This study indicated that aged 25–49 years, cadre/staff/teacher, unmarried, minority, high school or below, initial CD4 counts >500 cells/μL, no STD history, homosexual partners ≥10, special survey, long-term infection, and drug resistance were associated with clustering in molecular transmission networks, and clustering frequency in this population was significantly related to CD4 counts, year and city. This evidence concerns the gene CD4 and infection.