of total). There were particularly high levels of polymorphism in erythrocyte binding gene candidates including merozoite surface protein 1 (MSP1) and merozoite surface protein 3 (MSP3.5, MSP3.85 and MSP3.9). Two genes, MAEBL and MSP3.8 related to immunogenicity and erythrocyte binding function were detected with significant signals of positive selection. Variation in gene copy number was also concentrated in genes involved in host-parasite interactions, including the expansion of the Duffy binding protein gene (PvDBP) on chromosome 6 and MSP3.11 on chromosome 10. Based on the phylogeny constructed from the whole genome sequences, the expansion of these genes was an independent process among the P. vivax lineages in Ethiopia. We further inferred transmission patterns of P. vivax infections among study sites and showed various levels of gene flow at a small geographical scale. The genomic features of P. vivax provided baseline data for future comparison with those in Duffy-negative individuals and allowed us to develop a panel of informative Single Nucleotide Polymorphic markers diagnostic at a micro-geographical scale.
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- 2020
9. Unveiling the genomic landscape of malaria in natural infections
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Auburn, Sarah
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- 2023
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10. A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria
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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
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- 2022
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11. Genomic epidemiology of Plasmodium knowlesi reveals putative genetic drivers of adaptation in Malaysia.
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Westaway, Jacob, primary, Diez Benavente, Ernest, additional, Auburn, Sarah, additional, Kucharski, Michal, additional, Aranciaga, Nicolas, additional, Nayak, Sourav, additional, William, Timothy, additional, Rajahram, Giri S, additional, Piera, Kim A, additional, Braima, Kamil, additional, Tan, Angelica F, additional, Alaza, Danshy, additional, Barber, Bridget E, additional, Drakeley, Chris, additional, Amato, Roberto, additional, Sutanto, Edwin, additional, Trimarsanto, Hidayat, additional, Anstey, Nicholas M, additional, Bozdech, Zbynek, additional, Field, Matthew, additional, and Grigg, Matthew J, additional
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- 2024
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12. Longitudinal ex vivo and molecular trends of chloroquine and piperaquine activity against Plasmodium falciparum and P. vivax before and after introduction of artemisinin-based combination therapy in Papua, Indonesia
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Marfurt, Jutta, Wirjanata, Grennady, Prayoga, Pak, Chalfein, Ferryanto, Leonardo, Leo, Sebayang, Boni F., Apriyanti, Dwi, Sihombing, Maic A.E.M., Trianty, Leily, Suwanarusk, Rossarin, Brockman, Alan, Piera, Kim A., Luo, Irene, Rumaseb, Angela, MacHunter, Barbara, Auburn, Sarah, Anstey, Nicholas M., Kenangalem, Enny, Noviyanti, Rintis, Russell, Bruce, Poespoprodjo, Jeanne R., and Price, Ric N.
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- 2021
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13. A complexPlasmodium falciparumcryptotype circulating at low frequency across the African continent
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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
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- 2024
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14. Epidemiological profile of Plasmodium ovale spp. imported from Africa to Anhui Province, China, 2012–2019
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Zhang, Tao, Wang, Shuqi, Wang, Duoquan, Auburn, Sarah, Lu, Shenning, Xu, Xian, Jiang, Jingjing, Lyu, Xiaofeng, Yu, Chen, Tian, Cuicui, Li, Shizhu, and Li, Weidong
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- 2021
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15. Short-course primaquine for the radical cure of Plasmodium vivax malaria: a multicentre, randomised, placebo-controlled non-inferiority trial
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Taylor, Walter R J, Thriemer, Kamala, von Seidlein, Lorenz, Yuentrakul, Prayoon, Assawariyathipat, Thanawat, Assefa, Ashenafi, Auburn, Sarah, Chand, Krisin, Chau, Nguyen Hoang, Cheah, Phaik Yeong, Dong, Le Thanh, Dhorda, Mehul, Degaga, Tamiru Shibru, Devine, Angela, Ekawati, Lenny L, Fahmi, Fahmi, Hailu, Asrat, Hasanzai, Mohammad Anwar, Hien, Tran Tinh, Khu, Htee, Ley, Benedikt, Lubell, Yoel, Marfurt, Jutta, Mohammad, Hussein, Moore, Kerryn A, Naddim, Mohammad Nader, Pasaribu, Ayodhia Pitaloka, Pasaribu, Syahril, Promnarate, Cholrawee, Rahim, Awab Ghulam, Sirithiranont, Pasathron, Solomon, Hiwot, Sudoyo, Herawati, Sutanto, Inge, Thanh, Ngo Viet, Tuyet-Trinh, Nguyen Thi, Waithira, Naomi, Woyessa, Adugna, Yamin, Fazal Yamin, Dondorp, Arjen, Simpson, Julie A, Baird, J Kevin, White, Nicholas J, Day, Nicholas P, and Price, Ric N
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- 2019
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16. Imported malaria into Australia: surveillance insights and opportunities.
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Sohail, Asma, Barry, Alyssa, Auburn, Sarah, Cheng, Qin, Lau, Colleen L, Lee, Rogan, Price, Ric N, Furuya-Kanamori, Luis, Bareng, Paolo, McGuinness, Sarah L, and Leder, Karin
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MALARIA ,RAPID diagnostic tests ,YOUNG adults ,GENETIC mutation ,PLASMODIUM vivax - Abstract
Background Malaria continues to pose a significant burden in endemic countries, many of which lack access to molecular surveillance. Insights from malaria cases in travellers returning to non-endemic areas can provide valuable data to inform endemic country programmes. To evaluate the potential for novel global insights into malaria, we examined epidemiological and molecular data from imported malaria cases to Australia. Methods We analysed malaria cases reported in Australia from 2012 to 2022 using National Notifiable Disease Surveillance System data. Molecular data on imported malaria cases were obtained from literature searches. Results Between 2012 and 2022, 3204 malaria cases were reported in Australia. Most cases (69%) were male and 44% occurred in young adults aged 20–39 years. Incidence rates initially declined between 2012 and 2015, then increased until 2019. During 2012–2019, the incidence in travellers ranged from 1.34 to 7.71 per 100 000 trips. Cases were primarily acquired in Sub-Saharan Africa (n = 1433; 45%), Oceania (n = 569; 18%) and Southern and Central Asia (n = 367; 12%). The most common countries of acquisition were Papua New Guinea (n = 474) and India (n = 277). Plasmodium falciparum accounted for 58% (1871/3204) of cases and was predominantly acquired in Sub-Saharan Africa, and Plasmodium vivax accounted for 32% (1016/3204), predominantly from Oceania and Asia. Molecular studies of imported malaria cases to Australia identified genetic mutations and deletions associated with drug resistance and false-negative rapid diagnostic test results, and led to the establishment of reference genomes for P. vivax and Plasmodium malariae. Conclusions Our analysis highlights the continuing burden of imported malaria into Australia. Molecular studies have offered valuable insights into drug resistance and diagnostic limitations, and established reference genomes. Integrating molecular data into national surveillance systems could provide important infectious disease intelligence to optimize treatment guidelines for returning travellers and support endemic country surveillance programmes. [ABSTRACT FROM AUTHOR]
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- 2024
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17. Imported malaria into Australia: surveillance insights and opportunities
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Sohail, Asma, primary, Barry, Alyssa, additional, Auburn, Sarah, additional, Cheng, Qin, additional, Lau, Colleen L, additional, Lee, Rogan, additional, Price, Ric N, additional, Furuya-Kanamori, Luis, additional, Bareng, Paolo, additional, McGuinness, Sarah L, additional, and Leder, Karin, additional
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- 2023
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18. Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study
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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
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- 2018
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19. Host Genetic Components of the Erythrocyte Stimulatory G Protein Signal Pathway that Determine Susceptibility to Severe Malaria
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Auburn, Sarah
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572.8 - Abstract
The host stimulatory G protein signal transduction pathway has been functionally implicated in the modulation of erythrocyte invasion by Pjalciparum, and putatively implicated in the establishment of new permeability pathways in Pjalciparum-infected erythrocytes. The objective of this thesis was to identify whether the G protein pathway has genetic determinants involved in severe malaria pathogenesis. I investigated eleven components of the G protein pathway; GNAS, f3-2-AR, ADORA2A, ADORA2B, ADRBKJ, RGS2, GNB3, ADCY9, CFTR and P2RYJ. GNAS SNPs were genotyped in 7 studies (family and population-based) while f3-2-AR and all other genes were genotyped in either a single population-based study or a single family-based study, respectively. The most compelling association was observed at the GNAS locus, encoding G-alpha-s. Meta-analysis across 7 studies revealed significant association between an intronic variant, rs2057291, and severe malaria (P=O.002). I used allele-specific transcript quantification mapping in the attempt to map putative cis-regulatory polymorphisms in G-alpha-s transcription that might explain the rs2057291 association. Using B cells from fifteen HapMap individuals, I found evidence of relative allelic transcription imbalance in two cell lines (ratio C to T allele -1.3). However, mapping analysis was limited by sample size and failed to identify a plausible candidate for this regulatory effect. Analysis of P-2-AR and P-I-AR was limited due to difficulties in genotyping several key SNPs and, therefore, the role of these genes in severe malaria remains unclear. However, genotyping in the other genes revealed a promising association with a non-synonymous SNP in the catalytic domain of the ADCY9 gene, rs2230739 (ile772met), which had previously been shown to be functional in the regulation of cAMP production and [3-2-AR stimulation (P=O.027). This association requires validation in further studies. In conclusion, the involvement of the G protein pathway in severe malaria deserves further investigation. Future studies should focus on characterizing and replicating significant associations identified here and elucidating other important components of the pathway.
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- 2007
20. Genomic analysis of Plasmodium vivax identifies putative drivers of adaptation and connectivity across diverse districts in Ethiopia
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Kebede, Alebachew Messele, primary, Sutanto, Edwin, additional, Trimarsanto, Hidayat, additional, Benavente, Ernest Diez, additional, Barnes, Mariana, additional, Pearson, Richard, additional, Siegel, Sasha, additional, Erko, Berhanu, additional, Assefa, Ashenafi, additional, Getachew, Sisay, additional, Aseffa, Abraham, additional, Petros, Beyene, additional, Lo, Eugenia, additional, Mohammed, Rezika, additional, Yilma, Daniel, additional, Rumaseb, Angela, additional, Nosten, Francois, additional, Noviyanti, Rintis, additional, Rayner, Julian, additional, Kwiatkowski, Dominic, additional, Price, Ric, additional, Golassa, Lemu, additional, and Auburn, Sarah, additional
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- 2023
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21. Dissecting malaria biology and epidemiology using population genetics and genomics
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Auburn, Sarah and Barry, Alyssa E.
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- 2017
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22. Implementing parasite genotyping into national surveillance frameworks: feedback from control programmes and researchers in the Asia–Pacific region
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Noviyanti, Rintis, Miotto, Olivo, Barry, Alyssa, Marfurt, Jutta, Siegel, Sasha, Thuy-Nhien, Nguyen, Quang, Huynh Hong, Anggraeni, Nancy Dian, Laihad, Ferdinand, Liu, Yaobao, Sumiwi, Maria Endang, Trimarsanto, Hidayat, Coutrier, Farah, Fadila, Nadia, Ghanchi, Najia, Johora, Fatema Tuj, Puspitasari, Agatha Mia, Tavul, Livingstone, Trianty, Leily, Utami, Retno Ayu Setya, Wang, Duoquan, Wangchuck, Kesang, Price, Ric N., and Auburn, Sarah
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- 2020
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23. Increasing incidence of Plasmodium ovale and persistent reporting of Plasmodium vivax in imported malaria cases: an analysis of 9-year surveillance data in four areas of China
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Wang, Xiaoxiao, primary, Xu, Wenjie, additional, Luo, Fei, additional, Lin, Kangming, additional, Zhang, Tao, additional, Yao, Linong, additional, Zhang, Xuan, additional, Zhang, Jiaqi, additional, Auburn, Sarah, additional, Wang, Duoquan, additional, and Ruan, Wei, additional
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- 2023
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24. minSNPs: an R package for the derivation of resolution-optimised SNP sets from microbial genomic data
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Hoon, Kian Soon, primary, Holt, Deborah C., additional, Auburn, Sarah, additional, Shaw, Peter, additional, and Giffard, Philip M., additional
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- 2023
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25. Genomic analysis of Plasmodium vivax describes patterns of connectivity and putative drivers of adaptation in Ethiopia
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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
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- 2023
26. Genomics of Plasmodium vivax in Colombia reveals evidence of local bottle-necking and inter-country connectivity in the Americas
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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
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- 2023
27. Genomic Analysis Reveals a Common Breakpoint in Amplifications of the Plasmodium vivax Multidrug Resistance 1 Locus in Thailand
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Auburn, Sarah, Serre, David, Pearson, Richard D., Amato, Roberto, Sriprawat, Kanlaya, To, Sheren, Handayuni, Irene, Suwanarusk, Rossarin, Russell, Bruce, Drury, Eleanor, Stalker, Jim, Miotto, Olivo, Kwiatkowski, Dominic P., Nosten, Francois, and Price, Ric N.
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- 2016
28. Efficacy of Artesunate-mefloquine for Chloroquine-resistant Plasmodium vivax Malaria in Malaysia: An Open-label, Randomized, Controlled Trial
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Grigg, Matthew J., William, Timothy, Menon, Jayaram, Barber, Bridget E., Wilkes, Christopher S., Rajahram, Giri S., Edstein, Michael D., Auburn, Sarah, Price, Ric N., Yeo, Tsin W., and Anstey, Nicholas M.
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- 2016
29. Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples
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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, Apinjoh, Tobias, Arnaldo, Paulo, Ashley, Elizabeth, Auburn, Sarah, Awandare, Gordon, Ba, Hampate, Baraka, Vito, Barry, Alyssa, Bejon, Philip, Bertin, Gwladys, Boni, Maciej, Borrmann, Steffen, Bousema, Teun, Bouyou-Akotet, Marielle, Branch, Oralee, Bull, Peter, Cheah, Huch, Chindavongsa, Keobouphaphone, Chookajorn, Thanat, Chotivanich, Kesinee, Claessens, Antoine, Conway, David, 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, Egwang, Thomas, Enosse, Sonia Maria Mauricio, Erko, Berhanu, Fairhurst, Rick, Faiz, Abdul, Fanello, Caterina, Fleharty, Mark, Forbes, Matthew, Fukuda, Mark, Gamboa, Dionicia, Ghansah, Anita, Golassa, Lemu, Goncalves, Sonia, Harrison, G, Healy, Sara Anne, Hendry, Jason, Hernandez-Koutoucheva, Anastasia, Hien, Tran Tinh, Hill, Catherine, Hombhanje, Francis, Hott, Amanda, Htut, Ye, Hussein, Mazza, Imwong, Mallika, Ishengoma, Deus, Jackson, Scott, Jacob, Chris, Jeans, Julia, Johnson, Kimberly, Kamaliddin, Claire, Kamau, Edwin, Keatley, Jon, Kochakarn, Theerarat, Konate, Drissa, Konaté, Abibatou, Kone, Aminatou, Kwiatkowski, Dominic, Kyaw, Myat, Kyle, Dennis, Lawniczak, Mara, Lee, Samuel, Lemnge, Martha, Lim, Pharath, Lon, Chanthap, Loua, Kovana, Mandara, Celine, Marfurt, Jutta, Marsh, Kevin, Maude, Richard James, Mayxay, Mayfong, Maïga-Ascofaré, Oumou, Miotto, Olivo, Mita, Toshihiro, Mobegi, Victor, Mohamed, Abdelrahim Osman, Mokuolu, Olugbenga, Montgomery, Jaqui, Morang'A, Collins Misita, Mueller, Ivo, Murie, Kathryn, Newton, Paul, Ngo Duc, Thang, Nguyen, Thuy, Nguyen, Thuy-Nhien, Nguyen Thi Kim, Tuyen, Nguyen Van, Hong, Noedl, Harald, Nosten, François, Noviyanti, Rintis, Ntui, Vincent Ntui-Njock, Nzila, Alexis, Ochola-Oyier, Lynette Isabella, Ocholla, Harold, Oduro, Abraham, Omedo, Irene, Onyamboko, Marie, Ouedraogo, Jean-Bosco, Oyebola, Kolapo, Oyibo, Wellington Aghoghovwia, Pearson, Richard, Peshu, Norbert, Phyo, Aung, Plowe, Christopher, Price, Ric, Pukrittayakamee, Sasithon, Quang, Huynh Hong, Randrianarivelojosia, Milijaona, Rayner, Julian, Ringwald, Pascal, Rosanas-Urgell, Anna, Rovira-Vallbona, Eduard, Ruano-Rubio, Valentin, Ruiz, Lastenia, Saunders, David, Shayo, Alex, Siba, Peter, Simpson, Victoria, Sissoko, Mahamadou, 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, Wendler, Jason, White, Nicholas, Whitton, Georgia, Yavo, William, van der Pluijm, Rob, MalariaGEN, University of Khartoum, University of Cape Coast [Ghana], Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), The Wellcome Trust Sanger Institute [Cambridge], London School of Hygiene and Tropical Medicine [Fajara, Gambia], London School of Hygiene and Tropical Medicine (LSHTM), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), West African Centre for Cell Biology of Infectious Pathogens [Legon, Ghana] (WACCBIP), University of Ghana, Navrongo Health Research Centre [Navrongo, Ghana] (NHRC), Kenya Medical Research Institute (KEMRI), Texas Biomedical Research Institute [San Antonio, TX], Université d'Antananarivo, University of Buéa, Instituto Nacional de Saude [Maputo, Mozambique] (INS), Centre for Tropical Medicine and Global Health [Oxford, UK], Nuffield Department of Medicine [Oxford, UK] (Big Data Institute), University of Oxford-University of Oxford, Mahidol Oxford Tropical Medicine Research Unit (MORU), University of Oxford-Mahidol University [Bangkok]-Wellcome Trust, Menzies School of Health Research [Australia], Charles Darwin University [Australia], Nuffield Department of Clinical Medicine [Oxford], University of Oxford, Institut de Recherche pour le Développement (IRD), Laboratory of Pathogen and Host Immunity [Montpellier] (LPHI), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), and Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)
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data resource ,lnfectious Diseases and Global Health Radboud Institute for Health Sciences [Radboudumc 4] ,plasmodium falciparum ,genomics ,malaria ,Medicine (miscellaneous) ,genomic epidemiology ,General Biochemistry, Genetics and Molecular Biology ,[SDV.MHEP]Life Sciences [q-bio]/Human health and pathology - Abstract
Contains fulltext : 291985.pdf (Publisher’s version ) (Open Access) 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.
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- 2023
- Full Text
- View/download PDF
30. The changing epidemiology of Plasmodium vivax: Insights from conventional and novel surveillance tools
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Auburn, Sarah, Cheng, Qin, Marfurt, Jutta, and Price, Ric N.
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Plasmodium vivax -- Distribution -- Health aspects ,Malaria -- Causes of -- Diagnosis -- Demographic aspects ,Company distribution practices ,Biological sciences - Abstract
Author(s): Sarah Auburn 1,2,3,*, Qin Cheng 4,5, Jutta Marfurt 1, Ric N. Price 1,2,3 Summary points Renewed efforts to eliminate malaria have had greater impact on Plasmodium falciparum than Plasmodium [...]
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- 2021
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31. Glucose-6-phosphate dehydrogenase activity in individuals with and without malaria: Analysis of clinical trial, cross-sectional and case-control data from Bangladesh
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Ley, Benedikt, Alam, Mohammad Shafiul, Kibria, Mohammad Golam, Marfurt, Jutta, Phru, Ching Swe, Ami, Jenifar Quaiyum, Thriemer, Kamala, Auburn, Sarah, Jahan, Nusrat, Johora, Fatema Tuj, Hossain, Mohammad Sharif, Koepfli, Cristian, Khan, Wasif Ali, and Price, Ric N.
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Hemolysis and hemolysins -- Risk factors ,Dehydrogenases -- Physiological aspects -- Health aspects ,Malaria -- Physiological aspects ,Biological sciences - Abstract
Background Glucose-6-phosphate dehydrogenase (G6PD) activity is dependent upon G6PD genotype and age of the red blood cell (RBC) population, with younger RBCs having higher activity. Peripheral parasitemia with Plasmodium spp. induces hemolysis, replacing older RBCs with younger cells with higher G6PD activity. This study aimed to assess whether G6PD activity varies between individuals with and without malaria or a history of malaria. Methods and findings Individuals living in the Chittagong Hill Tracts of Bangladesh were enrolled into 3 complementary studies: (i) a prospective, single-arm clinical efficacy trial of patients (n = 175) with uncomplicated malaria done between 2014 and 2015, (ii) a cross-sectional survey done between 2015 and 2016 (n = 999), and (iii) a matched case-control study of aparasitemic individuals with and without a history of malaria done in 2020 (n = 506). G6PD activity was compared between individuals with and without malaria diagnosed by microscopy, rapid diagnostic test (RDT), or polymerase chain reaction (PCR), and in aparasitemic participants with and without a history of malaria. In the cross-sectional survey and clinical trial, 15.5% (182/1,174) of participants had peripheral parasitemia detected by microscopy or RDT, 3.1% (36/1,174) were positive by PCR only, and 81.4% (956/1,174) were aparasitemic. Aparasitemic individuals had significantly lower G6PD activity (median 6.9 U/g Hb, IQR 5.2-8.6) than those with peripheral parasitemia detected by microscopy or RDT (7.9 U/g Hb, IQR 6.6-9.8, p < 0.001), but G6PD activity similar to those with parasitemia detected by PCR alone (submicroscopic parasitemia) (6.1 U/g Hb, IQR 4.8-8.6, p = 0.312). In total, 7.7% (14/182) of patients with malaria had G6PD activity < 70% compared to 25.0% (248/992) of participants with submicroscopic or no parasitemia (odds ratio [OR] 0.25, 95% CI 0.14-0.44, p < 0.001). In the case-control study, the median G6PD activity was 10.3 U/g Hb (IQR 8.8-12.2) in 253 patients with a history of malaria and 10.2 U/g Hb (IQR 8.7-11.8) in 253 individuals without a history of malaria (p = 0.323). The proportion of individuals with G6PD activity < 70% was 11.5% (29/253) in the cases and 15.4% (39/253) in the controls (OR 0.7, 95% CI 0.41-1.23, p = 0.192). Limitations of the study included the non-contemporaneous nature of the clinical trial and cross-sectional survey. Conclusions Patients with acute malaria had significantly higher G6PD activity than individuals without malaria, and this could not be accounted for by a protective effect of G6PD deficiency. G6PD-deficient patients with malaria may have higher than expected G6PD enzyme activity and an attenuated risk of primaquine-induced hemolysis compared to the risk when not infected., Author(s): Benedikt Ley 1,*, Mohammad Shafiul Alam 2, Mohammad Golam Kibria 2, Jutta Marfurt 1, Ching Swe Phru 2, Jenifar Quaiyum Ami 2, Kamala Thriemer 1, Sarah Auburn 1, Nusrat [...]
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- 2021
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- View/download PDF
32. Whole genome sequencing of amplified Plasmodium knowlesi DNA from unprocessed blood reveals genetic exchange events between Malaysian Peninsular and Borneo subpopulations
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Benavente, Ernest Diez, Gomes, Ana Rita, De Silva, Jeremy Ryan, Grigg, Matthew, Walker, Harriet, Barber, Bridget E., William, Timothy, Yeo, Tsin Wen, de Sessions, Paola Florez, Ramaprasad, Abhinay, Ibrahim, Amy, Charleston, James, Hibberd, Martin L., Pain, Arnab, Moon, Robert W., Auburn, Sarah, Ling, Lau Yee, Anstey, Nicholas M., Clark, Taane G., and Campino, Susana
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- 2019
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33. Lineage-informative microhaplotypes for spatio-temporal surveillance of Plasmodium vivax malaria parasites
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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
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- 2023
- Full Text
- View/download PDF
34. Genomic characterization of recrudescent Plasmodium malariae after treatment with artemether/lumefantrine
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Rutledge, Gavin G., Marr, Ian, Huang, G. Khai Lin, Auburn, Sarah, Marfurt, Jutta, Sanders, Mandy, White, Nicholas J., Berriman, Matthew, Newbold, Chris I., Anstey, Nicholas M., Otto, Thomas D., and Price, Ric N.
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DNA sequencing -- Analysis -- Health aspects ,Plasmodium falciparum -- Analysis -- Health aspects ,Infection -- Analysis -- Health aspects ,Genomes -- Analysis -- Health aspects ,Malaria -- Analysis -- Health aspects ,Genomics -- Analysis -- Health aspects ,Health - Abstract
During the past decade, intensification of malaria control efforts has substantially reduced the global burden of malaria from Plasmodium falciparum. This trend has often been associated with increased recognition of [...]
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- 2017
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35. Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples
- Author
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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
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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
36. No association between thePlasmodium vivax crt-oMS334 or In9pvcrtpolymorphisms and chloroquine failure in a clinical cohort from Malaysia
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Rumaseb, Angela, primary, Moraes Barros, Roberto R., additional, Sá, Juliana M., additional, Juliano, Jonathan J., additional, William, Timothy, additional, Braima, Kamil A., additional, Barber, Bridget E., additional, Anstey, Nicholas M, additional, Price, Ric N., additional, Grigg, Matthew J., additional, Auburn, Sarah, additional, and Marfurt, Jutta, additional
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- 2022
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- View/download PDF
37. Plasmodium falciparum artemisinin resistance monitoring in Sabah, Malaysia: in vivo therapeutic efficacy and kelch13 molecular marker surveillance
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Grigg, Matthew J., William, Timothy, Piera, Kim A., Rajahram, Giri S., Jelip, Jenarun, Aziz, Ammar, Menon, Jayaram, Marfurt, Jutta, Price, Ric N., Auburn, Sarah, Barber, Bridget E., Yeo, Tsin W., and Anstey, Nicholas M.
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- 2018
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38. Novel highly-multiplexed AmpliSeq targeted assay for Plasmodium vivax genetic surveillance use cases at multiple geographical scales
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Kattenberg, Johanna Helena, primary, Nguyen, Hong Van, additional, Nguyen, Hieu Luong, additional, Sauve, Erin, additional, Nguyen, Ngoc Thi Hong, additional, Chopo-Pizarro, Ana, additional, Trimarsanto, Hidayat, additional, Monsieurs, Pieter, additional, Guetens, Pieter, additional, Nguyen, Xa Xuan, additional, Esbroeck, Marjan Van, additional, Auburn, Sarah, additional, Nguyen, Binh Thi Huong, additional, and Rosanas-Urgell, Anna, additional
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- 2022
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- View/download PDF
39. MinSNPs: an R package for derivation of resolution-optimised SNP sets from microbial genomic data
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Hoon, Kian Soon, primary, Holt, Deborah C, additional, Auburn, Sarah, additional, Shaw, Peter, additional, and Giffard, Philip M., additional
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- 2022
- Full Text
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40. A Prospective Comparative Study of Knowlesi, Falciparum, and Vivax Malaria in Sabah, Malaysia: High Proportion With Severe Disease From Plasmodium Knowlesi and Plasmodium Vivax But No Mortality With Early Referral and Artesunate Therapy
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Barber, Bridget E., William, Timothy, Grigg, Matthew J., Menon, Jayaram, Auburn, Sarah, Marfurt, Jutta, Anstey, Nicholas M., and Yeo, Tsin W.
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- 2013
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41. Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia
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Takala-Harrison, Shannon, Clark, Taane G., Jacob, Christopher G., Cummings, Michael P., Miotto, Olivo, Dondorp, Arjen M., Fukuda, Mark M., Nosten, Francois, Noedl, Harald, Imwong, Mallika, Bethell, Delia, Se, Youry, Lon, Chanthap, Tyner, Stuart D., Saunders, David L., Socheat, Duong, Ariey, Frederic, Phyo, Aung Pyae, Starzengruber, Peter, Fuehrer, Hans-Peter, Swoboda, Paul, Stepniewska, Kasia, Flegg, Jennifer, Arze, Cesar, Cerqueira, Gustavo C., Silva, Joana C., Ricklefs, Stacy M., Porcella, Stephen F., Stephens, Robert M., Adams, Matthew, Kenefic, Leo J., Campino, Susana, Auburn, Sarah, Maclnnis, Bronwyn, Kwiatkowski, Dominic P., Su, Xin-zhuan, White, Nicholas J., Ringwald, Pascal, and Plowe, Christopher V.
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- 2013
42. An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples
- Author
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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
43. Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution
- Author
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Rutledge, Gavin G., Böhme, Ulrike, Sanders, Mandy, Reid, Adam J., Cotton, James A., Maiga-Ascofare, Oumou, Djimdé, Abdoulaye A., Apinjoh, Tobias O., Amenga-Etego, Lucas, Manske, Magnus, Barnwell, John W., Renaud, François, Ollomo, Benjamin, Prugnolle, Franck, Anstey, Nicholas M., Auburn, Sarah, Price, Ric N., McCarthy, James S., Kwiatkowski, Dominic P., Newbold, Chris I., Berriman, Matthew, and Otto, Thomas D.
- Published
- 2017
- Full Text
- View/download PDF
44. minSNPs: an R package for the derivation of resolution-optimised SNP sets from microbial genomic data.
- Author
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Kian Soon Hoon, Holt, Deborah C., Auburn, Sarah, Shaw, Peter, and Giffard, Philip M.
- Subjects
SINGLE nucleotide polymorphisms ,COUNTRY of origin (Immigrants) ,SEQUENCE alignment - Abstract
Here, we present the R package, minSNPs. This is a re-development of a previously described Java application named Minimum SNPs. MinSNPs assembles resolution- optimised sets of single nucleotide polymorphisms (SNPs) from sequence alignments such as genome-wide orthologous SNP matrices. MinSNPs can derive sets of SNPs optimised for discriminating any user-defined combination of sequences from all others. Alternatively, SNP sets may be optimised to determine all sequences from all other sequences, i.e., to maximise diversity. MinSNPs encompasses functions that facilitate rapid and flexible SNP mining, and clear and comprehensive presentation of the results. The minSNPs' running time scales in a linear fashion with input data volume and the numbers of SNPs and SNPs sets specified in the output. MinSNPs was tested using a previously reported orthologous SNP matrix of Staphylococcus aureus and an orthologous SNP matrix of 3,279 genomes with 164,335 SNPs assembled from four S. aureus short read genomic data sets. MinSNPs was shown to be effective for deriving discriminatory SNP sets for potential surveillance targets and in identifying SNP sets optimised to discriminate isolates from different clonal complexes. MinSNPs was also tested with a large Plasmodium vivax orthologous SNP matrix. A set of five SNPs was derived that reliably indicated the country of origin within three south-east Asian countries. In summary, we report the capacity to assemble comprehensive SNP matrices that effectively capture microbial genomic diversity, and to rapidly and flexibly mine these entities for optimised marker sets. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
45. Phenotypic and genotypic characterisation of drug-resistant Plasmodium vivax
- Author
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Price, Ric N., Auburn, Sarah, Marfurt, Jutta, and Cheng, Qin
- Published
- 2012
- Full Text
- View/download PDF
46. Geographical distribution and genetic diversity of Plasmodium vivax reticulocyte binding protein 1a correlates with patient antigenicity
- Author
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Park, Ji-Hoon, primary, Kim, Min-Hee, additional, Sutanto, Edwin, additional, Na, Seok-Won, additional, Kim, Min-Jae, additional, Yeom, Joon Sup, additional, Nyunt, Myat Htut, additional, Abbas Elfaki, Mohammed Mohieldien, additional, Abdel Hamid, Muzamil Mahdi, additional, Cha, Seok Ho, additional, Alemu, Sisay Getachew, additional, Sriprawat, Kanlaya, additional, Anstey, Nicholas M., additional, Grigg, Matthew J., additional, Barber, Bridget E., additional, William, Timothy, additional, Gao, Qi, additional, Liu, Yaobao, additional, Pearson, Richard D., additional, Price, Ric N., additional, Nosten, Francois, additional, Yoon, Sung-Il, additional, No, Joo Hwan, additional, Han, Eun-Taek, additional, Auburn, Sarah, additional, Russell, Bruce, additional, and Han, JinHee, additional
- Published
- 2022
- Full Text
- View/download PDF
47. An open dataset of Plasmodium vivax genome variation in 1,895 worldwide samples
- Author
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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
48. Tumor Necrosis Factor and Lymphotoxin-α Polymorphisms and Severe Malaria in African Populations
- Author
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Clark, Taane G., Diakite, Mahamadou, Auburn, Sarah, Campino, Susana, Fry, Andrew E., Green, Angela, Richardson, Anna, Small, Kerrin, Teo, Yik Y., Wilson, Jonathan, Jallow, Muminatou, Sisay-Joof, Fatou, Pinder, Margaret, Griffiths, Michael J., Peshu, Norbert, Williams, Thomas N., Marsh, Kevin, Molyneux, Malcolm E., Taylor, Terrie E., Rockett, Kirk A., and Kwiatkowski, Dominic P.
- Published
- 2009
- Full Text
- View/download PDF
49. A novel locus of resistance to severe malaria in a region of ancient balancing selection
- Author
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Band, Gavin, Rockett, Kirk A., Spencer, Chris C.A., Kwiatkowski, Dominic P., Le, Quang Si, Clarke, Geraldine M., Kivinen, Katja, Leffler, Ellen M., Cornelius, Victoria, Conway, David J., Williams, Thomas N., Taylor, Terrie, Bojang, Kalifa A., Doumbo, Ogobara, Thera, Mahamadou A., Modiano, David, Sirima, Sodiomon B., Wilson, Michael D., Koram, Kwadwo A., Agbenyega, Tsiri, Achidi, Eric, Marsh, Kevin, Reyburn, Hugh, Drakeley, Chris, Riley, Eleanor, Molyneux, Malcolm, Jallow, Muminatou, Pinder, Margaret, Toure, Ousmane B., Konate, Salimata, Sissoko, Sibiri, Bougouma, Edith C., Mangano, Valentina D., Amenga-Etego, Lucas N., Ghansah, Anita K., Hodgson, Abraham V.O., Ansong, Daniel, Enimil, Anthony, Evans, Jennifer, Apinjoh, Tobias O., Macharia, Alexander, Ndila, Carolyne M., Newton, Charles, Peshu, Norbert, Uyoga, Sophie, Manjurano, Alphaxard, Kachala, David, Nyirongo, Vysaul, Mead, Daniel, Drury, Eleanor, Auburn, Sarah, Campino, Susana G., MacInnis, Bronwyn, Stalker, Jim, Gray, Emma, Hubbart, Christina, Jeffreys, Anna E., Rowlands, Kate, Mendy, Alieu, Craik, Rachel, Fitzpatrick, Kathryn, Molloy, Sile, Hart, Lee, Hutton, Robert, Kerasidou, Angeliki, and Johnson, Kimberly J.
- Published
- 2015
- Full Text
- View/download PDF
50. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples
- Author
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Ahouidi, Ambroise, Ali, Mozam, Almagro-Garcia, Jacob, Amambua-Ngwa, Alfred, Amaratunga, Chanaki, Amato, Roberto, Amenga-Etego, Lucas, Andagalu, Ben, Anderson, Tim JC, Andrianaranjaka, Voahangy, Apinjoh, Tobias, Ariani, Cristina, Ashley, Elizabeth A, Auburn, Sarah, Awandare, Gordon, Ba, Hampdate, Baraka, Vito, Barry, Alyssa E, Bejon, Philip, Bertin, Gwladys I, Boni, Maciej F, Borrmann, Steffen, Bousema, Teun, Branch, Oralee, Bull, Peter C, Busby, George BJ, Chookajorn, Thanat, Chotivanich, Kesinee, Claessens, Antoine, Conway, David, Craig, Alister, D'Alessandro, Umberto, Dama, Souleymane, Day, Nicholas PJ, Denis, Brigitte, Diakite, Mahamadou, Djimdé, Abdoulaye, Dolecek, Christiane, Dondorp, Arjen M, Drakeley, Chris, Drury, Eleanor, Duffy, Patrick, Echeverry, Diego F, Egwang, Thomas G, Erko, Berhanu, Fairhurst, Rick M, Faiz, Abdul, Fanello, Caterina A, Fukuda, Mark M, Gamboa, Dionica, Ghansah, Anita, Golassa, Lemu, Goncalves, Sonia, Hamilton, William L, Harrison, GL Abby, Hart, Lee, Henrichs, Christa, Hien, Tran Tinh, Hill, Catherine A, Hodgson, Abraham, Hubbart, Christina, Imwong, Mallika, Ishengoma, Deus S, Jackson, Scott A, Jacob, Chris G, Jeffery, Ben, Jeffreys, Anna E, Johnson, Kimberly J, Jyothi, Dushyanth, Kamaliddin, Claire, Kamau, Edwin, Kekre, Mihir, Kluczynski, Krzysztof, Kochakarn, Theerarat, Konaté, Abibatou, Kwiatkowski, Dominic P, Kyaw, Myat Phone, Lim, Pharath, Lon, Chanthap, Loua, Kovana M, Maïga-Ascofaré, Oumou, Malangone, Cinzia, Manske, Magnus, Marfurt, Jutta, Marsh, Kevin, Mayxay, Mayfong, Miles, Alistair, Miotto, Olivo, Mobegi, Victor, Mokuolu, Olugbenga A, Montgomery, Jacqui, Mueller, Ivo, Newton, Paul N, Nguyen, Thuy, Nguyen, Thuy-Nhien, Noedl, Harald, Nosten, Francois, Noviyanti, Rintis, Nzila, Alexis, Ochola-Oyier, Lynette I, Ahouidi, Ambroise, Ali, Mozam, Almagro-Garcia, Jacob, Amambua-Ngwa, Alfred, Amaratunga, Chanaki, Amato, Roberto, Amenga-Etego, Lucas, Andagalu, Ben, Anderson, Tim JC, Andrianaranjaka, Voahangy, Apinjoh, Tobias, Ariani, Cristina, Ashley, Elizabeth A, Auburn, Sarah, Awandare, Gordon, Ba, Hampdate, Baraka, Vito, Barry, Alyssa E, Bejon, Philip, Bertin, Gwladys I, Boni, Maciej F, Borrmann, Steffen, Bousema, Teun, Branch, Oralee, Bull, Peter C, Busby, George BJ, Chookajorn, Thanat, Chotivanich, Kesinee, Claessens, Antoine, Conway, David, Craig, Alister, D'Alessandro, Umberto, Dama, Souleymane, Day, Nicholas PJ, Denis, Brigitte, Diakite, Mahamadou, Djimdé, Abdoulaye, Dolecek, Christiane, Dondorp, Arjen M, Drakeley, Chris, Drury, Eleanor, Duffy, Patrick, Echeverry, Diego F, Egwang, Thomas G, Erko, Berhanu, Fairhurst, Rick M, Faiz, Abdul, Fanello, Caterina A, Fukuda, Mark M, Gamboa, Dionica, Ghansah, Anita, Golassa, Lemu, Goncalves, Sonia, Hamilton, William L, Harrison, GL Abby, Hart, Lee, Henrichs, Christa, Hien, Tran Tinh, Hill, Catherine A, Hodgson, Abraham, Hubbart, Christina, Imwong, Mallika, Ishengoma, Deus S, Jackson, Scott A, Jacob, Chris G, Jeffery, Ben, Jeffreys, Anna E, Johnson, Kimberly J, Jyothi, Dushyanth, Kamaliddin, Claire, Kamau, Edwin, Kekre, Mihir, Kluczynski, Krzysztof, Kochakarn, Theerarat, Konaté, Abibatou, Kwiatkowski, Dominic P, Kyaw, Myat Phone, Lim, Pharath, Lon, Chanthap, Loua, Kovana M, Maïga-Ascofaré, Oumou, Malangone, Cinzia, Manske, Magnus, Marfurt, Jutta, Marsh, Kevin, Mayxay, Mayfong, Miles, Alistair, Miotto, Olivo, Mobegi, Victor, Mokuolu, Olugbenga A, Montgomery, Jacqui, Mueller, Ivo, Newton, Paul N, Nguyen, Thuy, Nguyen, Thuy-Nhien, Noedl, Harald, Nosten, Francois, Noviyanti, Rintis, Nzila, Alexis, and Ochola-Oyier, Lynette I
- 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.
- Published
- 2021
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