A Simple-Probe real-time PCR assay for genotyping reassorted and non-reassorted isolates of Crimean-Congo hemorrhagic fever virus in southern Africa.

Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne viral zoonosis distributed widely in Africa, Asia, Russia and the Balkans. Occurrence of segment reassortment has been established and may be associated with pathogenicity. The ability to distinguish between an infection with a reassortant and a non-reassortant variant may have prognostic value. In this study the use of Simple-Probe technology and real-time PCR was investigated to detect rapidly CCHF viral nucleic acid and to distinguish between reassorted and non-reassorted variants of southern African CCHF virus (CCHFV) isolates. A Simple-Probe was designed based on multiple alignments of 19 CCHFV partial M segment sequences that included reassorted and non-reassorted isolates from two phylogenies. Real-time PCR followed by probe-specific melting-curve analysis allowed differentiation of three selected isolates representative of two phylogenetically distinct groups, SPU 431/85 (group IV), 383/87 (group IV) and 103/87 (group III) based on melting temperatures. Within group IV there are two distinct lineages which were represented in the optimization. A further 16 clinical isolates could be genotyped into groups III and IV using the Simple-Probe real-time PCR assay developed in this study. This assay provides a reliable and sensitive tool for the differentiation between reassorted and non-reassorted variants of CCHFV which finds application for diagnosis and epidemiologic and surveillance studies.