Homologous and nonhomologous retroviral pecombinations are both involved in the transfer by infectious particles of defective avian leukosis virus-derived transcomplementing genomes

We previously described avian leukosis virus-based packaging cell lines that produce stocks of retroviral vectors in which replication-competent viruses were not detectable. However, following infection of target cells with these retroviral stocks, we recently obtained colonies resulting from the transmission of recombinant genomes. Here, we have analyzed their genetic structure and shown that (i) each of them results from recombination between the packaging- and integration-defective transcomplementing genomes and the retroviral vector; (ii) recombination probably occurred during the reverse transcription step, involving strand switching of the reverse transcription growing point from the infectious retroviral vector to the transcomplementing RNA; and (iii) sequence identity and nonhomologous sequences were both used for the strand snitching.