Disclosed are methods and compositions for identifying viral-specific polynucleotide sequences in a biological sample, and particularly in samples of veterinary origin. Also disclosed are oligonucleotide primer pairs, as well as labeled oligonucleotide detection probes useful in detecting the presence of one or more particular species, strains, types, or subtypes of one or more mammalian pathogens of viral origin, as well as systems, diagnostic kits and articles of manufacture comprising virus-specific primers and labeled detection probes, including those useful in identifying viral components of a multivalent vaccine, and quantitating the potency of particular attenuated, live viruses that comprise a livestock vaccine. In certain embodiments, real-time, quantitative PCR methods have been utilized to identify and distinguish between the three known genetic subtypes of bovine viral diarrhea viruses (BVDV-1a, BVDV-1b, and BVDV-2) in a multivalent bovid shipping fever vaccine.