RT transcribes the viral genomic RNA to DNA. In the first step of integration, integrase removes two nucleotides from the 3' end of each strand of the linear DNA. This results in CA overhangs. The CA overhang is found on many retrotransposons.. The processed 3' ends of the DNA are joined to the 5' ends of the target DNA. Unpaired nucleotides are next removed from the 5' ends of the viral DNA and these are then joined to 3' ends of target DNA. This integrates the provirus into the host cell DNA

Integration can occur at many sites in the host cell chromosomes

For further information see: Alan Frankel and John A. T. Young, HIV-1: Fifteen proteins and an RNA Annual Review of Biochemistry 67: 1-25, 1998