Kinetics of <i>in vitro</i> replication of viruses recovered from the earliest-available plasma samples from R880F and R463F and IMCs corresponding to each subject's deduced T/F virus sequence.

<p>(A and B). Infection with virus isolates (A) or PBMC stocks derived from IMCs (B) was performed in either pools of human CD8 depleted PBMC isolated from 3 individual donors (A) or single individuals (B), and the data is representative of at least 3 independent experiments for each. Reverse transcriptase activity (measured in digital light units (DLU) or p24 antigen is plotted on a log₁₀ scale on the vertical axis against days following infection of cells in <i>in vitro</i> culture. HIV-1 NL4.3 is shown in (A) as a positive control for <i>in vitro</i> replication. (C). Analysis of the in vitro growth rates of viruses R880 and R463 from each of 9 experiments. The growth rate of each was calculated as the slope of increase in the logarithms of p24 or RT activity over the times when this increase was linear. A Wilcoxon signed-rank test was used to compare the ratios obtained in the experiments. (D). A competition growth assay was performed in triplicate as described in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004565#s4" target="_blank">Methods</a> with approximately equal input copies of R880F and R463F viral stocks. Relative amounts of each virus at days 2, 4, 6, 8, and 10 were determined by qPCR. (E). An amino acid sequence alignment of the B*5703 Gag CD8 T cell epitopes for the R880 transmission pair is shown.