The RNaseH activity of RVT digests most of the RNA genome . Selected portions of the RNA genome remain, however, to serve as primers. This produces dsDNA that is longer than genomic RNA, because it contains the LTRs. The provirus moves to the nucleus, and integrates into the host chromosome at random sites.
Integration requires viral integrase .
It removes 2 nucleotides from each end of the viral DNA, and duplicates a short sequence of cellular DNA flanking the insertion site. The virus can't replicate until it integrates . Then a frameshift occurs that allows translation of viral protease, and the Pol polyprotein . Other full-length transcripts will be spliced in the nucleus to yield a shorter mRNA encoding the Env polyprotein . They therefore all have the same 5' end.