Malaria prevalence estimates in Tanzania have been documented to decline in the recent
years. National malaria data shows prevalence rates have been reduced by half from 18% in
2008 to 9% in 2012 (THMIS 2009; 2013). This decline has been attributed to countrywide
implementation of malaria interventions, including indoor residual spraying (IRS), mass
distribution of insecticide treated nets (ITNs), long-lasting ITNs and the use of artemisinin
combination therapy (ACT), which aim at transmission reduction. Monitoring and evaluation
of malaria interventions requires accurate information on the remaining malaria burden in
the community. The rapid diagnostic tests (RDTs) and light microscopy (LM) are the
commonly used diagnostic tools for parasite detection and estimation of parasite prevalence
rates in many resource-limited areas such as Tanzania. However, owing to the low detection
limit of LM and RDTs of about 50-100 parasites/µL, their ability to capture low density
infections is limited (Moody 2002; MalEra 2011). The use of molecular techniques to detect
malaria parasites has been advocated to improve the accuracy of parasite prevalence
estimates, especially in moderate to low endemic settings