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Infections can be subpatent, falling below the limit of detection for conventional thick-film microscopy and rapid diagnostic testing (RDT). In this study, the prevalence of subclinical <jats:italic>P. falciparum<\/jats:italic> infections in school-aged children was characterised at the start of the dry season in the Upper River Region of The Gambia in 2017\/2018, with a goal to also compare the utility of different diagnostic tools.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>In a cross-sectional survey of children living in 29 villages on the south bank of the Gambia river (median age of 10 years), matched microscopy, rapid diagnostic test (RDT, detecting histidine-rich protein 2) and polymerase chain reaction (PCR, targeting either 18S rRNA or <jats:italic>var<\/jats:italic> gene acidic terminal sequence) were used to determine the prevalence of patent and subpatent infections and to compare the performance of the different diagnostic methods.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The prevalence of <jats:italic>var<\/jats:italic> gene acidic terminal sequence (<jats:italic>var<\/jats:italic>ATS) qPCR-detectable infections was 10.2% (141\/1381) with a median density of 3.12 parasites\/\u00b5L. Malaria prevalence was highly heterogeneous across the region, ranging from &lt;\u20091% to ~\u200940% prevalence in different village clusters. Compared to <jats:italic>var<\/jats:italic>ATS, 18S rRNA PCR detected fewer low-density infections, with an assay sensitivity of 50% and specificity of 98.8%. Parasite prevalence in the cohort was 2.9% by microscopy and 1.5% by RDT. Compared to <jats:italic>var<\/jats:italic>ATS qPCR, microscopy and RDT had sensitivities of 11.5% and 9.2%, respectively, although both methods were highly specific (&gt;\u200998%). Samples that were positive by all three tests (<jats:italic>var<\/jats:italic>ATS qPCR, RDT and microscopy) had significantly higher parasite densities (median\u2009=\u20091705 parasites\/\u00b5L) than samples that were positive by <jats:italic>var<\/jats:italic>ATS qPCR only (median\u2009=\u20092.4 parasites\/\u00b5L).<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>The majority of subclinical malaria infections in school-aged children were of extremely low parasite density and detectable only by ultra-sensitive PCR analysis. Understanding the duration of these low density infections, their physiological impact and their contribution to sustained parasite transmission is necessary to inform malaria elimination strategies.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12936-022-04184-9","type":"journal-article","created":{"date-parts":[[2022,6,7]],"date-time":"2022-06-07T08:05:45Z","timestamp":1654589145000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Dry season prevalence of Plasmodium falciparum in asymptomatic Gambian children, with a comparative evaluation of diagnostic methods"],"prefix":"10.1186","volume":"21","author":[{"given":"Jason P.","family":"Mooney","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sophia M.","family":"DonVito","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maimuna","family":"Jahateh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haddy","family":"Bittaye","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian","family":"Bottomley","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Umberto","family":"D\u2019Alessandro","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eleanor M.","family":"Riley","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2022,6,7]]},"reference":[{"key":"4184_CR1","unstructured":"WHO. 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Prior to enrolment, verbal assent was obtained from study participants and verbal or written consent was obtained from their parent or guardian.","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 the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential competing interest.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"171"}}