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For: Henden L, Lee S, Mueller I, Barry A, Bahlo M. Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens. PLoS Genet 2018;14:e1007279. [PMID: 29791438 DOI: 10.1371/journal.pgen.1007279] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 06/05/2018] [Accepted: 02/26/2018] [Indexed: 12/30/2022]  Open
Number Cited by Other Article(s)
1
Robertson E, Grinton B, Oliver K, Fearnley L, Hildebrand M, Sadleir L, Scheffer I, Berkovic S, Bennett M, Bahlo M. Identifying individuals with rare disease variants by inferring shared ancestral haplotypes from SNP array data. NAR Genom Bioinform 2025;7:lqaf033. [PMID: 40191585 PMCID: PMC11970371 DOI: 10.1093/nargab/lqaf033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2024] [Revised: 02/23/2025] [Accepted: 03/15/2025] [Indexed: 04/09/2025]  Open
2
Chen YA, Ng PY, Garcia-Ruiz D, Elliot A, Palmer B, Assunção Carvalho RMCD, Tseng LF, Lee CS, Tsai KH, Greenhouse B, Chang HH. Genetic surveillance reveals low but sustained malaria transmission with clonal replacement in Sao Tome and Principe. COMMUNICATIONS MEDICINE 2025;5:199. [PMID: 40425726 PMCID: PMC12116912 DOI: 10.1038/s43856-025-00905-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Accepted: 05/09/2025] [Indexed: 05/29/2025]  Open
3
Mehra S, Neafsey DE, White M, Taylor AR. Systematic bias in malaria parasite relatedness estimation. G3 (BETHESDA, MD.) 2025;15:jkaf018. [PMID: 39883524 PMCID: PMC12060250 DOI: 10.1093/g3journal/jkaf018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Accepted: 11/22/2024] [Indexed: 01/31/2025]
4
Guo B, Rowley E, O'Connor TD, Takala-Harrison S. Potential and pitfalls of using identity-by-descent for malaria genomic surveillance. Trends Parasitol 2025;41:387-400. [PMID: 40263027 PMCID: PMC12070291 DOI: 10.1016/j.pt.2025.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2025] [Revised: 03/24/2025] [Accepted: 03/25/2025] [Indexed: 04/24/2025]
5
Jigisha J, Ly J, Minadakis N, Freund F, Kunz L, Piechota U, Akin B, Balmas V, Ben-David R, Bencze S, Bourras S, Bozzoli M, Cotuna O, Couleaud G, Cséplő M, Czembor P, Desiderio F, Dörnte J, Dreiseitl A, Feechan A, Gadaleta A, Gauthier K, Giancaspro A, Giove SL, Handley-Cornillet A, Hubbard A, Karaoglanidis G, Kildea S, Koc E, Liatukas Ž, Lopes MS, Mascher F, McCabe C, Miedaner T, Martínez-Moreno F, Nellist CF, Okoń S, Praz C, Sánchez-Martín J, Sărăţeanu V, Schulz P, Schwartz N, Seghetta D, Martel IS, Švarta A, Testempasis S, Villegas D, Widrig V, Menardo F. Population genomics and molecular epidemiology of wheat powdery mildew in Europe. PLoS Biol 2025;23:e3003097. [PMID: 40315179 PMCID: PMC12047814 DOI: 10.1371/journal.pbio.3003097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2024] [Accepted: 03/04/2025] [Indexed: 05/04/2025]  Open
6
Aranda-Díaz A, Neubauer Vickers E, Murie K, Palmer B, Hathaway N, Gerlovina I, Boene S, García-Ulloa M, Cisteró P, Katairo T, Semakuba FD, Nsengimaana B, Gwarinda H, García-Fernández C, Louie W, Esayas E, Da Silva C, Datta D, Kiyaga S, Wiringilimaana I, Feleke SM, Bennett A, Smith JL, Gadisa E, Parr JB, Conrad MD, Raman J, Tukwasibwe S, Ssewanyana I, Rovira-Vallbona E, Tato CM, Briggs J, Mayor A, Greenhouse B. Sensitive and modular amplicon sequencing of Plasmodium falciparum diversity and resistance for research and public health. Sci Rep 2025;15:10737. [PMID: 40155691 PMCID: PMC11953298 DOI: 10.1038/s41598-025-94716-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Accepted: 03/17/2025] [Indexed: 04/01/2025]  Open
7
Minadakis N, Jigisha J, Cornetti L, Kunz L, Müller MC, Torriani SFF, Menardo F. Genomic Surveillance and Molecular Evolution of Fungicide Resistance in European Populations of Wheat Powdery Mildew. MOLECULAR PLANT PATHOLOGY 2025;26:e70071. [PMID: 40108778 PMCID: PMC11922816 DOI: 10.1111/mpp.70071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 02/10/2025] [Accepted: 02/19/2025] [Indexed: 03/22/2025]
8
Aranda-Díaz A, Vickers EN, Murie K, Palmer B, Hathaway N, Gerlovina I, Boene S, Garcia-Ulloa M, Cisteró P, Katairo T, Semakuba FD, Nsengimaana B, Gwarinda H, García-Fernández C, Louie W, Esayas E, Da Silva C, Datta D, Kiyaga S, Wiringilimaana I, Fekele SM, Bennett A, Smith JL, Gadisa E, Parr JB, Conrad M, Raman J, Tukwasibwe S, Ssewanyana I, Rovira-Vallbona E, Tato CM, Briggs J, Mayor A, Greenhouse B. Sensitive and modular amplicon sequencing of Plasmodium falciparum diversity and resistance for research and public health. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.08.22.609145. [PMID: 39229023 PMCID: PMC11370457 DOI: 10.1101/2024.08.22.609145] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
9
Wong W, Wang L, Schaffner SF, Li X, Cheeseman I, Anderson TJC, Vaughan A, Ferdig M, Volkman SK, Hartl DL, Wirth DF. MalKinID: A classification model for identifying malaria parasite genealogical relationships using identity-by-descent. Genetics 2025;229:iyae197. [PMID: 39579070 PMCID: PMC11796457 DOI: 10.1093/genetics/iyae197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Revised: 11/12/2024] [Accepted: 11/13/2024] [Indexed: 11/25/2024]  Open
10
Kattenberg JH, Mutsaers M, Nguyen VH, Nguyen THN, Umugwaneza A, Lara-Escandell M, Nguyen XX, Nguyen THB, Rosanas-Urgell A. Genetic surveillance shows spread of ACT resistance during period of malaria decline in Vietnam (2018-2020). Front Genet 2024;15:1478706. [PMID: 39687741 PMCID: PMC11646998 DOI: 10.3389/fgene.2024.1478706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2024] [Accepted: 11/13/2024] [Indexed: 12/18/2024]  Open
11
Taylor AR, Neubauer Vickers E, Greenhouse B. Review of MrsFreqPhase methods: methods designed to estimate statistically malaria parasite multiplicity of infection, relatedness, frequency and phase. Malar J 2024;23:308. [PMID: 39407242 PMCID: PMC11481338 DOI: 10.1186/s12936-024-05119-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 09/28/2024] [Indexed: 10/19/2024]  Open
12
Chen Y, Ng PY, Garcia D, Elliot A, Palmer B, Assunção Carvalho RMCD, Tseng LF, Lee CS, Tsai KH, Greenhouse B, Chang HH. Genetic surveillance reveals low, sustained malaria transmission with clonal replacement in Sao Tome and Principe. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.15.24309968. [PMID: 39072035 PMCID: PMC11275696 DOI: 10.1101/2024.07.15.24309968] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
13
Cabrera-Sosa L, Nolasco O, Kattenberg JH, Fernandez-Miñope C, Valdivia HO, Barazorda K, Arévalo de Los Rios S, Rodriguez-Ferrucci H, Vinetz JM, Rosanas-Urgell A, Van Geertruyden JP, Gamboa D, Delgado-Ratto C. Genomic surveillance of malaria parasites in an indigenous community in the Peruvian Amazon. Sci Rep 2024;14:16291. [PMID: 39009685 PMCID: PMC11250820 DOI: 10.1038/s41598-024-66925-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 07/05/2024] [Indexed: 07/17/2024]  Open
14
Guo B, Takala-Harrison S, O’Connor TD. Benchmarking and Optimization of Methods for the Detection of Identity-By-Descent in High-Recombining Plasmodium falciparum Genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.04.592538. [PMID: 38746392 PMCID: PMC11092787 DOI: 10.1101/2024.05.04.592538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
15
Kattenberg JH, Cabrera-Sosa L, Figueroa-Ildefonso E, Mutsaers M, Monsieurs P, Guetens P, Infante B, Delgado-Ratto C, Gamboa D, Rosanas-Urgell A. Plasmodium vivax genomic surveillance in the Peruvian Amazon with Pv AmpliSeq assay. PLoS Negl Trop Dis 2024;18:e0011879. [PMID: 38991038 PMCID: PMC11265702 DOI: 10.1371/journal.pntd.0011879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 07/23/2024] [Accepted: 06/12/2024] [Indexed: 07/13/2024]  Open
16
Sharma R, Khan Z, Mehan S, Das Gupta G, Narula AS. Unraveling the multifaceted insights into amyotrophic lateral sclerosis: Genetic underpinnings, pathogenesis, and therapeutic horizons. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024;794:108518. [PMID: 39491718 DOI: 10.1016/j.mrrev.2024.108518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 09/19/2024] [Accepted: 10/30/2024] [Indexed: 11/05/2024]
17
Vanhove M, Schwabl P, Clementson C, Early AM, Laws M, Anthony F, Florimond C, Mathieu L, James K, Knox C, Singh N, Buckee CO, Musset L, Cox H, Niles-Robin R, Neafsey DE. Temporal and spatial dynamics of Plasmodium falciparum clonal lineages in Guyana. PLoS Pathog 2024;20:e1012013. [PMID: 38870266 PMCID: PMC11206942 DOI: 10.1371/journal.ppat.1012013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 06/26/2024] [Accepted: 05/24/2024] [Indexed: 06/15/2024]  Open
18
Kwiatkowski D. Modelling transmission dynamics and genomic diversity in a recombining parasite population. Wellcome Open Res 2024;9:215. [PMID: 39554245 PMCID: PMC11569386 DOI: 10.12688/wellcomeopenres.19092.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2024] [Indexed: 11/19/2024]  Open
19
Fola AA, He Q, Xie S, Thimmapuram J, Bhide KP, Dorman J, Ciubotariu II, Mwenda MC, Mambwe B, Mulube C, Hawela M, Norris DE, Moss WJ, Bridges DJ, Carpi G. Genomics reveals heterogeneous Plasmodium falciparum transmission and selection signals in Zambia. COMMUNICATIONS MEDICINE 2024;4:67. [PMID: 38582941 PMCID: PMC10998850 DOI: 10.1038/s43856-024-00498-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/28/2024] [Indexed: 04/08/2024]  Open
20
Guo B, Borda V, Laboulaye R, Spring MD, Wojnarski M, Vesely BA, Silva JC, Waters NC, O'Connor TD, Takala-Harrison S. Strong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparum. Nat Commun 2024;15:2499. [PMID: 38509066 PMCID: PMC10954658 DOI: 10.1038/s41467-024-46659-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024]  Open
21
Kattenberg JH, Monsieurs P, De Meyer J, De Meulenaere K, Sauve E, de Oliveira TC, Ferreira MU, Gamboa D, Rosanas‐Urgell A. Population genomic evidence of structured and connected Plasmodium vivax populations under host selection in Latin America. Ecol Evol 2024;14:e11103. [PMID: 38529021 PMCID: PMC10961478 DOI: 10.1002/ece3.11103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 03/27/2024]  Open
22
Cabrera-Sosa L, Nolasco O, Kattenberg JH, Fernandez-Miñope C, Valdivia HO, Barazorda K, Rios SADL, Rodriguez-Ferrucci H, Vinetz JM, Rosanas-Urgell A, Geertruyden JPV, Gamboa D, Delgado-Ratto C. Genomic surveillance of malaria parasites in an indigenous community in the Peruvian Amazon. RESEARCH SQUARE 2024:rs.3.rs-3979991. [PMID: 38464169 PMCID: PMC10925399 DOI: 10.21203/rs.3.rs-3979991/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
23
He Q, Chaillet JK, Labbé F. Antigenic strain diversity predicts different biogeographic patterns of maintenance and decline of antimalarial drug resistance. eLife 2024;12:RP90888. [PMID: 38363295 PMCID: PMC10942604 DOI: 10.7554/elife.90888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]  Open
24
Fola AA, He Q, Xie S, Thimmapuram J, Bhide KP, Dorman J, Ciubotariu II, Mwenda MC, Mambwe B, Mulube C, Hawela M, Norris DE, Moss WJ, Bridges DJ, Carpi G. Genomics reveals heterogeneous Plasmodium falciparum transmission and population differentiation in Zambia and bordering countries. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.09.24302570. [PMID: 38370674 PMCID: PMC10871455 DOI: 10.1101/2024.02.09.24302570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
25
Kessel J, Rosanas-Urgell A, Dingwerth T, Goetsch U, Haller J, Huits R, Kattenberg JH, Meinecke A, Monsieurs P, Sroka M, Witte T, Wolf T. Investigation of an airport-associated cluster of falciparum malaria in Frankfurt, Germany, 2022. Euro Surveill 2024;29:2300298. [PMID: 38304950 PMCID: PMC10835754 DOI: 10.2807/1560-7917.es.2024.29.5.2300298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/19/2023] [Indexed: 02/03/2024]  Open
26
Vanhove M, Schwabl P, Clementson C, Early AM, Laws M, Anthony F, Florimond C, Mathieu L, James K, Knox C, Singh N, Buckee CO, Musset L, Cox H, Niles-Robin R, Neafsey DE. Temporal and spatial dynamics of Plasmodium falciparum clonal lineages in Guyana. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578156. [PMID: 38352461 PMCID: PMC10862847 DOI: 10.1101/2024.01.31.578156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
27
He Q, Chaillet JK, Labbé F. Antigenic strain diversity predicts different biogeographic patterns of maintenance and decline of anti-malarial drug resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531320. [PMID: 37987011 PMCID: PMC10659383 DOI: 10.1101/2023.03.06.531320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
28
Schaffner SF, Badiane A, Khorgade A, Ndiop M, Gomis J, Wong W, Ndiaye YD, Diedhiou Y, Thwing J, Seck MC, Early A, Sy M, Deme A, Diallo MA, Sy N, Sene A, Ndiaye T, Sow D, Dieye B, Ndiaye IM, Gaye A, Ndiaye A, Battle KE, Proctor JL, Bever C, Fall FB, Diallo I, Gaye S, Sene D, Hartl DL, Wirth DF, MacInnis B, Ndiaye D, Volkman SK. Malaria surveillance reveals parasite relatedness, signatures of selection, and correlates of transmission across Senegal. Nat Commun 2023;14:7268. [PMID: 37949851 PMCID: PMC10638404 DOI: 10.1038/s41467-023-43087-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023]  Open
29
Coonahan E, Gage H, Chen D, Noormahomed EV, Buene TP, Mendes de Sousa I, Akrami K, Chambal L, Schooley RT, Winzeler EA, Cowell AN. Whole-genome surveillance identifies markers of Plasmodium falciparum drug resistance and novel genomic regions under selection in Mozambique. mBio 2023;14:e0176823. [PMID: 37750720 PMCID: PMC10653802 DOI: 10.1128/mbio.01768-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 09/27/2023]  Open
30
Guo B, Borda V, Laboulaye R, Spring MD, Wojnarski M, Vesely BA, Silva JC, Waters NC, O'Connor TD, Takala-Harrison S. Strong Positive Selection Biases Identity-By-Descent-Based Inferences of Recent Demography and Population Structure in Plasmodium falciparum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.549114. [PMID: 37502843 PMCID: PMC10370022 DOI: 10.1101/2023.07.14.549114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
31
Fola AA, Moser KA, Aydemir O, Hennelly C, Kobayashi T, Shields T, Hamapumbu H, Musonda M, Katowa B, Matoba J, Stevenson JC, Norris DE, Thuma PE, Wesolowski A, Moss WJ, Bailey JA, Juliano JJ, the Southern, Central Africa International Center of Excellence for Malaria Research (ICEMR). Temporal and spatial analysis of Plasmodium falciparum genomics reveals patterns of parasite connectivity in a low-transmission district in Southern Province, Zambia. Malar J 2023;22:208. [PMID: 37420265 PMCID: PMC10327325 DOI: 10.1186/s12936-023-04637-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/30/2023] [Indexed: 07/09/2023]  Open
32
Amambua-Ngwa A, Button-Simons KA, Li X, Kumar S, Brenneman KV, Ferrari M, Checkley LA, Haile MT, Shoue DA, McDew-White M, Tindall SM, Reyes A, Delgado E, Dalhoff H, Larbalestier JK, Amato R, Pearson RD, Taylor AB, Nosten FH, D'Alessandro U, Kwiatkowski D, Cheeseman IH, Kappe SHI, Avery SV, Conway DJ, Vaughan AM, Ferdig MT, Anderson TJC. Chloroquine resistance evolution in Plasmodium falciparum is mediated by the putative amino acid transporter AAT1. Nat Microbiol 2023;8:1213-1226. [PMID: 37169919 PMCID: PMC10322710 DOI: 10.1038/s41564-023-01377-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/29/2023] [Indexed: 05/13/2023]
33
Holzschuh A, Lerch A, Gerlovina I, Fakih BS, Al-Mafazy AWH, Reaves EJ, Ali A, Abbas F, Ali MH, Ali MA, Hetzel MW, Yukich J, Koepfli C. Multiplexed ddPCR-amplicon sequencing reveals isolated Plasmodium falciparum populations amenable to local elimination in Zanzibar, Tanzania. Nat Commun 2023;14:3699. [PMID: 37349311 PMCID: PMC10287761 DOI: 10.1038/s41467-023-39417-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023]  Open
34
Argyropoulos DC, Tan MH, Adobor C, Mensah B, Labbé F, Tiedje KE, Koram KA, Ghansah A, Day KP. Performance of SNP barcodes to determine genetic diversity and population structure of Plasmodium falciparum in Africa. Front Genet 2023;14:1071896. [PMID: 37323661 PMCID: PMC10267394 DOI: 10.3389/fgene.2023.1071896] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 05/17/2023] [Indexed: 06/17/2023]  Open
35
Schaffner SF, Badiane A, Khorgade A, Ndiop M, Gomis J, Wong W, Ndiaye YD, Diedhiou Y, Thwing J, Seck MC, Early A, Sy M, Deme A, Diallo MA, Sy N, Sene A, Ndiaye T, Sow D, Dieye B, Ndiaye IM, Gaye A, Ndiaye A, Battle KE, Proctor JL, Bever C, Fall FB, Diallo I, Gaye S, Sene D, Hartl DL, Wirth DF, MacInnis B, Ndiaye D, Volkman SK. Malaria surveillance reveals parasite relatedness, signatures of selection, and correlates of transmission across Senegal. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.11.23288401. [PMID: 37131838 PMCID: PMC10153316 DOI: 10.1101/2023.04.11.23288401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
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Kattenberg JH, Fernandez-Miñope C, van Dijk NJ, Llacsahuanga Allcca L, Guetens P, Valdivia HO, Van geertruyden JP, Rovira-Vallbona E, Monsieurs P, Delgado-Ratto C, Gamboa D, Rosanas-Urgell A. Malaria Molecular Surveillance in the Peruvian Amazon with a Novel Highly Multiplexed Plasmodium falciparum AmpliSeq Assay. Microbiol Spectr 2023;11:e0096022. [PMID: 36840586 PMCID: PMC10101074 DOI: 10.1128/spectrum.00960-22] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 08/02/2022] [Indexed: 02/24/2023]  Open
37
Arambepola R, Bérubé S, Freedman B, Taylor SM, Prudhomme O’Meara W, Obala AA, Wesolowski A. Exploring how space, time, and sampling impact our ability to measure genetic structure across Plasmodium falciparum populations. FRONTIERS IN EPIDEMIOLOGY 2023;3:1058871. [PMID: 38516334 PMCID: PMC10956351 DOI: 10.3389/fepid.2023.1058871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/18/2023] [Indexed: 03/23/2024]
38
Camponovo F, Buckee CO, Taylor AR. Measurably recombining malaria parasites. Trends Parasitol 2023;39:17-25. [PMID: 36435688 PMCID: PMC9893849 DOI: 10.1016/j.pt.2022.11.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/02/2022] [Accepted: 11/02/2022] [Indexed: 11/24/2022]
39
Carrasquilla M, Early AM, Taylor AR, Knudson Ospina A, Echeverry DF, Anderson TJC, Mancilla E, Aponte S, Cárdenas P, Buckee CO, Rayner JC, Sáenz FE, Neafsey DE, Corredor V. Resolving drug selection and migration in an inbred South American Plasmodium falciparum population with identity-by-descent analysis. PLoS Pathog 2022;18:e1010993. [PMID: 36542676 PMCID: PMC9815574 DOI: 10.1371/journal.ppat.1010993] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 01/05/2023] [Accepted: 11/09/2022] [Indexed: 12/24/2022]  Open
40
Mbye H, Mane K, Diop MF, Demba MA, Bojang F, Mohammed NI, Jeffries D, Quashie NB, D'Alessandro U, Amambua-Ngwa A. Plasmodium falciparum merozoite invasion ligands, linked antimalarial resistance loci and ex vivo responses to antimalarials in The Gambia. J Antimicrob Chemother 2022;77:2946-2955. [PMID: 35904009 PMCID: PMC9616547 DOI: 10.1093/jac/dkac244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/23/2022] [Indexed: 11/14/2022]  Open
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Brashear AM, Cui L. Population genomics in neglected malaria parasites. Front Microbiol 2022;13:984394. [PMID: 36160257 PMCID: PMC9493318 DOI: 10.3389/fmicb.2022.984394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022]  Open
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Gerlovina I, Gerlovin B, Rodríguez-Barraquer I, Greenhouse B. Dcifer: an IBD-based method to calculate genetic distance between polyclonal infections. Genetics 2022;222:6674513. [PMID: 36000888 PMCID: PMC9526043 DOI: 10.1093/genetics/iyac126] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/04/2022] [Indexed: 11/23/2022]  Open
43
Kattenberg JH, Nguyen HV, Nguyen HL, Sauve E, Nguyen NTH, Chopo-Pizarro A, Trimarsanto H, Monsieurs P, Guetens P, Nguyen XX, Esbroeck MV, Auburn S, Nguyen BTH, Rosanas-Urgell A. Novel highly-multiplexed AmpliSeq targeted assay for Plasmodium vivax genetic surveillance use cases at multiple geographical scales. Front Cell Infect Microbiol 2022;12:953187. [PMID: 36034708 PMCID: PMC9403277 DOI: 10.3389/fcimb.2022.953187] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022]  Open
44
LaVerriere E, Schwabl P, Carrasquilla M, Taylor AR, Johnson ZM, Shieh M, Panchal R, Straub TJ, Kuzma R, Watson S, Buckee CO, Andrade CM, Portugal S, Crompton PD, Traore B, Rayner JC, Corredor V, James K, Cox H, Early AM, MacInnis BL, Neafsey DE. Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: A malaria case study. Mol Ecol Resour 2022;22:2285-2303. [PMID: 35437908 PMCID: PMC9288814 DOI: 10.1111/1755-0998.13622] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 03/05/2022] [Accepted: 04/05/2022] [Indexed: 11/28/2022]
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Cárdenas P, Corredor V, Santos-Vega M. Genomic epidemiological models describe pathogen evolution across fitness valleys. SCIENCE ADVANCES 2022;8:eabo0173. [PMID: 35857510 PMCID: PMC9278859 DOI: 10.1126/sciadv.abo0173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
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Mayor A, da Silva C, Rovira-Vallbona E, Roca-Feltrer A, Bonnington C, Wharton-Smith A, Greenhouse B, Bever C, Chidimatembue A, Guinovart C, Proctor JL, Rodrigues M, Canana N, Arnaldo P, Boene S, Aide P, Enosse S, Saute F, Candrinho B. Prospective surveillance study to detect antimalarial drug resistance, gene deletions of diagnostic relevance and genetic diversity of Plasmodium falciparum in Mozambique: protocol. BMJ Open 2022;12:e063456. [PMID: 35820756 PMCID: PMC9274532 DOI: 10.1136/bmjopen-2022-063456] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
47
Van Bortel W, Van den Poel B, Hermans G, Vanden Driessche M, Molzahn H, Deblauwe I, De Wolf K, Schneider A, Van Hul N, Müller R, Wilmaerts L, Gombeer S, Smitz N, Kattenberg JH, Monsieurs P, Rosanas-Urgell A, Van Esbroeck M, Bottieau E, Maniewski-Kelner U, Rebolledo J. Two fatal autochthonous cases of airport malaria, Belgium, 2020. EURO SURVEILLANCE : BULLETIN EUROPEEN SUR LES MALADIES TRANSMISSIBLES = EUROPEAN COMMUNICABLE DISEASE BULLETIN 2022;27. [PMID: 35451360 PMCID: PMC9027149 DOI: 10.2807/1560-7917.es.2022.27.16.2100724] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Naung MT, Martin E, Munro J, Mehra S, Guy AJ, Laman M, Harrison GLA, Tavul L, Hetzel M, Kwiatkowski D, Mueller I, Bahlo M, Barry AE. Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens. PLoS Comput Biol 2022;18:e1009801. [PMID: 35108259 PMCID: PMC8843232 DOI: 10.1371/journal.pcbi.1009801] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 02/14/2022] [Accepted: 01/03/2022] [Indexed: 12/30/2022]  Open
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Han J, Munro JE, Kocoski A, Barry AE, Bahlo M. Population-level genome-wide STR discovery and validation for population structure and genetic diversity assessment of Plasmodium species. PLoS Genet 2022;18:e1009604. [PMID: 35007277 PMCID: PMC8782505 DOI: 10.1371/journal.pgen.1009604] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 01/21/2022] [Accepted: 12/14/2021] [Indexed: 11/18/2022]  Open
50
Ndiaye YD, Hartl DL, McGregor D, Badiane A, Fall FB, Daniels RF, Wirth DF, Ndiaye D, Volkman SK. Genetic surveillance for monitoring the impact of drug use on Plasmodium falciparum populations. Int J Parasitol Drugs Drug Resist 2021;17:12-22. [PMID: 34333350 PMCID: PMC8342550 DOI: 10.1016/j.ijpddr.2021.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/24/2021] [Accepted: 07/07/2021] [Indexed: 11/23/2022]
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