This review examines the mechanisms of reverse transcription in retroviruses, focusing on discontinuities and template switches (jumps) during plus-strand DNA synthesis. Retroviruses convert their RNA genome into double-stranded DNA through reverse transcriptase, requiring two template switches. The article addresses variations among retroviral subfamilies: oncoviruses exhibit multiple discontinuities in their plus-strand DNA, while lentiviruses (HIV-1) and spumaviruses contain a single gap at an invariant position near the 3' end of the pol gene, adjacent to a duplicated polypurine tract (PPT). This dual priming mechanism differs from classical models and suggests that plus-strand synthesis initiates from two sites. A revised model proposes that the second jump involves strand displacement rather than simple circularization, with implications for viral replication efficiency and proviral integration. The gap and associated orphan long terminal repeats (LTRs) detected in HIV-1 and spumavirus-infected cells support this alternative mechanism. The authors speculate that discontinuous plus-strand synthesis may facilitate protein binding for nuclear transport or integration, or may enhance replication speed. These findings suggest retroviral reverse transcription mechanics are more complex than previously understood and warrant further investigation.

Key findings

• Lentiviruses and spumaviruses possess a single-stranded gap in their linear unintegrated DNA at an invariant position near the pol gene, associated with a duplicated polypurine tract, indicating dual initiation of plus-strand DNA synthesis.
• A revised model for the second template jump proposes strand displacement of strong-stop plus DNA rather than simple circularization, requiring at least two plus-strand priming events.
• Orphan double-stranded LTR sequences have been detected in HIV-1 and spumavirus-infected cells, consistent with the strand displacement model when displaced DNA fragments fail to reanneal at the correct location.
• The specific function of plus-strand discontinuities remains unclear but may involve protein binding for proviral integration or nuclear transport, or could enhance reverse transcription efficiency.