Proviruses with identical sequences comprise a large fraction of the replication-competent HIV reservoir

Abstract

The major obstacle to curing HIV infection is the persistence of cells with intact proviruses that can produce replication-competent virus. This HIV reservoir is believed to exist primarily in CD4 ⁺ T-cells and is stable despite years of suppressive antiretroviral therapy. A potential mechanism for HIV persistence is clonal expansion of infected cells, but how often such clones carry replication-competent proviruses has been controversial. Here, we used single-genome sequencing to probe for identical HIV sequence matches among viruses recovered in different viral outgrowth cultures and between the sequences of outgrowth viruses and proviral or intracellular HIV RNA sequences in uncultured blood mononuclear cells from eight donors on suppressive ART with diverse proviral populations. All eight donors had viral outgrowth virus that was fully susceptible to their current ART drug regimen. Six of eight donors studied had identical near full-length HIV RNA sequences recovered from different viral outgrowth cultures, and one of the two remaining donors had identical partial viral sequence matches between outgrowth virus and intracellular HIV RNA. These findings provide evidence that clonal expansion of HIV-infected cells is an important mechanism of reservoir persistence that should be targeted to cure HIV infection.

Author summary

Antiretroviral therapy (ART) can reduce plasma HIV viral loads to undetectable levels. However, HIV-infected cells can persist despite years of antiretroviral suppression and contribute to rebound viremia following cessation of ART. It is unclear whether HIV-infected cells are maintained by ongoing viral replication, prolonged survival of infected cells, or clonal expansion of infected cells. No studies to date have definitively determined whether clonal expansion is a common mechanism of persistence for replication-competent HIV. To investigate, we used single-genome sequencing to detect identical HIV sequence matches between replication-competent viruses, proviruses, and/or cell-associated RNA from eight donors who were on long-term suppressive ART without evidence of ongoing viral replication. Six of eight donors had identical near full-length sequences between unique replication-competent viruses. One of the two remaining donors had identical partial viral sequences between a replication-competent virus and cell-associated HIV RNA. These findings suggest that clonal expansion is an important mechanism of persistence of replication-competent HIV and should be targeted by HIV cure efforts.