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In this study, we explored the genomic profile of 18 <jats:italic>P. falciparum<\/jats:italic> samples collected in the Peruvian Amazon Basin (Loreto) and 6 from the Peruvian North Coast (Tumbes). Our results showed the presence of three subpopulations that matched previously typed lineages in Peru: Bv1 (n\u2009=\u200917), Clonet D (n\u2009=\u20094) and Acre-Loreto type (n\u2009=\u20093). Gene coverage analysis showed that none of the Bv1 samples presented coverage for <jats:italic>pfhrp2<\/jats:italic> and <jats:italic>pfhrp3<\/jats:italic>. Genotyping of drug resistance markers showed a high prevalence of Chloroquine resistance mutations S1034C\/N1042D\/D1246Y in <jats:italic>pfmdr1<\/jats:italic> (62.5%) and K45T in <jats:italic>pfcrt<\/jats:italic> (87.5%). Mutations associated with sulfadoxine and pyrimethamine treatment failure were found on 88.8% of the Bv1 samples which were triple mutants for <jats:italic>pfdhfr<\/jats:italic> (50R\/51I\/108N) and <jats:italic>pfdhps<\/jats:italic> (437G\/540E\/581G). Analysis of the <jats:italic>pfS47<\/jats:italic> gene that allows <jats:italic>P. falciparum<\/jats:italic> to evade mosquito immune responses showed that the Bv1 lineage presented one <jats:italic>pfS47<\/jats:italic> haplotype exclusive to Loreto and another haplotype that was present in both Loreto and Tumbes. Furthermore, a possible expansion of Bv1 was detected since 2011 in Loreto. This replacement could be a result of the high prevalence of CQ resistance polymorphisms in Bv1, which could have provided a selective advantage to the indirect selection pressures driven by the use of CQ for <jats:italic>P. vivax<\/jats:italic> treatment.<\/jats:p>","DOI":"10.1038\/s41598-021-00806-5","type":"journal-article","created":{"date-parts":[[2021,10,27]],"date-time":"2021-10-27T10:04:13Z","timestamp":1635329053000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["Population genomics and evidence of clonal replacement of Plasmodium falciparum in the Peruvian Amazon"],"prefix":"10.1038","volume":"11","author":[{"given":"Fredy E.","family":"Villena","sequence":"first","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":"Hugo O.","family":"Valdivia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,10,27]]},"reference":[{"key":"806_CR1","unstructured":"Organization, W. 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