The development of new molecular approaches for identification or discovery of known and unknown pathogens is essential. The purpose of this study was to evaluate the utility of a new method designated primer extension enrichment reaction (PEER) in detecting viral genomes from highly divergent viral families (ssDNA, dsDNA, ssRNA, dsRNA) in infected cell lines. Findings indicate that the PEER methodology is a powerful tool since it permitted successful ex vivo detection of infectious agents from the Circoviridae, Herpesviridae, Paramyxoviridae, Picornaviridae and Reoviridae families. The great potential of PEER was further confirmed in tests using serial dilutions of West Nile virus (Flaviviridae) and in a "blind" test in which a member of the Poxviridae family was successfully identified. The technique was shown to be useful for identifying causative viral pathogens, following inoculation of susceptible cell lines with clinical biological samples.