All HPV virion preparations were quantified for encapsidated viral genomes using TaqMan qPCR specific to the HPV long control region (LCR), a noncoding segment of the viral genome, as previously described [12,13]. HPV stocks were diluted (e.g., 1:50 and 1:500) in carrier DNA (sheared salmon sperm DNA [Invitrogen] or human placental DNA [Millipore Sigma]) at a carrier concentration of 50 ng/ul. qPCR reactions were performed using 5 µL of the 1:50 and 1:500 virus stocks using primers targeted to the HPV LCR (Bio-Rad SsoFast EvaGreen Supermix) (see Supplemental Table 2). For each assay a calibration curve spanning 108–100 genome copies was run in triplicate and was generated by serial dilutions of cloned HPV genomes. Data were collected on a Bio-Rad CFX96 and analysed using Bio-Rad CFX Manager (version1.6.541.1068). Only experiments with calibration curve R2 values of ≥0.995 and amplification efficiencies between 90 and 100% were included.

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