Reverse transcription primers are used in PCR but in vivo reverse transcription begins when the viral particle that enters the cytoplasm of a target cell with its reverse transcriptase. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex that has not been well characterized. The process of reverse transcription generates, in the cytoplasm, a linear DNA via an intricate series of steps. This DNA is collinear with its RNA template, but it contains terminal duplications known as the long terminal repeats (LTRs) that are not present in viral RNA . Extant models for reverse transcription propose that two specialized template switches known as strand-transfer reactions or “jumps” are required to generate the LTRs.
