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Recent outbreaks in Brazil underscore the importance of\n                    <jats:italic>P. simium<\/jats:italic>\n                    spillovers from non-human primates. Genomic studies are crucial for identifying molecular markers of host adaptation and improving diagnostic tools; however, a high-quality reference genome is needed. To address this, we used Oxford Nanopore and Illumina sequencing platforms to generate a high-quality\n                    <jats:italic>P. simium<\/jats:italic>\n                    reference (Ps_S\u00e3oPaulo, 21.8\u00a0Mb). Comparative genomic analyses confirmed known differences with\n                    <jats:italic>P. vivax<\/jats:italic>\n                    , including mitochondrial mutations, deletions in reticulocyte-invasion genes (\n                    <jats:italic>RBP2a, DBP<\/jats:italic>\n                    ), and variants in blood-stage antigen genes (\n                    <jats:italic>msp3.1, msp3.2<\/jats:italic>\n                    ). Genome-wide analyses of 38\n                    <jats:italic>P. simium<\/jats:italic>\n                    samples from Brazil revealed expected divergence from\n                    <jats:italic>P. vivax<\/jats:italic>\n                    and potential unique signatures of selection and host adaptation. This study provides the most comprehensive\n                    <jats:italic>P. simium<\/jats:italic>\n                    reference genome, advancing our understanding of its genomic diversity, with insights for malaria control in Brazil.\n                  <\/jats:p>","DOI":"10.1038\/s41598-025-27554-0","type":"journal-article","created":{"date-parts":[[2025,12,12]],"date-time":"2025-12-12T11:16:05Z","timestamp":1765538165000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Novel zoonotic cases of Plasmodium simium from S\u00e3o Paulo with a reference genome of the Brazilian strain"],"prefix":"10.1038","volume":"15","author":[{"given":"Emilia","family":"Manko","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nina","family":"Billows","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew","family":"Higgins","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Ward","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amy","family":"Ibrahim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Susana","family":"Campino","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Silvia Maria","family":"Di Santi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Taane G.","family":"Clark","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,12,12]]},"reference":[{"key":"27554_CR1","unstructured":"World Health Organization., World Malaria Report 2024. 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