No fitness costs of the early CD8⁺ T cell escape mutation R355K in Env.

<p>(A) The frequency of the R355K mutation in the Env_352–360T cell epitope different time points (days post Fiebig stage I/II). The viral sequences obtained by SGA were compared to the T/F virus. Amino acid substitutions at the R355K mutation site were highlighted in red. Relative fitness of the R355K mutant was determined by comparing to the cognate T/F virus in the single-passage assay (B) and the multiple-passage assay (C) as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102734#pone-0102734-g003" target="_blank">Figure 3</a>. The percentage of each virus in the inoculum stock and the culture supernatant was determined by PASS. Mean ± standard deviations are shown.</p

Impact of the V247I or G248A mutation alone on the fitness of their cognate T/F virus.

<p>The fitness impact of the V247I or G248A mutation alone was determined by comparing the mutant V247I (A and B) or G248A (C and D) to their cognate T/F virus in the single-passage assay (A and C) and the multiple-passage assay (B and D). The percentage of each virus in the inoculum stock and the culture supernatant was determined by PASS. Mean ± standard deviations are shown.</p

No fitness costs of the early reversion mutation I64T in Tat/Rev overlapping region.

<p>(A) Frequencies of the I64T mutation in the Tat protein at different time points (days post Fiebig stage I/II). The viral sequences obtained by SGA were compared to the T/F virus and the subtype B consensus sequence (ConB). Amino acid substitutions at the I64T mutation site were highlighted in red. Relative fitness of the I64T mutant was determined by comparing to the cognate T/F virus in the single-passage assay (B) and the multiple-passage assay (C). The percentage of each virus in the inoculum stock and the culture supernatant was determined by PASS. Mean ± standard deviations are shown.</p

Partial restoration of the fitness loss of the T242N mutant by compensatory mutations.

<p>The relative fitness was determined between the T242N mutant and the NI (A and B) and NA (C and D) mutant as well as between the T/F virus and NI (E and F) or NA (G and H) mutant in the single-passage assay (left panels) and the multiple-passage assay (right panels). Same amount (5 ng p24) of each compared virus was mixed to infect 10⁶ of purified CD4⁺ T cells in triplicates. In the single-passage assay, the viruses were cultured for three days and the culture supernatant were harvested daily by completely replacing the medium. In the multiple-passage assay, 200 µl of cell-free virus harvested at day 3 at each passage was used to infect 10⁶ of fresh CD4⁺ T cells. The viruses were subsequently passaged three additional times. The percentage of each virus in the inoculum stock and the culture supernatant was determined by PASS. Mean ± standard deviations are shown. The relative fitness was determined by modeling the replication slope of each virus in the single- and multiple-passage assays as previously described <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102734#pone.0102734-Song1" target="_blank">[25]</a>.</p

Structural modeling of mutations in the TW10 epitope in p24 Gag.

<p>(A) Homology models of the p24 monomer for the sequences of the T/F virus (cyan), the T242N mutant (magenta) and the NIA mutant (green) show similar structures of the helix 6 region with modest structural differences in the neighboring N-terminal hairpin and CypA binding loop. Side chains at mutation positions are shown as stick representation. (B) Mutations at position 242 (red) and positions 247/248 (green) in helix 6 were mapped to the hexameric p24 crystal structure <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102734#pone.0102734-Pornillos1" target="_blank">[49]</a>. The mutation positions did not occur at p24 subunit interfaces. Helix 6 is located between the N-terminal hairpin (magenta) and cyclophilin-binding loop (orange) on the surface of the hexamer. (C) Mutation at position 242 (red) and positions 247/248 (green) in helix 6 (yellow) were mapped to a hexamer of hexamers in the capsid assembly <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0102734#pone.0102734-Zhao1" target="_blank">[40]</a>. The T242N (red) and V247I/G248A (magenta) mutations face outward in the assembly and do not occur at hexamer-hexamer interfaces.</p

Determination of T cell responses by ELISpot.

<p>(A) Frequencies of the mutations in the TW10 epitope at different time points (days post Fiebig stage I/II). The viral sequences obtained by SGA were compared to the T/F virus and the subtype B consensus sequence (ConB). Amino acid substitutions at positions 242, 247 and 248 are highlighted in red. (B) T cell response to the wild type and mutant TW10 peptides at day 102 in subject CH77 were determined using an <i>ex vivo</i> IFN-γ ELISpot assay. Peptides containing T242N, V247I or G248A mutation alone as well as in various combinations were analyzed. ELISpot data are expressed as the mean spot forming units (SFU) per million PBMC (SFU/10⁶PBMC)±SEM. Positive T cell responses were defined as: ≥30 SFU/million and >4 times above background (indicated by the dotted line). All assays were performed in triplicate.</p

Quantifying the Diversification of Hepatitis C Virus (HCV) during Primary Infection: Estimates of the In Vivo Mutation Rate

<div><p>Hepatitis C virus (HCV) is present in the host with multiple variants generated by its error prone RNA-dependent RNA polymerase. Little is known about the initial viral diversification and the viral life cycle processes that influence diversity. We studied the diversification of HCV during acute infection in 17 plasma donors, with frequent sampling early in infection. To analyze these data, we developed a new stochastic model of the HCV life cycle. We found that the accumulation of mutations is surprisingly slow: at 30 days, the viral population on average is still 46% identical to its transmitted viral genome. Fitting the model to the sequence data, we estimate the median <em>in vivo</em> viral mutation rate is 2.5×10⁻⁵ mutations per nucleotide per genome replication (range 1.6–6.2×10⁻⁵), about 5-fold lower than previous estimates. To confirm these results we analyzed the frequency of stop codons (N = 10) among all possible non-sense mutation targets (M = 898,335), and found a mutation rate of 2.8–3.2×10⁻⁵, consistent with the estimate from the dynamical model. The slow accumulation of mutations is consistent with slow turnover of infected cells and replication complexes within infected cells. This slow turnover is also inferred from the viral load kinetics. Our estimated mutation rate, which is similar to that of other RNA viruses (e.g., HIV and influenza), is also compatible with the accumulation of substitutions seen in HCV at the population level. Our model identifies the relevant processes (long-lived cells and slow turnover of replication complexes) and parameters involved in determining the rate of HCV diversification.</p> </div

Kinetic and simulation parameters for each subject studied.

<p><i>r</i> – exponential growth rate; t₂ – doubling time; VL_max – maximum viral load; Plateau – time that the virus remains at the plateau; I_ss – percentage of cells infected at viral plateau, assuming that there are 10¹¹ hepatocytes <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002881#ppat.1002881-BioulacSage1" target="_blank">[40]</a>; Q1/Q2/5 h – quarter 1, quarter 2 and 5′ half HCV genome, respectively. Other symbols described in text. The mutation rate is μ×10⁻⁵ per nucleotide per replication cycle.</p

Changes in viral load and mutation profile predicted by the model.

<p>(A) different values for the half-life of replication complexes (ln 2/ρ), and (B) the emergence of a cytolytic immune response at 30 days post-infection. Note that if there were less than 5 runs leading to establishment of infection, no line is plotted, because the noise is too large. Thus in (A) for short half-life of replication complexes (i.e., <i>t</i>_1/2 = 0.74 d in cyan) the line may not appear, because the infection was not established, or the line may disappear, because an initial infection was aborted.</p

Profile of (A) viral load and (B) ALT in the subjects studied.

<p>The black symbols are the observed viral loads, the lines are the simulated trajectories with the model described in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002881#s4" target="_blank">methods</a>, and the dashed lines correspond to 95% CI based on 100 simulations. The parameters used for the simulations are given in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002881#ppat-1002881-t001" target="_blank">Table 1</a>. (The first week of increase in virus is very variable due to the stochastic nature of the process, and it is not represented in the graphs.). The profiles of ALT in (B) are about normal (the upper limit of normal – ULN – is ∼40 IU/ml <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002881#ppat.1002881-Kariv1" target="_blank">[33]</a>, <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002881#ppat.1002881-Ruhl1" target="_blank">[34]</a>) and much less than typical later in primary infection, where they can reach 10× to 20× the normal value <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002881#ppat.1002881-Hoofnagle1" target="_blank">[37]</a>.</p