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Background Identifying efficient and effective strategies to reach and monitor populations at greatest risk of malaria in low-transmission settings is a key challenge for malaria elimination. In Namibia’s Zambezi Region, transmission is ongoing yet its drivers remain poorly understood. A growing literature suggests that night-time social activities may lead to malaria exposure that is beyond the reach of conventional preventive interventions, such as insecticide treated bed nets and indoor residual spraying. Methods Formative research was conducted with community members in March, 2015 in the catchment areas of six randomly selected health facilities in the western Zambezi Region to identify night-time locations where large numbers of individuals regularly congregate. Using time-location sampling, a survey was conducted between March and May, 2015 at community-identified venues (bars and evening church services) to develop representative estimates of the prevalence of parasite infection and risk factors among venue-goers. Results When compared to a contemporaneous household survey of the general population aged 15 and older (N = 1160), venue-goers (N = 480) were more likely to have spent the night away from their home recently (17.3% vs. 8.9%, P = 0.008), report recent fever (65.2% vs. 36.9%, P

Background Subpatent malaria infections, or low-density infections below the detection threshold of microscopy or standard rapid diagnostic testing (RDT), can perpetuate persistent transmission and, therefore, may be a barrier for countries like Namibia that are pursuing malaria elimination. This potential burden in Namibia has not been well characterized. Methods Using a two-stage cluster sampling, cross-sectional design, subjects of all age were enrolled during the end of the 2015 malaria transmission season in Zambezi region, located in northeast Namibia. Malaria RDTs were performed with subsequent gold standard testing by loop-mediated isothermal amplification (LAMP) using dried blood spots. Infection prevalence was measured and the diagnostic accuracy of RDT calculated. Relationships between recent fever, demographics, epidemiological factors, and infection were assessed. Results Prevalence of Plasmodium falciparum malaria infection was low: 0.8% (16/1919) by RDT and 2.2% (43/1919) by LAMP. All but one LAMP-positive infection was RDT-negative. Using LAMP as gold standard, the sensitivity and specificity of RDT were 2.3% and 99.2%, respectively. Compared to LAMP-negative infections, a higher portion LAMP-positive infections were associated with fever (45.2% vs. 30.4%, p = 0.04), though 55% of infections were not associated with fever. Agricultural occupations and cattle herding were significantly associated with LAMP-detectable infection (Adjusted ORs 5.02, 95% CI 1.77–14.23, and 11.82, 95% CI 1.06–131.81, respectively), while gender, travel, bed net use, and indoor residual spray coverage were not. Conclusions This study presents results from the first large-scale malaria cross-sectional survey from Namibia using molecular testing to characterize subpatent infections. Findings suggest that fever history and standard RDTs are not useful to address this burden. Achievement of malaria elimination may require active case detection using more sensitive point-of-care diagnostics or presumptive treatment and targeted to high-risk groups. Electronic supplementary material The online version of this article (10.1186/s12936-018-2626-5) contains supplementary material, which is available to authorized users.