(A) Three-point moving averages of mean KSHV mRNA levels in KS biopsy specimens from the patients with low CD4 counts (solid line) and patients with undetectable HIV load and CD4 counts of ≥200 (open circles). Since real-time qPCR is quantitative within an extended linear range, we calculated the relative abundance of each viral mRNA compared to LANA mRNA as 1.8^{−ΔCT(LANA)} and expressed it as percentage of LANA mRNA on a logarithmic scale (vertical axis). (B) Pairwise comparisons of individual KSHV mRNAs. Shown are box plots for the levels of two KSHV lytic mRNAs (v-cyclin [cyc], vGPCR) relative to a KSHV latent mRNA (LANA). The vertical axis is on a log₁₀ scale. The horizontal labels signify patients with AIDS or nondetectable HIV KS. The bold horizontal line indicates the median, box ends the lower and upper quartiles, and dotted lines the range of the data. Outliers are indicated by dots. (C) Pairwise correlations of log₂ mRNA levels (C_T) for the two cellular genes coding for actin (hu. actin) and hypoxanthine-guanine phosphoribosyltransferase (HPRT) and two latent viral genes coding for the viral cyclin (orf72f1) and LANA (lat273F), which originate from the same constitutive promoter. Note that higher mRNA levels correspond to lower C_T numbers. Shown are scatter plots and a linear regression fit line below the diagonal, distribution of C_Ts for the individual genes across all samples on the diagonal, and pairwise Pearson correlation coefficients above the diagonal of this panel matrix.

Unsupervised cluster analysis of KSHV transcription in KS (heat map representation). Shown are relative levels of KSHV mRNAs in KS biopsy specimens obtained from patients with low CD4 counts and detectable HIV viral loads (pre) or with CD4 ≥200 and no detectable HIV (post). Red indicates maximal, yellow intermediate, and white low levels of individual mRNAs. With the exception of a single case (arrow at bottom), none of the post-HAART KS biopsy specimens show evidence of KSHV lytic mRNAs. In contrast, in >50% of lesions from pre-HAART KS, the full complement of lytic mRNAs was detectable.