{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T10:22:57Z","timestamp":1771928577442,"version":"3.50.1"},"reference-count":77,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,2,3]],"date-time":"2026-02-03T00:00:00Z","timestamp":1770076800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      Global efforts to control and eventually eliminate malaria have been less effective for\n                      <jats:italic>Plasmodium vivax<\/jats:italic>\n                      relative to\n                      <jats:italic>Plasmodium falciparum<\/jats:italic>\n                      due to its unique biology, including dormant liver stages that cause later relapse, and earlier commitment to transmission stages. After the nationwide distribution of long-lasting insecticide treated nets (LLIN) in Papua New Guinea (PNG),\n                      <jats:italic>P. vivax<\/jats:italic>\n                      initially reduced to low prevalence, but again resurged to levels similar to those before LLIN distributions.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Method<\/jats:title>\n                    <jats:p>\n                      To explore changes in\n                      <jats:italic>P. vivax<\/jats:italic>\n                      population structure and identify sources of resurgence over this period, we applied a previously validated genome-wide SNP barcode to genotype 336\n                      <jats:italic>P. vivax<\/jats:italic>\n                      isolates obtained from serial cross-sectional surveys conducted over a decade in East Sepik (2005, 2012, 2016) and Madang Province (2006, 2010, 2014).\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Population genetic analyses of the resulting parasite genotypes revealed contrasting spatiotemporal patterns between the two provinces. In Madang, the complexity of infection, genetic diversity, and population structure varied with prevalence, with a possible population bottleneck and early clonal expansion at low transmission, and rapid recovery of the population with resurgence. In East Sepik, there was a less dramatic impact on the parasite population after prevalence decline, and ongoing transmission of multiple residual lineages throughout the study period.\n                      <jats:italic>P. vivax<\/jats:italic>\n                      decline was also accompanied by an increase in genetic differentiation between the two areas, which reduced with resurgence suggesting changes in parasite migration between areas associated with prevalence.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      The earlier implementation of LLIN in East Sepik, smaller rebound, heterogeneity in transmission and relative isolation, compared to Madang may have contributed to these differing patterns. The results demonstrate that long term sustained control efforts are essential to make a lasting impact on the\n                      <jats:italic>P. vivax<\/jats:italic>\n                      population, and that SNP barcodes can provide valuable insights into parasite transmission dynamics as a result of control efforts.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fgene.2025.1621920","type":"journal-article","created":{"date-parts":[[2026,2,3]],"date-time":"2026-02-03T04:15:01Z","timestamp":1770092101000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Population genetics of Plasmodium vivax with transmission decline and rebound in two endemic areas of Papua New Guinea"],"prefix":"10.3389","volume":"16","author":[{"given":"Abebe A.","family":"Fola","sequence":"first","affiliation":[{"name":"Population Health and Immunity Division, Walter and Eliza Hall Institute","place":["Parkville, VIC, Australia"]},{"name":"Department of Medical Biology, University of Melbourne","place":["Carlton, VIC, Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Somya","family":"Mehra","sequence":"additional","affiliation":[{"name":"Population Health and Immunity Division, Walter and Eliza Hall Institute","place":["Parkville, VIC, Australia"]},{"name":"Department of Medical Biology, University of Melbourne","place":["Carlton, VIC, Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zahra","family":"Razook","sequence":"additional","affiliation":[{"name":"Population Health and Immunity Division, Walter and Eliza Hall Institute","place":["Parkville, VIC, Australia"]},{"name":"IMPACT\/School of Medicine, Deakin University","place":["Geelong, VIC, Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dulcie","family":"Lautu-Gumal","sequence":"additional","affiliation":[{"name":"Population Health and Immunity Division, Walter and Eliza Hall Institute","place":["Parkville, VIC, Australia"]},{"name":"Department of Medical Biology, University of Melbourne","place":["Carlton, VIC, Australia"]},{"name":"Life Sciences Discipline, Burnet Institute","place":["Melbourne, VIC, Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elma","family":"Nate","sequence":"additional","affiliation":[{"name":"Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research","place":["Yagaum, Madang, Papua New Guinea"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stuart","family":"Lee","sequence":"additional","affiliation":[{"name":"Population Health and Immunity Division, Walter and Eliza Hall Institute","place":["Parkville, VIC, Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Johanna Helena","family":"Kattenberg","sequence":"additional","affiliation":[{"name":"Population Health and Immunity Division, Walter and Eliza Hall Institute","place":["Parkville, VIC, Australia"]},{"name":"Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research","place":["Yagaum, Madang, Papua New Guinea"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cristian","family":"Koepfli","sequence":"additional","affiliation":[{"name":"Population Health and Immunity Division, Walter and Eliza Hall Institute","place":["Parkville, VIC, Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James","family":"Kazura","sequence":"additional","affiliation":[{"name":"Centre for Global Health and Diseases, Case Western Reserve University","place":["Cleveland, OH, United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria","family":"Ome-Kaius","sequence":"additional","affiliation":[{"name":"Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research","place":["Yagaum, Madang, Papua New Guinea"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Moses","family":"Laman","sequence":"additional","affiliation":[{"name":"Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research","place":["Yagaum, Madang, Papua New Guinea"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leanne J.","family":"Robinson","sequence":"additional","affiliation":[{"name":"Population Health and Immunity Division, Walter and Eliza Hall Institute","place":["Parkville, VIC, Australia"]},{"name":"Department of Medical Biology, University of Melbourne","place":["Carlton, VIC, Australia"]},{"name":"Life Sciences Discipline, Burnet Institute","place":["Melbourne, VIC, Australia"]},{"name":"Central Clinical School, Monash University","place":["Melbourne, VIC, Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ivo","family":"Mueller","sequence":"additional","affiliation":[{"name":"Population Health and Immunity Division, Walter and Eliza Hall Institute","place":["Parkville, VIC, Australia"]},{"name":"Department of Medical Biology, University of Melbourne","place":["Carlton, VIC, Australia"]},{"name":"Department of Parasites and Vectors, Institut Pasteur Paris","place":["Paris, France"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alyssa E.","family":"Barry","sequence":"additional","affiliation":[{"name":"Population Health and Immunity Division, Walter and Eliza Hall Institute","place":["Parkville, VIC, Australia"]},{"name":"Department of Medical Biology, University of Melbourne","place":["Carlton, VIC, Australia"]},{"name":"IMPACT\/School of Medicine, Deakin University","place":["Geelong, VIC, Australia"]},{"name":"Life Sciences Discipline, Burnet Institute","place":["Melbourne, VIC, Australia"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2026,2,3]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"a025585","DOI":"10.1101\/cshperspect.a025585","article-title":"The biology of Plasmodium vivax","volume":"7","author":"Adams","year":"2017","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"B2","doi-asserted-by":"publisher","first-page":"1467","DOI":"10.1093\/oxfordjournals.molbev.a026247","article-title":"Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum","volume":"17","author":"Anderson","year":"2000","journal-title":"Mol. Biol. Evol."},{"key":"B3","volume-title":"FastQC: a quality control tool for high throughput sequence data","author":"Andrews","year":"2010"},{"key":"B4","doi-asserted-by":"publisher","first-page":"188","DOI":"10.4269\/ajtmh.12-0774","article-title":"High genetic diversity of Plasmodium vivax on the north coast of Papua New Guinea","volume":"89","author":"Arnott","year":"2013","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"B5","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1016\/j.ijpara.2016.08.006","article-title":"Dissecting malaria biology and epidemiology using population genetics and genomics","volume":"47","author":"Auburn","year":"2017","journal-title":"Int. J. Parasitol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"e32891","DOI":"10.1371\/journal.pone.0032891","article-title":"Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data","volume":"7","author":"Auburn","year":"2012","journal-title":"PLoS One"},{"key":"B7","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1186\/s12936-015-0879-9","article-title":"Significant geographical differences in prevalence of mutations associated with Plasmodium falciparum and Plasmodium vivax drug resistance in two regions from Papua New Guinea","volume":"14","author":"Barnadas","year":"2015","journal-title":"Malar. J."},{"key":"B8","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1179\/2047773215Y.0000000012","article-title":"Uncovering the transmission dynamics of Plasmodium vivax using population genetics","volume":"109","author":"Barry","year":"2015","journal-title":"Pathog. Glob. Health"},{"key":"B9","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"B10","doi-asserted-by":"publisher","first-page":"e0008962","DOI":"10.1371\/journal.pntd.0008962","article-title":"Population genomics of Plasmodium vivax in Panama to assess the risk of case importation on malaria elimination","volume":"14","author":"Buyon","year":"2020","journal-title":"PLoS Negl. Trop. Dis."},{"key":"B11","doi-asserted-by":"publisher","first-page":"1488109","DOI":"10.3389\/fgene.2024.1488109","article-title":"Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon","volume":"15","author":"Cabrera-Sosa","year":"2024","journal-title":"Front. Genet."},{"key":"B12","doi-asserted-by":"publisher","first-page":"e1005348","DOI":"10.1371\/journal.pcbi.1005348","article-title":"The real McCOIL: a method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites","volume":"13","author":"Chang","year":"2017","journal-title":"PLoS Comput. Biol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"e43481","DOI":"10.7554\/eLife.43481","article-title":"Mapping imported malaria in Bangladesh using parasite genetic and human mobility data","volume":"8","author":"Chang","year":"2019","journal-title":"Elife"},{"key":"B14","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1186\/s40249-016-0151-8","article-title":"Malaria: global progress 2000 - 2015 and future challenges","volume":"5","author":"Cibulskis","year":"2016","journal-title":"Infect. Dis. Poverty"},{"key":"B15","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1186\/s12936-021-03804-0","article-title":"Spatial prediction of malaria prevalence in Papua New Guinea: a comparison of Bayesian decision network and multivariate regression modelling approaches for improved accuracy in prevalence prediction","volume":"20","author":"Cleary","year":"2021","journal-title":"Malar. J."},{"key":"B16","doi-asserted-by":"publisher","first-page":"980795","DOI":"10.3389\/fepid.2022.980795","article-title":"A review of malaria epidemiology and control in Papua New Guinea 1900 to 2021: progress made and future directions","volume":"2","author":"Cleary","year":"2022","journal-title":"Front. Epidemiol."},{"key":"B17","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1093\/emph\/eou018","article-title":"Phylogenetic tree shapes resolve disease transmission patterns","volume":"2014","author":"Colijn","year":"2014","journal-title":"Evol. Med. Public Health"},{"key":"B18","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1186\/s12936-019-2784-0","article-title":"Use cases for genetic epidemiology in malaria elimination","volume":"18","author":"Dalmat","year":"2019","journal-title":"Malar. J."},{"key":"B19","doi-asserted-by":"publisher","first-page":"e60780","DOI":"10.1371\/journal.pone.0060780","article-title":"Genetic surveillance detects both clonal and epidemic transmission of malaria following enhanced intervention in Senegal","volume":"8","author":"Daniels","year":"2013","journal-title":"PLoS One"},{"key":"B20","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1111\/1755-0998.12157","article-title":"NeEstimator v2: re-implementation of software for the estimation of contemporary effective population size (Ne) from genetic data","volume":"14","author":"Do","year":"2014","journal-title":"Mol. Ecol. Resour."},{"key":"B21","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1007\/s12686-011-9548-7","article-title":"Structure Harvester: a website and program for visualizing Structure output and implementing the evanno method","volume":"4","author":"Earl","year":"2012","journal-title":"Conserv. Genet. Resour."},{"key":"B22","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: summarize analysis results for multiple tools and samples in a single report","volume":"32","author":"Ewels","year":"2016","journal-title":"Bioinformatics"},{"key":"B23","doi-asserted-by":"publisher","first-page":"100051","DOI":"10.1016\/j.lansea.2022.100051","article-title":"Quantifying spatial heterogeneity of malaria in the endemic Papua region of Indonesia: analysis of epidemiological surveillance data","volume":"5","author":"Fadilah","year":"2022","journal-title":"Lancet Regional Health - Southeast Asia"},{"key":"B24","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1179\/2047772415Z.000000000263","article-title":"Challenges for Plasmodium vivax malaria elimination in the genomics era","volume":"109","author":"Ferreira","year":"2015","journal-title":"Pathog. Glob. Health"},{"key":"B25","doi-asserted-by":"publisher","first-page":"630","DOI":"10.4269\/ajtmh.16-0716","article-title":"Higher complexity of infection and genetic diversity of Plasmodium vivax than Plasmodium falciparum across all malaria transmission zones of Papua New Guinea","volume":"96","author":"Fola","year":"2017","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"B26","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1016\/j.meegid.2017.11.028","article-title":"Nationwide genetic surveillance of Plasmodium vivax in Papua New Guinea reveals heterogeneous transmission dynamics and routes of migration amongst subdivided populations","volume":"58","author":"Fola","year":"2018","journal-title":"Infect. Genet. Evol."},{"key":"B27","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1186\/s12936-020-03440-0","article-title":"SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics","volume":"19","author":"Fola","year":"2020","journal-title":"Malar. J."},{"key":"B28","doi-asserted-by":"crossref","DOI":"10.1101\/2023.03.02.23286711","volume-title":"Clonal spread ofPlasmodium falciparumcandidate artemisinin partial resistanceKelch13622I mutation and co-occurrence withpfhrp2\/3deletions in Ethiopia","author":"Fola","year":"2023"},{"key":"B29","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1186\/1471-2105-13-87","article-title":"PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods","volume":"13","author":"Francisco","year":"2012","journal-title":"BMC Bioinforma."},{"key":"B30","doi-asserted-by":"publisher","first-page":"2678","DOI":"10.1093\/bioinformatics\/bts503","article-title":"Qualimap: evaluating next-generation sequencing alignment data","volume":"28","author":"Garc\u00eda-Alcalde","year":"2012","journal-title":"Bioinformatics"},{"key":"B31","doi-asserted-by":"publisher","first-page":"16540","DOI":"10.1038\/s41598-021-95959-8","article-title":"Investigating differences in village-level heterogeneity of malaria infection and household risk factors in Papua New Guinea","volume":"11","author":"Gul","year":"2021","journal-title":"Sci. Rep."},{"key":"B32","doi-asserted-by":"publisher","first-page":"880","DOI":"10.1017\/S0031182013002278","article-title":"The Sri Lankan paradox: high genetic diversity in Plasmodium vivax populations despite decreasing levels of malaria transmission","volume":"141","author":"Gunawardena","year":"2014","journal-title":"Parasitology"},{"key":"B33","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1093\/bioinformatics\/16.9.847","article-title":"LIAN 3.0: detecting linkage disequilibrium in multilocus data","volume":"16","author":"Haubold","year":"2000","journal-title":"Bioinformatics"},{"key":"B34","doi-asserted-by":"publisher","first-page":"e1007279","DOI":"10.1371\/journal.pgen.1007279","article-title":"Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens","volume":"14","author":"Henden","year":"2018","journal-title":"PLoS Genet."},{"key":"B35","doi-asserted-by":"publisher","first-page":"1745","DOI":"10.1111\/tmi.12616","article-title":"Prevalence of malaria across Papua New Guinea after initial roll-out of insecticide-treated mosquito nets","volume":"20","author":"Hetzel","year":"2015","journal-title":"Trop. Med. Int. Health"},{"key":"B36","doi-asserted-by":"publisher","first-page":"695","DOI":"10.2471\/BLT.16.189902","article-title":"Insecticide-treated nets and malaria prevalence, Papua New Guinea, 2008-2014","volume":"95","author":"Hetzel","year":"2017","journal-title":"Bull. World Health Organ."},{"key":"B37","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1007\/s40471-021-00266-5","article-title":"Antimalarial drug resistance and implications for the WHO global technical strategy","volume":"8","author":"Ippolito","year":"2021","journal-title":"Curr. Epidemiol. Rep."},{"key":"B38","doi-asserted-by":"publisher","first-page":"e0003634","DOI":"10.1371\/journal.pntd.0003634","article-title":"Plasmodium vivax populations are more genetically diverse and less structured than sympatric Plasmodium falciparum populations","volume":"9","author":"Jennison","year":"2015","journal-title":"PLoS Negl. Trop. Dis."},{"key":"B39","doi-asserted-by":"publisher","first-page":"20138","DOI":"10.1073\/pnas.1007068107","article-title":"Exposing malaria in-host diversity and estimating population diversity by capture-recapture using massively parallel pyrosequencing","volume":"107","author":"Juliano","year":"2010","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B40","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1038\/sj.hdy.6801010","article-title":"Detecting population structure using STRUCTURE software: effect of background linkage disequilibrium","volume":"99","author":"Kaeuffer","year":"2007","journal-title":"Hered. (Edinb.)"},{"key":"B41","doi-asserted-by":"publisher","first-page":"e0164054","DOI":"10.1371\/journal.pone.0164054","article-title":"Spatial effects on the multiplicity of Plasmodium falciparum infections","volume":"11","author":"Karl","year":"2016","journal-title":"PLoS One"},{"key":"B42","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1186\/s12936-020-03265-x","article-title":"The epidemiology of Plasmodium falciparum and Plasmodium vivax in east sepik province, Papua New Guinea, pre- and post-implementation of national malaria control efforts","volume":"19","author":"Kattenberg","year":"","journal-title":"Malar. J."},{"key":"B43","doi-asserted-by":"publisher","first-page":"4525","DOI":"10.1111\/mec.15654","article-title":"Monitoring Plasmodium falciparum and Plasmodium vivax using microsatellite markers indicates limited changes in population structure after substantial transmission decline in Papua New Guinea","volume":"29","author":"Kattenberg","year":"","journal-title":"Mol. Ecol."},{"key":"B44","doi-asserted-by":"publisher","first-page":"e0005930","DOI":"10.1371\/journal.pntd.0005930","article-title":"Substantial population structure of Plasmodium vivax in Thailand facilitates identification of the sources of residual transmission","volume":"11","author":"Kittichai","year":"2017","journal-title":"PLoS Negl. Trop. Dis."},{"key":"B45","doi-asserted-by":"publisher","first-page":"e1424","DOI":"10.1371\/journal.pntd.0001424","article-title":"Multiplicity and diversity of Plasmodium vivax infections in a highly endemic region in Papua New Guinea","volume":"5","author":"Koepfli","year":"2011","journal-title":"PLoS Negl. Trop. Dis."},{"key":"B46","doi-asserted-by":"publisher","first-page":"e66041","DOI":"10.1371\/journal.pone.0066041","article-title":"A large Plasmodium vivax reservoir and little population structure in the south Pacific","volume":"8","author":"Koepfli","year":"2013","journal-title":"PLoS One"},{"key":"B47","doi-asserted-by":"publisher","first-page":"1434","DOI":"10.1093\/infdis\/jix507","article-title":"Sustained malaria control over an 8-Year period in Papua New Guinea: the challenge of low-density asymptomatic plasmodium infections","volume":"216","author":"Koepfli","year":"2017","journal-title":"J. Infect. Dis."},{"key":"B48","doi-asserted-by":"publisher","first-page":"ofy240","DOI":"10.1093\/ofid\/ofy240","article-title":"Multiplicity of infection is a poor predictor of village-level Plasmodium vivax and P. falciparum population prevalence in the southwest Pacific","volume":"5","author":"Koepfli","year":"2018","journal-title":"Open Forum Infect. Dis."},{"key":"B49","doi-asserted-by":"publisher","first-page":"1179","DOI":"10.1111\/1755-0998.12387","article-title":"Clumpak: a program for identifying clustering modes and packaging population structure inferences across K","volume":"15","author":"Kopelman","year":"2015","journal-title":"Mol. Ecol. Resour."},{"key":"B50","doi-asserted-by":"publisher","first-page":"2453","DOI":"10.1046\/j.1365-294x.2002.01643.x","article-title":"Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review","volume":"11","author":"Li","year":"2002","journal-title":"Mol. Ecol."},{"key":"B51","doi-asserted-by":"publisher","first-page":"1451","DOI":"10.1093\/bioinformatics\/btp187","article-title":"DnaSP v5: a software for comprehensive analysis of DNA polymorphism data","volume":"25","author":"Librado","year":"2009","journal-title":"Bioinformatics"},{"key":"B52","doi-asserted-by":"publisher","first-page":"298","DOI":"10.1093\/bioinformatics\/btr642","article-title":"PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs","volume":"28","author":"Lischer","year":"2012","journal-title":"Bioinformatics"},{"key":"B53","doi-asserted-by":"publisher","first-page":"e1009133","DOI":"10.1371\/journal.ppat.1009133","article-title":"Emergence of artemisinin-resistant Plasmodium falciparum with kelch13 C580Y mutations on the island of new Guinea","volume":"16","author":"Miotto","year":"2020","journal-title":"PLoS Pathog."},{"key":"B54","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1186\/1475-2875-8-41","article-title":"High sensitivity detection of plasmodium species reveals positive correlations between infections of different species, shifts in age distribution and reduced local variation in Papua New Guinea","volume":"8","author":"Mueller","year":"","journal-title":"Malar. J."},{"key":"B55","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1016\/S1473-3099(09)70177-X","article-title":"Key gaps in the knowledge of Plasmodium vivax, a neglected human malaria parasite","volume":"9","author":"Mueller","year":"","journal-title":"Lancet Infect. Dis."},{"key":"B56","doi-asserted-by":"publisher","first-page":"131","DOI":"10.4269\/ajtmh.21-1336","article-title":"Asia-Pacific ICEMR: understanding malaria transmission to accelerate malaria elimination in the Asia Pacific region","volume":"107","author":"Mueller","year":"2022","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"B57","doi-asserted-by":"publisher","first-page":"1046","DOI":"10.1038\/ng.2373","article-title":"The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum","volume":"44","author":"Neafsey","year":"2012","journal-title":"Nat. Genet."},{"key":"B58","doi-asserted-by":"publisher","first-page":"502","DOI":"10.1038\/s41576-021-00349-5","article-title":"Advances and opportunities in malaria population genomics","volume":"22","author":"Neafsey","year":"2021","journal-title":"Nat. Rev. Genet."},{"key":"B59","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1111\/mec.12099","article-title":"Population genetic correlates of declining transmission in a human pathogen","volume":"22","author":"Nkhoma","year":"2013","journal-title":"Mol. Ecol."},{"key":"B60","doi-asserted-by":"publisher","first-page":"e0003739","DOI":"10.1371\/journal.pntd.0003739","article-title":"Contrasting transmission dynamics of Co-endemic Plasmodium vivax and P. falciparum: implications for malaria control and elimination","volume":"9","author":"Noviyanti","year":"2015","journal-title":"PLoS Negl. Trop. Dis."},{"key":"B61","doi-asserted-by":"publisher","first-page":"10","DOI":"10.12688\/wellcomeopenres.10784.2","article-title":"Micro-epidemiological structuring of Plasmodium falciparum parasite populations in regions with varying transmission intensities in Africa","volume":"2","author":"Omedo","year":"2017","journal-title":"Wellcome Open Res."},{"key":"B62","doi-asserted-by":"publisher","first-page":"945","DOI":"10.1093\/genetics\/155.2.945","article-title":"Inference of population structure using multilocus genotype data","volume":"155","author":"Pritchard","year":"2000","journal-title":"Genetics"},{"key":"B63","doi-asserted-by":"publisher","first-page":"e1002456","DOI":"10.1371\/journal.pmed.1002456","article-title":"malERA: an updated research agenda for malaria elimination and eradication","volume":"14","author":"Rabinovich","year":"2017","journal-title":"PLoS Med."},{"key":"B64","doi-asserted-by":"publisher","first-page":"e1001891","DOI":"10.1371\/journal.pmed.1001891","article-title":"Strategies for understanding and reducing the Plasmodium vivax and Plasmodium ovale hypnozoite reservoir in Papua New Guinean children: a randomised placebo-controlled trial and mathematical model","volume":"12","author":"Robinson","year":"2015","journal-title":"PLoS Med."},{"key":"B65","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1016\/j.pt.2023.11.006","article-title":"Molecular markers for malaria genetic epidemiology: progress and pitfalls","volume":"40","author":"Ruybal-Pes\u00e1ntez","year":"2024","journal-title":"Trends Parasitol."},{"key":"B66","doi-asserted-by":"publisher","first-page":"e1001195","DOI":"10.1371\/journal.pmed.1001195","article-title":"Intermittent preventive treatment for malaria in Papua New Guinean infants exposed to Plasmodium falciparum and P. vivax: a randomized controlled trial","volume":"9","author":"Senn","year":"2012","journal-title":"PLoS Med."},{"key":"B67","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1186\/1475-2875-12-447","article-title":"A call to arms: on refining Plasmodium vivax microsatellite marker panels for comparing global diversity","volume":"12","author":"Sutton","year":"2013","journal-title":"Malar. J."},{"key":"B80","doi-asserted-by":"crossref","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: molecular evolutionary genetics analysis version 11","volume":"38","author":"Tamura","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"B68","doi-asserted-by":"publisher","first-page":"e1007065","DOI":"10.1371\/journal.pgen.1007065","article-title":"Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent","volume":"13","author":"Taylor","year":"2017","journal-title":"PLoS Genet."},{"key":"B69","doi-asserted-by":"publisher","first-page":"1337","DOI":"10.1534\/genetics.119.302120","article-title":"Estimating relatedness between malaria parasites","volume":"212","author":"Taylor","year":"2019","journal-title":"Genetics"},{"key":"B70","doi-asserted-by":"publisher","first-page":"e43510","DOI":"10.7554\/eLife.43510","article-title":"Using parasite genetic and human mobility data to infer local and cross-border malaria connectivity in Southern Africa","volume":"8","author":"Tessema","year":"2019","journal-title":"Elife"},{"key":"B71","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1016\/B978-0-12-800099-1.00003-X","article-title":"Measuring changes in Plasmodium falciparum transmission: precision, accuracy and costs of metrics","volume":"84","author":"Tusting","year":"2014","journal-title":"Adv. Parasitol."},{"key":"B72","first-page":"314","article-title":"Efficient architecture-aware acceleration of BWA-MEM for multicore systems","author":"Vasimuddin","year":"2019"},{"key":"B73","doi-asserted-by":"publisher","first-page":"324","DOI":"10.1016\/j.actatropica.2011.12.002","article-title":"Application of genomics to field investigations of malaria by the international centers of excellence for malaria research","volume":"121","author":"Volkman","year":"2012","journal-title":"Acta Trop."},{"key":"B74","doi-asserted-by":"publisher","first-page":"e0006146","DOI":"10.1371\/journal.pntd.0006146","article-title":"Increasingly inbred and fragmented populations of Plasmodium vivax associated with the eastward decline in malaria transmission across the southwest Pacific","volume":"12","author":"Waltmann","year":"2018","journal-title":"PLoS Negl. Trop. Dis."},{"key":"B75","volume-title":"World malaria report","year":"2024"},{"key":"B76","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1186\/s12936-018-2322-5","article-title":"Molecular approaches to determine the multiplicity of plasmodium infections","volume":"17","author":"Zhong","year":"2018","journal-title":"Malar. J."}],"updated-by":[{"DOI":"10.3389\/fgene.2026.1805349","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2026,2,16]],"date-time":"2026-02-16T00:00:00Z","timestamp":1771200000000}}],"container-title":["Frontiers in Genetics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2025.1621920\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T09:31:41Z","timestamp":1771925501000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fgene.2025.1621920\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,3]]},"references-count":77,"alternative-id":["10.3389\/fgene.2025.1621920"],"URL":"https:\/\/doi.org\/10.3389\/fgene.2025.1621920","relation":{},"ISSN":["1664-8021"],"issn-type":[{"value":"1664-8021","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,3]]},"article-number":"1621920"}}