Most Retroviruses penetrate into a cell by fusion with the plasma membrane, but some use the endosomal pathway. Once inside the cell, reverse transcription takes place in a subviral particle to produce a full-length, linear dsDNA copy of the RNA. The composition of this subviral particle is not well defined. It certainly contains RT and its associated activities as well as components derived from Gag, but which Gag components are present and whether cellular proteins form part of this particle are not known.

Reverse transcription begins in the cytoplasm. In most viruses, the full-length dsDNA is produced in the cytoplasm, but in some the finishing touches occur after transfer to the nucleus. After transfer to the nucleus, the viral DNA is integrated into the host chromosome, essentially t random, in a process that requires the activity of IN. In the simple viruses, transfer to the nucleus occurs during cell division, when the nuclear envelope is disassembled. At least some of the complex retroviruses, however, such as HIV, encode proteins that allow the DNA-containing complex to traverse the nuclear membrane. Thus, the simple Retroviruses can only productively infect dividing cells, whereas HIV can infect non-dividing cells.