Developing diagnostic tools and strategies is the main driver to improve surveillance and research of emerging viral diseases. A strategic choice was made to link syndromes to an etiological agent, including hemorrhagic syndromes. To isolate and diagnose highly pathogenic viruses, a progressive and diversified methodology was applied. The first approach used real-time virus-specific PCR (qRT-PCR). If the first approach was not successful, conventional RT-PCR was implemented using degenerate consensus primers targeting conserved regions of the genome. Ultimately, random amplification of nucleotide sequences was directly applied to the original biological material (DNA chip re-sequencing, meta-genomic pyrosequencing (454 Life Sciences, Branford, CT)).