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From 2013 to 2020, the total number of malaria cases have decreased, from 37,741 to 4474 (an 88.1% reduction). However, infections with <jats:italic>Plasmodium knowlesi<\/jats:italic>, a monkey malarial pathogen that can also infect humans, have been increasingly observed. This study focused on the molecular analysis of <jats:italic>P. knowlesi<\/jats:italic> parasites causing malaria in Thailand.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>Under Thailand\u2019s integrated Drug Efficacy Surveillance (iDES), which includes drug-resistance monitoring as part of routine case-based surveillance and responses, specimens were collected from malaria patients (n = 966) between 2018 and 2020. Thirty-one mono\u00a0<jats:italic>P. knowlesi<\/jats:italic> infections (3.1%), most of which were from eastern and southern Thailand, were observed and confirmed by nested PCR assay and DNA sequencing. To evaluate whether these pathogens were from different lineages, cluster analysis based on seven microsatellite genotyping markers and the merozoite surface protein 1 (<jats:italic>pkmsp1<\/jats:italic>) gene was carried out. The <jats:italic>P. knowlesi<\/jats:italic> pyrimethamine resistance gene dihydrofolate reductase (<jats:italic>pkdhfr<\/jats:italic>) was sequenced and homology modelling was constructed.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The results of analysing the seven microsatellite markers and <jats:italic>pkmsp1<\/jats:italic> sequence demonstrated that <jats:italic>P. knowlesi<\/jats:italic> parasites from eastern Thailand were of the same lineage as those isolated in Cambodia, while the parasites causing malaria in southern Thailand were the same lineage as those isolated from Malaysia. The sequencing results for the <jats:italic>pkdhfr<\/jats:italic> genes indicated the presence of two mutations, Arg34Leu and a deletion at position 105. On analysis with homology modelling, the two mutations were not associated with anti-malarial drug resistance.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>This report compared the genetic populations of <jats:italic>P. knowlesi<\/jats:italic> parasites in Thailand from 2018 to 2020 and have shown similar lineages as those isolated in Cambodia and Malaysia of <jats:italic>P. knowlesi<\/jats:italic> infection in Thailand and demonstrated that the <jats:italic>P. knowlesi<\/jats:italic> parasites were of the same lineages as those isolated in Cambodia and Malaysia. The parasites were also shown to be sensitive to pyrimethamine.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12936-021-03990-x","type":"journal-article","created":{"date-parts":[[2021,12,3]],"date-time":"2021-12-03T10:06:29Z","timestamp":1638525989000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Genetic population of Plasmodium knowlesi during pre-malaria elimination in Thailand"],"prefix":"10.1186","volume":"20","author":[{"given":"Rungniran","family":"Sugaram","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patcharida","family":"Boondej","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Suttipat","family":"Srisutham","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chanon","family":"Kunasol","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Watcharee","family":"Pagornrat","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Usa","family":"Boonyuen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arjen M","family":"Dondorp","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aungkana","family":"Saejeng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Prayuth","family":"Sudathip","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0857-1855","authenticated-orcid":false,"given":"Mallika","family":"Imwong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,12,3]]},"reference":[{"key":"3990_CR1","volume-title":"The \u201cWorld malaria report 2019\u201d at a glance","author":"WHO","year":"2019","unstructured":"World Health Organization. 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For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","order":6,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare that they have no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Ethical approvals for the study were obtained from the ethical review committees of the Faculty of Tropical Medicine, Mahidol University (MUTM2020-082-01). Informed consent was obtained from all participants. Approval for this study was obtained from the Ethics Review Committee for Research in Human Subjects, Faculty of Tropical Medicine, Mahidol University, Thailand (EC approval number: MUTM2020-082-01). Informed consent was obtained from all participants.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"454"}}