Last in first out: SIV proviruses seeded later in infection are harbored in short-lived CD4+ T cells

Abstract

HIV can persist in a latent form as integrated DNA (provirus) in resting CD4⁺ T cells of infected individuals and as such is unaffected by antiretroviral therapy (ART). Despite being a major obstacle for eradication efforts, the genetic variation and timing of formation of this latent reservoir remains poorly understood. Previous studies on when virus is deposited in the latent reservoir have come to contradictory conclusions. To reexamine the genetic variation of HIV in CD4⁺ T cells during ART, we determined the divergence in envelope sequences collected from 10 SIV infected rhesus macaques. We found that the macaques displayed a biphasic decline of the viral divergence over time, where the first phase lasted for an average of 11.6 weeks (range 4-28 weeks). Motivated by recent observations that the HIV-infected CD4⁺ T cell population is composed of short- and long-lived subsets, we developed a model to study the divergence dynamics. We found that SIV in short-lived cells was on average more diverged, while long-lived cells harbored less diverged virus. This suggests that the long-lived cells harbor virus deposited starting earlier in infection and continuing throughout infection, while short-lived cells predominantly harbor more recent virus. As these cell populations decayed, the overall proviral divergence decline matched that observed in the empirical data. This model explains previous seemingly contradictory results on the timing of virus deposition into the latent reservoir, and should provide guidance for future eradication efforts.

Keywords: HIV; SIV; antiviral treatment; genetic divergence; latency.

Fig. 1.

Biphasic divergence decline of non-defective provirus env sequences in 10 macaques infected with SIVmac₂₅₁ stock, sampled longitudinally during 3 years on ART (mean divergence curve shown in red), with an initial rapid decline followed by a second slower decline. Divergence in individual experimental sequences shown in circles (non-defective proviral divergence in grey, plasma viral RNA divergence in blue). The first slope is shown by a dashed line, using non-defective proviral DNA at the start of ART in grey, and using plasma viral RNA at the start of ART in blue. The second slope is shown by a grey dash-dot line. Divergence was computed from the consensus sequence of MAC.US.x.239.M3. Plasma viral RNA could not be collected for T624.

Fig. 2.

Mutational profiles of short- (orange) and long-lived (grey) populations at the start of ART, in 10 macaques infected with SIV sampled longitudinally during 3 years on ART. Orange and grey curves show the smoothed-out histograms. Solid vertical lines correspond to the mean divergence of short- (orange) and long-lived (grey) populations. Vertical green dashed lines show the median divergence of the total population.

Fig. 3.

Empirically observed mean divergence dynamics (red lines) compared to model simulated divergence in 10 macaques infected with SIV sampled longitudinally during 3 years on ART. Divergence dynamics using half-lives estimated by first pooling the data of all 10 macaques, and then adjusting for individual variations are shown by blue lines. Divergence dynamics using half-lives learnt separately for each individual macaque are shown by green lines. Bold blue/green lines show the means of 10³ simulations. Thin blue/green lines show individual stochastic simulations of divergence obtained by sampling according to experimental sampling times and number of sequences. Turquoise is the result of the thin blue and green lines overlapping. For macaques T624 and T625, green lines are absent as the data was insufficient to estimate half-lives individually. In T624 the thin blue lines overlap exactly with the thick blue line after ≈ 20 weeks. The red tick marks on the x-axis show the times when experimental samples were obtained.

Fig. 4.

Schematic figure of the decay model used in this work. Divergence is computed using Eq. 1