The majority of simian immunodeficiency virus/mne circle junctions result from ligation of unintegrated viral DNA ends that are aberrant for integration.

SIV/Mne circle junctions were amplified by the polymerase chain reaction (PCR) and cloned in a bacterial plasmid. Sequence analysis of clones isolated from 11 independent PCRs reveals that the start site for plus DNA synthesis is 5' ACTG. . ., and thus an asymmetric cleavage must occur during viral integration. In addition, most of the sequences found resulted from the ligation of aberrant proviral DNA ends that were apparently generated by priming errors, primer removal errors, or integrase processing errors. The results suggest that in this virus, as in Moloney murine leukemia virus, two good ends may be required for efficient integration.