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Most infections are low-parasitemia, with an unknown proportion below routine microscopy detection thresholds. Molecular surveillance tools optimizing the limit of detection (LOD) would allow more accurate estimates of zoonotic malaria prevalence.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec002\">\n                    <jats:title>Methodology\/Principal findings<\/jats:title>\n                    <jats:p>\n                      An established ultra-sensitive\n                      <jats:italic>Plasmodium<\/jats:italic>\n                      genus quantitative-PCR (qPCR) assay targeting the 18S rRNA gene underwent LOD evaluation with and without reverse transcription (RT) for\n                      <jats:italic>P<\/jats:italic>\n                      .\n                      <jats:italic>knowlesi<\/jats:italic>\n                      ,\n                      <jats:italic>P<\/jats:italic>\n                      .\n                      <jats:italic>cynomolgi<\/jats:italic>\n                      and\n                      <jats:italic>P<\/jats:italic>\n                      .\n                      <jats:italic>vivax<\/jats:italic>\n                      using total nucleic acid preserved (DNA\/RNA Shield) isolates and archived dried blood spots (DBS). LODs for selected\n                      <jats:italic>P<\/jats:italic>\n                      .\n                      <jats:italic>knowlesi-<\/jats:italic>\n                      specific assays, and reference\n                      <jats:italic>P<\/jats:italic>\n                      .\n                      <jats:italic>vivax-<\/jats:italic>\n                      and\n                      <jats:italic>P<\/jats:italic>\n                      .\n                      <jats:italic>cynomolgi<\/jats:italic>\n                      -specific assays were determined with reverse transcription (RT). Assay specificities were assessed using clinical malaria samples and malaria-negative controls.\n                    <\/jats:p>\n                    <jats:p>\n                      The use of reverse transcription improved\n                      <jats:italic>Plasmodium<\/jats:italic>\n                      species detection by up to 10,000-fold (\n                      <jats:italic>Plasmodium<\/jats:italic>\n                      genus), 2759-fold (\n                      <jats:italic>P<\/jats:italic>\n                      .\n                      <jats:italic>knowlesi<\/jats:italic>\n                      ) and 1000-fold (\n                      <jats:italic>P<\/jats:italic>\n                      .\n                      <jats:italic>vivax<\/jats:italic>\n                      and\n                      <jats:italic>P<\/jats:italic>\n                      .\n                      <jats:italic>cynomolgi<\/jats:italic>\n                      ).\n                    <\/jats:p>\n                    <jats:p>\n                      The Kamau et al.\n                      <jats:italic>Plasmodium<\/jats:italic>\n                      genus RT-qPCR assay was highly sensitive for\n                      <jats:italic>P<\/jats:italic>\n                      .\n                      <jats:italic>knowlesi<\/jats:italic>\n                      detection with a median LOD of \u22640.0002 parasites\/\u03bcL compared to 0.002 parasites\/\u03bcL for\n                      <jats:italic>P<\/jats:italic>\n                      .\n                      <jats:italic>cynomolgi<\/jats:italic>\n                      and\n                      <jats:italic>P<\/jats:italic>\n                      .\n                      <jats:italic>vivax<\/jats:italic>\n                      . The LODs with RT for\n                      <jats:italic>P<\/jats:italic>\n                      .\n                      <jats:italic>knowlesi<\/jats:italic>\n                      -specific PCRs were enhanced for the Imwong et al. 18S rRNA (0.0007 parasites\/\u03bcL) and Divis et al. real-time 18S rRNA (0.0002 parasites\/\u03bcL) assays, but not for the Lubis et al. hemi-nested\n                      <jats:italic>SICAvar<\/jats:italic>\n                      (1.1 parasites\/\u03bcL) and Lee et al. nested 18S rRNA (11 parasites\/\u03bcL). The LOD for\n                      <jats:italic>P<\/jats:italic>\n                      .\n                      <jats:italic>vivax-<\/jats:italic>\n                      and\n                      <jats:italic>P<\/jats:italic>\n                      .\n                      <jats:italic>cynomolgi-<\/jats:italic>\n                      specific assays with RT were moderately improved at 0.02 and 0.002 parasites\/\u03bcL, respectively (1000-fold change). For DBS\n                      <jats:italic>P<\/jats:italic>\n                      .\n                      <jats:italic>knowlesi<\/jats:italic>\n                      samples the use of RT also markedly improved the\n                      <jats:italic>Plasmodium<\/jats:italic>\n                      genus qPCR LOD from 19.89 to 0.08 parasites\/\u03bcL (249-fold change); no LOD improvement was demonstrated in DBS archived beyond 6 years. The\n                      <jats:italic>Plasmodium<\/jats:italic>\n                      genus and\n                      <jats:italic>P<\/jats:italic>\n                      .\n                      <jats:italic>knowlesi<\/jats:italic>\n                      -assays were 100% specific for\n                      <jats:italic>Plasmodium<\/jats:italic>\n                      species and\n                      <jats:italic>P<\/jats:italic>\n                      .\n                      <jats:italic>knowlesi<\/jats:italic>\n                      detection, respectively, from 190 clinical infections and 48 healthy controls. Reference\n                      <jats:italic>P<\/jats:italic>\n                      .\n                      <jats:italic>vivax-<\/jats:italic>\n                      specific primers demonstrated known cross-reactivity with\n                      <jats:italic>P<\/jats:italic>\n                      .\n                      <jats:italic>cynomolgi<\/jats:italic>\n                      .\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec003\">\n                    <jats:title>Conclusions\/Significance<\/jats:title>\n                    <jats:p>\n                      Our findings support the use of an 18S rRNA\n                      <jats:italic>Plasmodium<\/jats:italic>\n                      genus qPCR and species-specific nested PCR protocol with RT for highly-sensitive surveillance of zoonotic and human\n                      <jats:italic>Plasmodium<\/jats:italic>\n                      species infections.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1371\/journal.pntd.0012129","type":"journal-article","created":{"date-parts":[[2025,2,6]],"date-time":"2025-02-06T13:56:31Z","timestamp":1738850191000},"page":"e0012129","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":8,"title":["Improved limit of detection for zoonotic Plasmodium knowlesi and P. cynomolgi surveillance using reverse transcription for total nucleic acid preserved samples or dried blood spots"],"prefix":"10.1371","volume":"19","author":[{"given":"Kamil A.","family":"Braima","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kim A.","family":"Piera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7075-9491","authenticated-orcid":true,"given":"Inke N. 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