Table 1.
Initial relative fitnessa (±s.e.m.) of wt and mt virus
Table 2.
Relative fitnessa (±s.e.m.) of wt and mt virus after 110 days of culture in the MT4 T-cell line
Figure 1.
Change in relative fitness of viruses cultured on two distinct T-cell lines.
A) The 6 wildtype replicates that are cultured on MT4 T-cells show a linear increase in fitness. The inset shows a single representative example of replicate wt-1. B) The 6 mutant MT4 cultured replicates show an initial fitness increase that seems to reach a maximum at around a relative fitness of 1.04±0.02. All trajectories are best described by an exponential regression model with an upper limit (F-test, p<0.05). The inset shows a single representative example of replicate mt-1 (see Table 2 for relative fitness values at day 110). C and D) relative fitness of 6 wt and 6 mt C8166 cultured viruses, respectively. Relative fitness did not significantly deviate from the starting virus over the course of the experiment (ANOVA, p>>0.05; see Table 3 for relative fitness values at day 110). Fitness is relative to reference strain v13 (also see materials and methods section.
Table 3.
Relative fitnessa (±s.e.m.) of wt and mt virus after 110 days of culture in the C8166 T-cell line
Table 4.
Nucleotide diversity (π±s.e.m.)
Table 5.
Transition/transversion ratio (R) in LTR and Env and non-synonymous (dN)/synonymous (dS) ratio in Env (±s.e.m.).
Figure 2.
Genetic variation in the Long Terminal Repeat (LTR) and envelope region (Env) of MT4 and C8166 cultured viruses.
For each culture, ten clones of both the LTR and Env region were sequenced and this was repeated for five points in time. Thus, each data point corresponds to the amount of genetic variation within a single serial passage line at a certain point in time. Genetic variation (Kimura 2 parameter) is plotted separately for the two cell-lines. A) No correlation in genetic variation in MT4 evolved viruses was observed (n = 44, r2 = 0.011, p = 0.49). B) There is a strong linear correlation in genetic variation between the LTR and Env in C8166 cultured viruses (n = 39, r2 = 0.745, p<0.0001). Even if the two outliers are taken out, the strong correlation remains (n = 37, r2 = 0.475, p<0.0001).
Table 6.
Recombination in MT4 and C8166 cells