Evidence for a gapped linear duplex DNA intermediate in the replicative cycle of human and simian spumaviruses

Two forms of linear DNAs have been found in simian (SFV1) and human (HSRV) spumaviruses: a linear duplex unsensitive to nuclease S1 and a sensitive structure with a single-stranded gap. Two nuclease S1 sensitive sites, mapping at the same position for both viruses, have been identified in the gapped structure. Using different molecular subgenomic clones of HSRV as probes in Southern blot analysis, one S1 site was localized in the 3'LTR and the other near the middle of the molecule at about 6.5 kbp from the 5' end of the viral genome. The latter site was shown to correspond to a single stranded region within the linear duplex DNA. Nucleotide sequence analysis revealed that the polypurine tract (PPT) usually found at the 5' boundary of the 3'LTR of retroviruses, is duplicated in HSRV at the 3' end of the pol gene, near the gap. This suggests that the synthesis of plus strand DNA is discontinuous, generating the gap.