Detection of Subgenomic cDNAs and Mapping of Feline Foamy Virus mRNAs Reveals Complex Patterns of Transcription

AbstractFeline foamy virus (FeFV) belongs to the group of spumaretroviruses that contain in addition togag, pol,andenvaccessory genes collectively calledbelgenes. Primate FVs have been shown to utilize internal promoters in addition to the 5′ LTR promoters. In contrast to other known retroviruses, the FVpolgenes are expressed via spliced transcripts. Northern blot analysis and reverse transcription-coupled polymerase chain reactions (RT-PCR) were used to amplify, clone, and characterize cDNAs generated from subgenomic viral transcripts. Sequencing of the splice site junctions of the different FeFV mRNAs showed that singly and multiply spliced subgenomic transcripts were expressed in virus-infected cells. The relative amount of the splicedpol-specific transcripts was quantitated and FeFVpolmRNA found to be expressed at about one-half of that of the genomic mRNA. The major FeFV internal start site of transcription was identified at RNA position 7925. Comparison of the FeFV transcriptional patterns to those of the human foamy virus revealed that the FeFVbel 1mRNA was expressedexclusivelyfrom the internal promoter in contrast to primate foamy viruses that use both the LTR and the internal promoter for Bel 1 expression. Unexpectedly, anenv-bel 2mRNA was identified in FeFV-infected cells. In addition, cDNAs from FeFV-infected cells were directly amplified by PCR without RT reactions and found to correspond to genomic and to a subset of different subgenomic FeFV mRNAs