No evidence of ongoing evolution in replication competent latent HIV-1 in a patient followed up for two years

Abstract

The persistence of infected T cells harbouring intact HIV proviruses is the barrier to the eradication of HIV. This reservoir is stable over long periods of time despite antiretroviral therapy. There has been controversy on whether low level viral replication is occurring at sanctuary sites periodically reseeding infected cells into the latent reservoir to account its durability. To study viral evolution in a physiologically relevant population of latent viruses, we repeatedly performed virus outgrowth assays on a stably treated HIV positive patient over two years and sequenced the reactivated latent viruses. We sought evidence of increasing sequence pairwise distances with time as evidence of ongoing viral replication. 64 reactivatable latent viral sequences were obtained over 103 weeks. We did not observe an increase in genetic distance of the sequences with the time elapsed between sampling. No evolution could be discerned in these reactivatable latent viruses. Thus, in this patient, the contribution of low-level replication to the maintenance of the latent reservoir detectable in the blood compartment is limited.

Figure 1

Dendrogram constructed using the neighbour joining method from 64 gag sequences obtained from replication competent virus activated from resting CD4⁺ T cells from the patient donor. Branch lengths as indicated by the scale bar represent the p-distance between sequence pairs. Grey boxes represent isolates which could not be distinguished using their gag sequence alone. The pink box highlights eight viruses with identical gag sequences which could not be discriminated by sequencing env. The dots are coloured according to the key to show date of sampling. There is no apparent clustering by time of sampling.

Figure 2

Linear regression of p-distance and time between sampling. For each pair of samples we compared the pairwise distance and the time elapsed between the samples being taken. No association between time of sampling and p-distance was identified (r² = 0.00016, p = 0.573).