Configuration and terminal sequences of the simian varicella virus genome

The simian varicella virus (SVV) genome is a linear DNA molecule consisting of a unique short (Us) and a unique long (UL) region. The Us is bounded by internal (IR) and terminal inverted repeats and inverts such that virion DNA contains equimolar amounts of two genome isomers. We have sequenced the right and leftward termini and the UL-IR junction region of the SVV genome. A sequence motif common to other herpesviruses, consisting of A and T residues surrounded by G+C-rich regions, was found near the rightward terminus of the SVV genome. Sequence analysis showed no repeats surrounding the UL region of the genome. Nucleic acid hybridization and polymerase chain reaction (PCR) amplification using primers from the right and leftward ends of the SVV genome indicated that the UL region inverts. PCR amplification also showed that, compared with virion DNA, SVV genomes with connected termini are increased in infected cell DNA, suggesting the presence of circular or concatemeric genomic molecules.