Defective HIV-1 proviruses produce viral proteins

Abstract

HIV-1 proviruses persist in the CD4+ T cells of HIV-infected individuals despite years of combination antiretroviral therapy (cART) with suppression of HIV-1 RNA levels <40 copies/mL. Greater than 95% of these proviruses detected in circulating peripheral blood mononuclear cells (PBMCs) are referred to as “defective” by virtue of having large internal deletions and lethal genetic mutations. As these defective proviruses are unable to encode intact and replication-competent viruses, they have long been thought of as biologically irrelevant “graveyard” of viruses with little significance to HIV-1 pathogenesis. Contrary to this notion, we have recently demonstrated that these defective proviruses are not silent, are capable of transcribing novel unspliced forms of HIV-RNA transcripts with competent open reading frames (ORFs), and can be found in the peripheral blood CD4+ T cells of patients at all stages of HIV-1 infection. In the present study, by an approach of combining serial dilutions of CD4+ T cells and T cell–cloning technologies, we are able to demonstrate that defective proviruses that persist in HIV-infected individuals during suppressive cART are translationally competent and produce the HIV-1 Gag and Nef proteins. The HIV-RNA transcripts expressed from these defective proviruses may trigger an element of innate immunity. Likewise, the viral proteins coded in the defective proviruses may form extracellular virus-like particles and may trigger immune responses. The persistent production of HIV-1 proteins in the absence of viral replication helps explain persistent immune activation despite HIV-1 levels below detection, and also presents new challenges to HIV-1 eradication.

The Atlas of the In Vivo HIV CD4 T Cell Reservoir

“…Second, cells sorted based on PP-SLIDE were enriched for genome-intact and replication-competent reservoir cells in the expected populations. Of note, our PP-SLIDE characterization had charted the translation-competent reservoir, defined as latent cells able to produce viral proteins upon stimulation (Baxter et al, 2018), which may include some replication-incompetent HIV provirus (Baxter et al, 2016;Imamichi et al, 2020). Nevertheless, our viral outgrowth results closely aligned with the enrichment of kNN latent cells, confirming that PP-SLIDE identifies markers of the replicationcompetent HIV reservoir most relevant for a cure.…”

HIV-1 Persistence and Chronic Induction of Innate Immune Responses in Macrophages

“…In fact, in HIV + individuals or SIV-infected NHPs on suppressive cART, viral gag RNAs (i.e., icRNA) are still detectable in various tissues [46,[132][133][134][135][136]. Although the majority of integrated proviruses are defective, containing large internal deletions and/or hyper mutations [137,138], these defective proviruses remain transcriptionally active and can lead to expression of icRNA [139,140]. It is conceivable that HIV icRNA from intact or defective proviruses are transcribed even in the presence of the current ART drugs, leading to chronic immune activation.…”

Differences in HIV Markers between Infected Individuals Treated with Different ART Regimens: Implications for the Persistence of Viral Reservoirs

“…As these defective proviruses are incapable of triggering viral rebound following ART interruption, it has been suggested to restrict the definition of the HIV reservoir to the "replication-competent reservoir", a small number of intact proviruses that should be eliminated in order to avoid viral resurgence after therapy interruption [21]. This definition ignores >90% of all proviruses that are replication-defective, but can nevertheless produce viral (or novel) RNA species, proteins, or even defective virus particles, potentially contributing to chronic immune activation and inflammation despite ART [22][23][24][25][26][27][28][29]. The definition of the HIV reservoir thus could be extended to include defective proviruses, as long as they contribute to residual HIV pathogenesis under ART -something that is yet to be shown.…”