The low representation of viral sequences was not unexpected because viruses causing acute infections should be difficult to detect in healthy animals. Retroviruses integrate into the host genome as part of their replication cycle, thus transcription of viral genes can be persistent in infected animals. Overall four transcript-tags were assigned to gamma retroviruses of the family Retroviridae. Based on the transcript-tag from the MD Bonner-pool and an upstream region that is conserved in gamma retroviruses, PCR fragments were amplified and sequenced from MD 191 cDNA, which was used in the MD Bonner-pool, and from genomic DNA of MD 80228. These sequences were compared to other gamma retrovirus sequences using maximum likelihood methods (Fig. 4) . The mule deer gamma retrovirus forms a distinct clade within the gamma retroviruses, which has many well-described members of primate, murine, and feline origin. A newly described gamma retrovirus from killer whale (Orcinus orca) [38] is the closest relative of this mule deer retrovirus. The killer whale virus was described as an endogenous retrovirus based on its finding in various tissues and individuals. However, our detection of transcripts to this virus in only three of the libraries and the sequence variation in the PCR fragment between genomic (MD 80228) and transcript-derived (MD 191) mule deer samples suggest that both endogenous and exogenous gamma retroviruses might be present.