The right end of the unique region of the genome of human herpesvirus 6 U1102 contains a candidate immediate early gene enhancer and a homologue of the human cytomegalovirus US22 gene family.

The nucleotide sequence of a 12 kbp HindIII fragment (HindIII C) from the right end of the unique component of the genome of human herpesvirus 6 (HHV-6) (strain U1102) was determined. The sequence has a mean G + C content of 42% and contains approximately 28 copies of a tandemly repeated 104 to 107 bp element, which, with a single exception, contain a cleavage site for KpnI (the KpnI repeats). Each of these elements contains potential binding sites for transcription factors NF-kappa B and AP2. The KpnI repeats lie immediately upstream of a region previously identified as a candidate immediate early (IE) gene locus and therefore may constitute an IE gene enhancer element. One incomplete and six complete open reading frames (ORFs) were identified in the unique sequence of the HindIII C fragment. The predicted products of these ORFs do not include homologues of proteins encoded by members of the alpha- or gamma-herpesvirus sub-family. However, the HindIII C fragment does contain a homologue of the US22 gene family, previously found only in the beta-herpesvirus human cytomegalovirus (HCMV). These findings provide evidence that the close phylogenetic relationship between HHV-6 and HCMV is not confined to the beta-herpesvirus-specific arrangement of conserved replicative and structural genes which has been demonstrated previously.