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Background  Onchocerciasis is a parasitic disease caused by the filarial nematode  Onchocerca volvulus.  In endemic areas, the diagnosis is commonly confirmed by microscopic examination of skin snip samples, though this technique is considered to have low sensitivity. The available melting-curve based quantitative real-time PCR (qPCR) using degenerated primers targeting the O-150 repeat of  O. volvulus  was considered insufficient for confirming the individual diagnosis, especially in elimination studies. This study aimed to improve detection of  O. volvulus  DNA in clinical samples through the development of a highly sensitive qPCR assay.    Methods  A novel hydrolysis probe based qPCR assay was designed targeting the specific sequence of the  O. volvulus  O-5S rRNA gene. A total of 200 clinically suspected onchocerciasis cases were included from Goma district in South-west Ethiopia, from October 2012 through May 2013. Skin snip samples were collected and subjected to microscopy, O-150 qPCR, and the novel O-5S qPCR.    Results  Among the 200 individuals, 133 patients tested positive (positivity rate of 66.5%) and 67 negative by O-5S qPCR, 74 tested positive by microscopy (37.0%) and 78 tested positive by O-150 qPCR (39.0%). Among the 133 O-5S qPCR positive individuals, microscopy and O-150 qPCR detected 55.6 and 59.4% patients, respectively, implying a higher sensitivity of O-5S qPCR than microscopy and O-150 qPCR. None of the 67 individuals who tested negative by O-5S qPCR tested positive by microscopy or O-150 qPCR, implying 100% specificity of the newly designed O-5S qPCR assay.    Conclusions  The novel O-5S qPCR assay is more sensitive than both microscopic examination and the existing O-150 qPCR for the detection of  O. volvulus  from skin snip samples. The newly designed assay is an important step towards appropriate individual diagnosis and control of onchocerciasis.    Electronic supplementary material  The online version of this article (10.1186/s13071-017-2382-3) contains supplementary material, which is available to authorized users.

O-5S quantitative real-time PCR: a new diagnostic tool for laboratory confirmation of human onchocerciasis