Nucleotide sequence analysis of a 30-kilobase-pair region of human herpesvirus-6B (HHV-6B) genome and strain-specific variations in major immediate-early genesNucleotide sequence analysis of a 30-kilobase-pair region of human herpesvirus-6B (HHV-6B) genom

Human herpesvirus 6 (HHV-6) is now classified into two distinct variants such as HHV-6 variant A(HHV-6A) and B(HHV-6B) (Ablashi et al., Arch. Virol. 129, 1993, 1–4) and the DNA of HHV-6A strain U1102 was completely sequenced (Gompels et al., Virology 209, 1995, 29–51). We have sequenced a 30-kilobase pair (kbp) (genomic positions around 111–141 kb) of HHV-6B strain HST, and a sequence of this region was compared with that of HHV-6A strain U1102. Dodecameric repeats, G/T and Kpn repeat elements, putative major immediate early 1 (MIE1) and major immediate early 2 (MIE2) genes were found in this region. The DNA sequences of HHV-6A (U1102) and HHV-6B (HSI) were markedly different in the MIE1 region, Kpn repeat elements and the putative MIE2 region. Dodecameric repeat element was located in the putative MIE2 locus of HHV-6. When primers covering dodecameric repeat region were used to amplify HHV-6 DNA of clinical isolates from patients with exanthem subitum (ES) by polymerase chain reaction (PCR), variations in size of PCR products in each isolate were found, indicating strain-specific features. Furthermore, the results of molecular biological analysis by PCR using DNA samples in a family suggest that HHV-6 infects within a family.