design: SupT1 cells were seeded and transduced with HIV-1 OGH, HIV-2 OGH or HIV-2 eGFP for 3 days. After 3 days, the cells were washed twice with PBS and kept in culture for at least 10 days to allow non-integrated DNA to be diluted. Next, genomic DNA was extracted using the GenElute Mammalian Genomic DNA miniprep kit (Sigma-Aldrich) and sheared by sonication with the Covaris M220. Linkers were added to the sheared DNA ends and integration sites were amplified by nested PCR with primers complementary to the linker and the viral LTR. Finally, the PCR products were sequenced by Illumina Miseq (paired-end, 300 cycles)