Figure 2.

Principle of HIV-1 integration sites detection. (A) Genomic DNA of resting CD4⁺ T cells were extracted. (B) DNA fragments were randomly interrupted, and fragments possess both HIV-1 genome and human genome are targeted. Different cells with the same integration sites have diverse break point. (C) End repair and LTR digestion were conducted on the fragments, and several rounds of PCR were applied for targeted amplification. (D) Fragments from former step were sequenced and mapped to human genome to identify various integration sites. For the same integration sites, the variety of fragments with different length represents the number of clonally expanded HIV-1-infected cells. LTR: long terminal repeat; PCR: Polymerase chain reaction.