Integrated human papillomavirus type 16 (HPV-16) viral loads are currently estimated by quantification with real-time PCR of and E2 (RT-E2-1) DNA. We assessed the influence of HPV-16 E2 polymorphism on quantification of integrated HPV-16 DNA in anogenital specimens. HPV-16 E2 was sequenced from 135 isolates (123 from European and 12 from non-European lineages). An assay targeting conserved HPV-16 E2 sequences (RT-E2-2) was optimized and applied with RT-E6 and RT-E2-1 on 139 HPV-16-positive cervicovaginal lavages collected from 74 women [58 human immunodeficiency virus (HIV)-seropositive and 16 HIV-seronegative]. Ratios of HPV-16 copies measured with RT-E2-2 and RT-E2-1 obtained with African 2 (median53.23, range51.92-3.49) or Asian-American (median53.78, range51.47-37) isolates were greater than those obtained with European isolates (median51.02, range50.64-1.80; P,0.02 for each comparison). The distribution of HPV-16 E2 copies measured in 139 samples with RT-E2-2 (median56150) and RT-E2-1 (median58960) were different (P,0.0001). The risk of high-grade cervical intraepithelial neoplasia (CIN-2,3) compared with women without CIN was increased with higher HPV-16 total [odds ratio (OR)52.17, 95 % confidence interval (CI)51.11-4.23], episomal (OR52.14, 95 % CI51.09-4.19), but not for , after controlling for age, race, CD4 count, HIV and HPV-16 polymorphism. The proportion of samples with an E6/E2 ratio .2 in women without squamous intraepithelial lesion (7 of 35) was similar to that of women with CIN-2,3 (5 of 11, P50.24) or CIN-1 (5 of 14, P50.50). HPV-16 E2 polymorphism was a significant factor that influenced measures of HPV-16 integrated viral load.
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