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This study explored the population genetics of 63 <jats:italic>Plasmodium falciparum<\/jats:italic> and 170 <jats:italic>P. vivax<\/jats:italic> cases collected in the Peruvian Amazon Basin between 2015 and 2019. Microscopy and PCR were used for malaria detection and positive samples were genotyped at neutral and drug resistance-associated regions. The <jats:italic>P. falciparum<\/jats:italic> population exhibited a low nucleotide diversity (\u03c0\u2009=\u20090.02) whereas the <jats:italic>P. vivax<\/jats:italic> population presented a higher genetic diversity (\u03c0\u2009=\u20090.34). All <jats:italic>P. falciparum<\/jats:italic> samples (n\u2009=\u200963) carried chloroquine (CQ) resistant mutations on <jats:italic>Pfcrt<\/jats:italic>. Most <jats:italic>P. falciparum<\/jats:italic> samples (53 out of 54) carried sulfadoxine (SD) resistant mutations on <jats:italic>Pfdhfr<\/jats:italic> and <jats:italic>Pfdhps<\/jats:italic>. No evidence was found of artemisinin resistance mutations on <jats:italic>kelch13<\/jats:italic>. Population structure showed that a single cluster accounted for 93.4% of the <jats:italic>P. falciparum<\/jats:italic> samples whereas three clusters were found for <jats:italic>P. vivax<\/jats:italic>. Our study shows a low genetic diversity for both species with significant differences in genetic sub-structuring. The high prevalence of CQ-resistance mutations could be a result of indirect selection pressures driven by the <jats:italic>P. vivax<\/jats:italic> treatment scheme. These results could be useful for public health authorities to safeguard the progress that Peru has achieved towards malaria elimination.<\/jats:p>","DOI":"10.1038\/s41598-022-21028-3","type":"journal-article","created":{"date-parts":[[2022,10,1]],"date-time":"2022-10-01T09:07:09Z","timestamp":1664615229000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Drug resistance and population structure of Plasmodium falciparum and Plasmodium vivax in the Peruvian Amazon"],"prefix":"10.1038","volume":"12","author":[{"given":"Fredy E.","family":"Villena","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan F.","family":"Sanchez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oscar","family":"Nolasco","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Greys","family":"Braga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leonila","family":"Ricopa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keare","family":"Barazorda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carola J.","family":"Salas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carmen","family":"Lucas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen E.","family":"Lizewski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christie A.","family":"Joya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dionicia","family":"Gamboa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Delgado-Ratto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hugo O.","family":"Valdivia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,10,1]]},"reference":[{"key":"21028_CR1","unstructured":"WHO. 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