PMC2642736_01
Viral RNA load in acute HIV-1 subtype C infection. (A) Individual curves of viral RNA load in eight cases of acute infection. The timeline shows days from detected seroconversion. Time 0 corresponds to the first seropositive test. Plasma viral RNA load is expressed as log10 copies per ml of plasma. Measurements of viral RNA before time 0 are pre-seroconversion. Numbers at top of boxes correspond to subject cases. Dotted lines with arrows indicate initiation of ART. (B) Early viral RNA set point in acute HIV-1 subtype C infection. The level of viral RNA at early set point was defined as a mean +- standard deviation of measurements from 50 to 200 days from detected seroconversion (after assuming reduction of viral RNA peak). N shows the number of viral RNA measurements for the period from 50 to 200 days per subject. Dashed line shows a median of early viral RNA set point computed for all eight subjects at 4.53 log10 copies/ml. The first four subjects 1811, 2865, 3312, and 5018 correspond to the group of slow decline of viral RNA and high early viral RNA set point. Subjects 3430, 3505, 3603, and 5582 correspond to the group of fast decline of viral RNA and low early viral RNA set point.
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F1
The early viral RNA set point defined as mean+-standard deviation of plasma RNA measurements from 50 to 200 days differed between subjects with slow and fast decline of viral RNA (Fig. 1; 5.25+-0.22 vs. 3.62+-0.45 log10 for slow and fast decline of viral RNA, p<0.001). The mean values and standard deviations are shown in figures as fractions of 1, and presented as percentages in the text for convenience.
Intra-patient viral diversity in gp120. Mean values+-standard deviation of pairwise maximum likelihood nucleotide distances are shown. The timeline shows days from detected seroconversion. (A) Individual trajectories of viral diversity in gp120. Numbers within boxes correspond to subject cases. The extent of total viral diversity per time point per subject is shown by crosses. The intra-cluster diversity in subjects 1811 and 5018 is designated by triangles (recombinant sequences are removed). Dotted lines with arrows indicate initiation of ART. (B) Levels of proviral diversity in gp120 between subjects with slow (filled circles) and fast (open circles) decline of viral RNA. (C) Viral diversity within groups defined on viral RNA decline, fast and slow decline of viral RNA. The slow decline group is presented by uncorrected distances (defined as total intra-patient pairwise distances) and cluster-corrected distances (sequences within clusters used separately, no recombinants included). Analysis was performed for two time intervals: 0 to 200 days and 201+ days after seroconversion. Comparison between groups is performed by t-test or Mann-Whitney Rank Sum Test (shown with *).
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F5
Time of ART initiation is indicated by arrows in Figs. 5 and 6.
Diversification of viral gp120 in acute HIV-1 subtype C infection. Mean values+-standard deviation are shown. Viral diversification at each time point was compared to the per-subject MRCA sequence reconstructed from viral quasispecies at all time points (red triangle), and consensus sequence reconstructed from the earliest available quasispecies (green square). The timeline shows days from detected seroconversion. (A) Individual trajectories of viral diversification. Numbers within boxes correspond to subject cases. Dotted lines with arrows indicate initiation of ART. (B) Viral diversification from MRCA that was reconstructed from viral quasispecies is compared between groups defined on viral RNA phenotype, fast and slow decline of viral RNA. The slow decline group is presented in two ways: by uncorrected distances (defined as total intra-patient pairwise distances to MRCA) and cluster-corrected distances (defined as intra-cluster pairwise distances to MRCA, no recombinants were included). Analysis was performed for two time intervals: 0 to 200 days and 201+ days after seroconversion. Comparison between groups is performed by t-test or Mann-Whitney Rank Sum Test (shown with *).
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F6
Time of ART initiation is indicated by arrows in Figs. 5 and 6.