CD4 and infection: To evaluate our hypothesis that the gene pathways harboring integrated HIV differ between the ART-acute-HIV versus ART-chronic-HIV groups, ISs were derived (16) from negatively selected CD4+ T cells and compared to a set of approximately 66,000 ISs derived from in vitro infection of unstimulated primary CD4+ T cells infected with HIV-1 strain BaL (HIV-1BaL) and cultured for 48 hours (11), and primary resting CD4+ T cells infected with HIV NL4-3 for 96 hours (27) (referred to as “in vitro IS”) (see Methods).