From orphan virus to pathogen: the path to the clinical lab

Viral metagenomics has recently yielded numerous previously uncharacterized viral genomes from human and animal samples. We review some of the metagenomics tools and strategies to determine which orphan viruses are pathogenic. Disease association studies compare viral prevalence in patients with unexplained symptoms versus healthy individuals but require these case and control groups to be closely matched epidemiologically. The development of an antibody response in convalescent serum can temporarily link symptoms with a recent infection. Neutralizing antibody detection requires often difficult cell culture virus amplification. Antibody binding assays require synthesis of properly folded antigen and known positive and negative sera to set assay thresholds. High levels of viral genetic diversity within orphan viral groups, frequent co-infections, low or rare pathogenicity, and chronic viral replication, can all complicate disease association studies. The limited availability of large biological sample sets from patients with unexplained diseases and epidemiologically matched controls from different geographic areas and age groups are major hurdles for estimating the pathogenic potential of recently characterized orphan viruses. Current limitations on the practical use of deep sequencing for viral diagnostics are listed.