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Defective HIV-1 genomes and their potential impact on HIV pathogenesis

Retrovirology volume 19, Article number: 13 (2022) Cite this article

Abstract

Defective HIV-1 proviruses represent a population of viral genomes that are selected for by immune pressures, and clonally expanded to dominate the persistent HIV-1 proviral genome landscape. There are examples of RNA and protein expression from these compromised genomes which are generated by a variety of mechanisms. Despite the evidence that these proviruses are transcribed and translated, their role in HIV pathogenesis has not been fully explored. The potential for these genomes to participate in immune stimulation is particularly relevant considering the accumulation of cells harboring these defective proviruses over the course of antiretroviral therapy in people living with HIV. The expression of defective proviruses in different cells and tissues could drive innate sensing mechanisms and inflammation. They may also alter antiviral T cell responses and myeloid cell functions that directly contribute to HIV-1 associated chronic comorbidities. Understanding the impact of these defective proviruses needs to be considered as we advance cure strategies that focus on targeting the diverse population of HIV-1 proviral genomes.

Graphical abstract

Introduction

Virus replication requires successful entry into a host cell, generation of the viral genome, packaging of virion contents, and transmission of these contents to a new target cell. However, intrinsic host cell restriction factors and the inefficient and error-prone nature of viral replicative processes lead to the generation of defective virus genomes and particles. Defective viruses are generated by several RNA viruses including Measles, Sendai and Ebola Viruses [1,2,3,4,5,6,7]. They are also generated by retroviruses including human immunodeficiency virus-1 (HIV-1) [8,9,10], the focus of this review. Defective proviruses accumulate crippling mutations during infection and replication which render them unable to complete their replication cycle. Despite their inability to contribute to new infections, these defective viruses still potentially influence viral pathogenesis by diverting productive anti-viral immunity and propagating damaging inflammatory responses. Therefore, defective viruses may be critical contributors to viral immune escape, persistence, and pathogenesis and not simply viral genome “junk”.

The focus of HIV cure strategies has primarily been on eliminating or suppressing the intact latent provirus genomes that fuel the rebound of HIV replication upon interruption of antiretroviral therapy [11, 12]. However, the number of intact proviral genomes that are small, estimated to be 2% of all infected cells which includes a rarer population that contributes to viral rebound (one in 100,000 to 1 × 106 cells in peripheral blood and lymph nodes) in people living with HIV (PLWH) on antiretroviral therapy (ART). Secondary lymphoid tissues also harbor HIV-1 infected CD4+ T cells with frequencies of intact, defective and inducible proviral genomes similar to those observed in blood suggesting peripheral blood is an appropriate surrogate for evaluating persistent proviral sequences [13]. Furthermore, intact and defective proviral genomes are found in most CD4+ T cells subsets in comparable frequencies indicating multiple CD4+ cell types in multiple tissues contribute to HIV-1 persistence and latency [14]. However, it will be critical to have standardized clinically validated assays to evaluate latent reservoirs and persistent proviral genomes in blood and immune tissues to monitor the effectiveness of therapeutic approaches for HIV-1 cure [15].

With the majority of proviral sequences harboring deleterious mutations [8] how these defective HIV proviruses contribute to various persistent comorbidities and pathogenesis in people living with HIV remains an important unanswered question. When considering different cure strategies, whether genome editing to cripple HIV-1, “block-and-lock”, or “shock-and-kill” approaches, it will be critical to determine whether remnants of viral genomes are expressed and biologically active. In this review we highlight findings that demonstrate that HIV infection results in dynamic populations of defective genomes, discuss the expression and evolution of these defective proviruses in PLWH, and consider whether their expression contributes to HIV immune evasion, persistent inflammation, and pathogenesis.

Defective HIV-1 genomes dominate the proviral landscape

Characterization of the HIV-1 proviral reservoir in different CD4+ T cell subsets through deep sequencing, single-cell approaches, ex vivo viral outgrowth assays, and quantitative droplet digital PCR has led to insights into how persistent infection and latency are established, maintained, and reactivated [8, 9, 14, 16,17,18,19,20,21,22,23]. From these efforts it has become apparent that the proviral landscape is dynamic and evolving during chronic HIV-1 infection [24,25,26,27,28,29]. Intact HIV-1 proviruses which have the potential to support viral rebound, have been estimated to represent 2–5% of the persistent provirus pool as measured in peripheral blood mononuclear cells (PBMCs) [8, 9]. Longitudinal tracking of intact provirus sequences in PLWH before and after ART initiation suggests that most of the latent intact HIV reservoir has been seeded at the time of ART initiation and there is no additional infection post-ART [30,31,32], although ART initiation has been suggested to shape the latent reservoir [30,31,32]. It has also been suggested that the virus circulating at the time of ART initiation is overrepresented in the reservoir [30]. The size of the persistent provirus population varies among individuals and the mechanisms that determine if a proviral genome is capable of reactivation remain inadequately understood. Studies of CD4+ T cells from individuals who naturally control HIV-1 infection demonstrated that intact proviruses are enriched in heterochromatic regions of the host genome while defective proviruses are detected in euchromatic regions [19, 33]. These observations support that enhanced immune detection and clearance in these individuals shapes the persistent provirus reservoir over time, relegating intact proviruses to relatively silent loci of the host genome [34]. Examining the reactivation of provirus from peripheral blood obtained from PLWH that are undergoing ART indicates that relatively small subsets of latently infected cells are easily induced to express new virions while a second larger subset of infected cells harbor intact provirus that are more resistant to reactivation [9]. The mechanisms that are responsible for this spectrum of inducibility of intact proviruses is unclear and may reflect phenotypes and functions of cells that harbor HIV-1 infections, proviral integration sites, or even stochastic mechanisms such as bursts of Tat-dependent transcriptional activity [35,36,37,38,39,40,41,42].

The majority of proviral sequences detected, greater than 90%, are defective [8, 9, 16]. These defective genomes harbor large deletions, sequence inversions, hypermutations, and defective splice donor and acceptor sites that prevent viral replication. During the course of treatment, the persistent proviral landscape shifts with outgrowths of dominant clones that include defective proviral genomes [24]. Proposed mechanisms that drive the shaping, selection, and expansion of HIV-1 proviral clones include depletion of cells that express HIV antigens, antigen driven and cytokine driven clonal expansion, homeostasis of T cell subsets that harbor HIV proviruses, and expansion of proviruses integrated near genes that influence cell survival and proliferation [24, 25, 43,44,45,46,47]. Longitudinal studies have revealed that defective proviruses are subjected to different levels of immunological targeting and clearance depending on their transcriptional and translation competence [24, 26, 48]. Proviruses which retain the ability to transcribe HIV-1 RNAs and translate viral proteins can be preferentially cleared during sustained immunological pressure [29] leading to proviruses with little transcriptional or translational activity clonally expand to form the majority of the reservoir [24, 25, 29]. However, HIV-1 proviral genomes that are transcriptionally active and express gag have also been posited to drive clonal expansion [25]. Sequencing proviral genomes have suggested that persistent defective proviruses are established within the first few weeks following infection, although initiation of antiretroviral therapy may influence repertoire of defective HIV proviral sequences [8, 26]. It remains unclear whether defective proviruses play a role in subverting the anti-HIV immune responses or perpetuating the chronic inflammation which has been described in PLWH on ART.

Generation of defective HIV-1 genomes

Multiple mechanisms contribute to the generation of defective HIV-1 proviruses including the inefficiency of reverse transcription and the activity of host cell restriction factors. HIV reverse transcriptase lacks proofreading ability and is error prone, introducing approximately 1.4 × 10–5 mutations per base pair per cycle [49, 50]. Successful reverse transcription also requires dissociation and re-initiation of reverse transcription on the RNA genome template leading to a propensity to produce mutated and truncated HIV DNA intermediates [51,52,53]. For example, sequence analysis of HIV proviral sequences obtained from CD4+ T cells from PLWH on ART attributed approximately 40% of the internal deletions detected to negative strand synthesis during reverse transcription [54]. Recombination, a process by which genetic diversity is introduced through template-switching between the two copies of the HIV RNA genome packaged in virions, also contributes to the mutation rate of reverse transcription products [55,56,57,58].

Intrinsic host defenses and anti-viral restriction factors limit replication and reverse transcription efficiency contributing to the generation of defective HIV genomes. APOBEC 3G, a cytosine deaminase, targets single-stranded DNA intermediates and promotes HIV-1 hypermutation by inducing guanine-to-adenine changes during the process of reverse transcription [59,60,61,62,63]. Sterile Alpha Motif- and HD-domain containing protein 1 (SAMHD1), a host viral restriction factor which reduces the concentration of intracellular nucleotides in resting CD4+ T cells and myeloid cells, limiting the efficiency and completion of reverse transcription [64,65,66,67].

RNAs and translation products from intact and defective HIV-1 proviruses

HIV-1 transcription is regulated by multiple mechanisms and combinatorial events which have been extensively reviewed (recent reviews include [68,69,70]). In general, the HIV-1 long terminal repeat (LTR) acts as an enhancer and promoter, recruiting host cell transcriptional activators, repressors, chromatin remodeling factors, and the RNAP II complex which all influence transcriptional activation or repression. HIV Tat binds the TAR stem loop element at the 5ʹ end of the HIV-1 initiated transcript to recruit PTEFb a cofactor that enhances RNAPII processivity and recruits cofactors that influence proviral chromatin organization and transcription [71,72,73]. Current antiretroviral therapies do not target HIV transcription; however, during ART there is immune selection against cells actively transcribing HIV genes. The function of intrinsic transcription factors and repressive epigenetic regulators contribute to the repression of HIV-1 transcription in intact latent proviruses. However, it is important to note that HIV-1 transcripts are detected in individuals on ART [74,75,76,77]. Single-genome HIV RNA sequencing at limiting dilution showed that up to 7% of HIV-1 provirus in PBMCs from patients undergoing ART remain transcriptionally active [78].

A potential source of residual HIV-1 transcripts detected during ART are defective proviruses (Fig. 1). Defective HIV-1 proviruses are transcribed despite mutations that compromise efficient transcription and replication such as deletions of the 5ʹLTR or altered splice acceptor and donor sites, including the psi packaging element [24, 54]. Despite these defects, spurious transcription, possibly through alternative transcriptional start sites and/or alternative splice site usage, has been reported [24]. Proviruses with defects in their major splice donor sequence overcome this defect by using alternative splicing mechanisms. The use of alternative and cryptic splice sites is suspected to enable translation of chimeric and non-canonical HIV-1 fusion proteins [79]. Antisense transcription from the 3ʹ LTR is another mechanism for generating HIV-1 transcripts; however, whether antisense transcription is regulated by the same signaling cascades as transcription from the 5ʹ LTR, and its functional relevance, is unclear [80,81,82,83].

Fig. 1
figure 1

Summary of a subset of RNAs that are transcribed by HIV-1 outlined in the review. Dashes represent spliced sequences

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Intragenic cis-acting elements have been proposed for HIV-1 and other retroviruses and represent additional mechanisms to support the transcription of defective proviruses [84,85,86,87,88]. The presence of intragenic transcriptional elements in the HIV-1 genome has been postulated for decades but the function and regulation of such elements have not been fully appreciated. Cis-acting repressive sequences (CRS) have been reported and have been proposed to limit HIV-1 transcription, splicing, and nuclear export [89, 90]. CRS functions are partially achieved through interactions with host cellular transcription factors [90]. Such interactions have also been described for cis-acting elements involved in regulating the alternative splicing of HIV-1 transcripts [91]. In addition, sequences within the HIV-1 env gene have been identified as potential elements that control intragenic transcriptional activity and include transcription binding sites, the presence of methylated CpG islands, and increased DNAse I sensitivity which correlates with transcriptionally active elements [92,93,94]. We have extended these observations using 5ʹ RACE PCR to demonstrate that HIV transcripts are generated from an intragenic promoter within the envelope gene in in vitro infected primary cells [95]. Potential aberrant RNAs that contained env and nef but lacked 5ʹ LTR derived untranslated regions (UTRs) were detected in cDNAs generated from cell-associated RNA from PLWH on ART using multiplex reverse transcriptase droplet digital PCR [92]. A limitation with cDNA synthesis is that prematurely terminated cDNAs molecules would be included in the library. However, taken together these results lead to speculation that spurious transcription driven by cis-acting elements that remain active in defective HIV-1 proviruses could provide a mechanism for the generation of RNA when LTR-mediated transcription is repressed or compromised. Whether this transcription from defective proviruses is relevant to HIV-1 pathogenesis is an outstanding question as are mechanisms that regulate these intragenic promoters.

A critical question regarding potential roles of these cryptic or alternative RNA sequences is whether they are translated. It has been shown that point mutations within the HIV-1 provirus generate alternative reading frames and these can allow for translation of proteins [96, 97]. Similarly, internal deletions and inversions within defective proviral genomes can generate novel open reading frames and translation of proteins [54, 98]. HIV-1 proteins are also translated from transcripts generated from intragenic promoters and there have been reports of an antisense protein [80, 82, 95, 99]. Translation from these aberrant or spurious RNAs would be consistent with the detection of HIV-1 proteins in PWLH on ART and in latently infected cells in the absence of viral replication. For example, Nef and Gag have been observed intracellularly in PBMCs from PLWH on ART, although technical concerns have been raised about these studies and protein detection has often required ex vivo stimulation [100,101,102]. HIV-1 Gag has been shown to be a source of defective ribosomal products (DRiPs) which are rapidly degraded by the proteasome and loaded onto MHC-I molecules [103]. HIV-1 antisense protein (ASP) has been reported in infected cell samples from PLWH and antibodies against this protein have been detected in the sera of a subset of infected individuals [82, 104, 105]. The possible generation of viral transcripts and proteins from defective HIV-1 proviruses begs the question of whether these viral products play an immunomodulatory role in chronically infected individuals.

Defective viruses, immune dysfunction, and cure strategies

Immunological selection and clonal expansion of cells harboring HIV proviral genomes shapes the persistent reservoir [24, 33, 46, 106, 107]. For example, cells that express HIV-1 generate MHC-I associated peptides that are targeted and eliminated by CD8+ T cells. This pool of HIV peptides includes cryptic epitopes produced from alternative reading frames (ARFs) throughout the HIV-1 genome [97, 105, 108, 109]. ELISA and ELISpot assays demonstrated that CD8+ T cells from PLWH on ART are activated by peptides predicted to be generated by ARFs which exist in sense and antisense orientations in the HIV-1 genome [24, 105]. These responses were greater in magnitude for CD8+ T cells from chronically infected PLWH as opposed to those with an acute infection. These data support a model whereby ARFs shape the composition of persistent proviruses by being targets for CD8+ T cells and driving the homeostasis of CD8+ T cell-mediated immunity against these cryptic proteins. Studies that have demonstrated the ability of defective proviruses to produce viral proteins suggest that subsets of the defective provirus population could contribute to this phenomenon [98, 101, 102]. We speculate that defective proviral genomes act as one source of ARF generated peptides. Ex vivo expression of defective HIV-1 provirus clones has shown that defective HIV-1 genomes can be translated into proteins which activate cytotoxic T lymphocytes (CTLs) specific for HIV-1 peptides [24]. These data support that the adaptive immune response is influenced by protein expression from a subset of defective proviruses (Fig. 2).

Fig. 2
figure 2

Mechanisms by which cryptic HIV-1 peptides could influence T cell responses

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One consequence of chronic HIV infection is the functional exhaustion of HIV-specific CD8+ T cells [110, 111]. Polyfunctional HIV-specific CD8+ T cells, those which produce a wide breadth of cytokines, chemokines, and cytotoxic molecules, correlate with control of HIV-1 in non-progressors who control HIV infection [110, 111]. Longitudinal analysis of polyfunctional HIV-specific CD8+ T cells in vivo has shown that, in the context of persistent antigen stimulation, the breadth of cytokines produced declines, and this correlates with increased expression of PD-1, TIGIT, and LAG-3, molecules associated with exhaustion [110, 112, 113]. While HIV-1 specific CD8+ T cell numbers remain high in chronically infected individuals, they produce less IFNγ, express relatively high levels of co-inhibitory receptors like PD-1, and have altered metabolomic profiles [114,115,116]. Additionally, CD4+ T cell depletion promotes exhaustion by diminishing helper T-cells that facilitate antiviral CD8+ T cell responses [117, 118]. In addition, there is evidence that cryptic peptides may have the capacity to drive viral escape from cellular immunity driving escape mutations which prevent proteasomal cleavage and antigen presentation of these otherwise protective epitopes [119]. Therefore, during chronic HIV infection, spurious and chronic antigen expression from the defective persistent provirus pool could subvert anti-HIV immunity by driving T cell exhaustion, diversion and depletion.

Chronic HIV infection is associated with persistent inflammation which has been implicated in various comorbidities and associated HIV-1 disease sequela consistent with inflammaging in PLWH [120]. For example, PLWH receiving ART have increased risk of coronary heart disease, various cancers, HIV-associated neurological disorders (HAND), leaky gut syndrome, and other end-organ diseases [121,122,123,124,125,126,127]. These HIV associated conditions have been correlated with an accumulation of age-related epigenetic marks in cells from the blood and brain leading to the hypothesis that HIV-1 infection promotes accelerated aging [128,129,130,131]. Importantly, the inflammaging phenomenon does not correlate with plasma viremia and is observed in PLWH even when viremia is largely controlled by ART. This inflammatory response may be driven by recognition of HIV proteins and RNAs activating innate intracellular antiviral responses. Markers of chronic inflammation in PLWH on ART do not correlate with measurements of intact provirus genomes but do correlate with cell associated HIV-1 RNA [132]. Whether residual transcription from defective proviral genomes contribute to this inflammation is undefined.

HIV-1 proviruses generate a diverse set of transcripts which include RNAs with complex secondary structures, retention of intronic sequence, and post-transcriptional modifications including m6A modifications [133,134,135,136]. These features of HIV-1 transcripts provide multiple targets for detection by cellular innate nucleic acid innate immune sensors which can initiate signaling events that activate interferon responses and inflammatory cytokine production [133, 135, 137,138,139,140,141]. For example, the expression of intron-containing HIV-1 RNA exported from the nucleus in infected myeloid cells and microglia has been demonstrated to perpetuate inflammatory responses [134, 135]. Detection of these RNAs and the induction of IFN type 1 responses alter macrophage and dendritic cell function (Fig. 3) including antigen presentation thus influencing CD4+ and CD8+ T cell responses. Together, these studies support that the residual transcription described in PLWH on ART have the potential to contribute to CD8+ T cell dysfunction and systemic inflammation.

Fig. 3
figure 3

Mechanisms by which HIV-1 RNAs potentially activate innate immune responses

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Current cure strategies focus on either purging the HIV-1 provirus reservoir, permanently inactivating latent proviruses, or targeting the provirus with gene editing approaches [12, 142,143,144,145,146,147]. Examples of some these proposed approaches include shock-and-kill to activate the latent pool so it can be immunologically targeted, block-and-lock approaches that rely on compounds or engineered transcriptional repressors that inactivate or repress HIV proviral transcription such as didehydro-Cortistatin, dCas9-KRAB or dCasDMNTs and targeting and inactivating proviruses using CRISPR-cas9 or zinc finger nucleases [148,149,150,151,152,153,154,155,156,157,158]. These approaches, in general, target the expression or elimination of intact proviruses and would have minimum impact on the presence of defective proviruses. Since there is scant information as to how these defective proviral sequences are transcriptionally regulated, it is unknown whether latency reversal agents or transcriptional repressors will impact the activity of intragenic cis-transcriptional elements and the expression of cryptic peptides. Depending on the sequences targeted by engineered nucleases, gene editing approaches have the potential to create additional defective proviral genomes. Furthermore, CRISPR–cas9 approaches have been reported to promote viral escape through nonhomologous end joining and generate transcriptionally active LTR circles [159, 160]. As we explore ways to target the latent reservoir, continued understanding of the regulation and functional impact of defective proviruses need to be considered.

Conclusions

The persistent HIV-1 proviral genome landscape consists of mostly defective HIV-1 proviruses. Although RNAs and proteins are expressed from these proviral genomes their impact in HIV pathogenesis is unclear. We speculate that spurious expression of these RNAs and proteins contribute to immune dysfunction and T cell exhaustion that are associated with comorbidities of chronic HIV-1 infection including inflammaging. Future cure strategies will need to address the importance of targeting the complete array of intact and defective proviral genomes.

Availability of data and materials

Not applicable.

References

  1. Baczko K, Liebert UG, Billeter M, Cattaneo R, Budka H, ter Meulen V. Expression of defective measles virus genes in brain tissues of patients with subacute sclerosing panencephalitis. J Virol. 1986;59(2):472–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Sidhu MS, Crowley J, Lowenthal A, Karcher D, Menonna J, Cook S, et al. Defective measles virus in human subacute sclerosing panencephalitis brain. Virology. 1994;202(2):631–41.

    Article  CAS  PubMed  Google Scholar 

  3. Genoyer E, López CB. Defective viral genomes alter how Sendai virus interacts with cellular trafficking machinery, leading to heterogeneity in the production of viral particles among infected cells. J Virol. 2018;93(4):e01579-e1618.

    Google Scholar 

  4. Xu J, Sun Y, Li Y, Ruthel G, Weiss SR, Raj A, et al. Replication defective viral genomes exploit a cellular pro-survival mechanism to establish paramyxovirus persistence. Nat Commun. 2017;8(1):1–13.

    Article  Google Scholar 

  5. Calain P, Roux L, Kolakofsky D. Defective interfering genomes and Ebola virus persistence. Lancet. 2016;388:659–60.

    Article  PubMed  Google Scholar 

  6. Manzoni TB, López CB. Defective (interfering) viral genomes re-explored: impact on antiviral immunity and virus persistence. Future Virol. 2018;13(7):493–503. https://doi.org/10.2217/fvl-2018-0021.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Calain P, Monroe MC, Nichol ST. Ebola virus defective interfering particles and persistent infection. Virology. 1999;262(1):114–28.

    Article  CAS  PubMed  Google Scholar 

  8. Bruner KM, Murray AJ, Pollack RA, Soliman MG, Laskey SB, Capoferri AA, et al. Defective proviruses rapidly accumulate during acute HIV-1 infection. Nat Med. 2016;22(9):1043–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Ho YC, Shan L, Hosmane NN, Wang J, Laskey SB, Rosenbloom DIS, et al. Replication-competent noninduced proviruses in the latent reservoir increase barrier to HIV-1 cure. Cell. 2013;155(3):540.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Katz RA, Skalka AM. Generation of diversity in retroviruses. Annu Rev Genet. 1990;24(1):409–43.

    Article  CAS  PubMed  Google Scholar 

  11. Churchill MJ, Deeks SG, Margolis DM, Siliciano RF, Swanstrom R. HIV reservoirs: what, where and how to target them. Nat Rev Microbiol. 2016;14(1):55–60.

    Article  CAS  PubMed  Google Scholar 

  12. Vansant G, Bruggemans A, Janssens J, Debyser Z. Block-and-lock strategies to cure HIV infection. Viruses. 2020;12(1):84.

    Article  CAS  PubMed Central  Google Scholar 

  13. Martin AR, Bender AM, Hackman J, Kwon KJ, Lynch BA, Bruno D, et al. Similar frequency and inducibility of intact human immunodeficiency virus-1 proviruses in blood and lymph nodes. J Infect Dis. 2021;224(2):258.

    Article  CAS  PubMed  Google Scholar 

  14. Gálvez C, Grau-Expósito J, Urrea V, Clotet B, Falcó V, Buzón MJ, et al. Atlas of the HIV-1 reservoir in peripheral CD4 T cells of individuals on successful antiretroviral therapy. MBio. 2021;12(6):e03078-21.

    Article  PubMed Central  Google Scholar 

  15. Abdel-Mohsen M, Kuri-Cervantes L, Grau-Exposito J, Spivak AM, Nell RA, Tomescu C, et al. CD32 is expressed on cells with transcriptionally active HIV but does not enrich for HIV DNA in resting T cells. Sci Transl Med. 2018;10(437):eaar6759. https://doi.org/10.1126/scitranslmed.aar6759.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Bruner KM, Wang Z, Simonetti FR, Bender AM, Kwon KJ, Sengupta S, et al. A novel quantitative approach for measuring the reservoir of latent HIV-1 proviruses. Nature. 2019;566(7742):120.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Lorenzi JCC, Cohen YZ, Cohn LB, Kreider EF, Barton JP, Learn GH, et al. Paired quantitative and qualitative assessment of the replication-competent HIV-1 reservoir and comparison with integrated proviral DNA. Proc Natl Acad Sci USA. 2016;113(49):E7908–16. https://doi.org/10.1073/pnas.1617789113.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Siliciano JD, Kajdas J, Finzi D, Quinn TC, Chadwick K, Margolick JB, et al. Long-term follow-up studies confirm the stability of the latent reservoir for HIV-1 in resting CD4+ T cells. Nat Med. 2003;9(6):727–8.

    Article  CAS  PubMed  Google Scholar 

  19. Jiang C, Lian X, Gao C, Sun X, Einkauf KB, Chevalier JM, et al. A unique viral reservoir landscape in HIV-1 elite controllers. Nature. 2020;585(7824):261.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Cohn LB, Silva IT, Oliveira TY, Rosales RA, Parrish EH, Learn GH, et al. HIV-1 integration landscape during latent and active infection. Cell. 2015;160(3):420–32.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Chun TW, Carruth L, Finzi D, Shen X, DiGiuseppe JA, Taylor H, et al. Quantification of latent tissue reservoirs and total body viral load in HIV-1 infection. Nature. 1997;387(6629):183–8.

    Article  CAS  PubMed  Google Scholar 

  22. Sannier G, Dubé M, Dufour C, Richard C, Brassard N, Delgado GG, et al. Combined single-cell transcriptional, translational, and genomic profiling reveals HIV-1 reservoir diversity. Cell Rep. 2021;36(9):109643.

    Article  CAS  PubMed  Google Scholar 

  23. Grau-Expósito J, Luque-Ballesteros L, Navarro J, Curran A, Burgos J, Ribera E, et al. Latency reversal agents affect differently the latent reservoir present in distinct CD4+ T subpopulations. PLOS Pathog. 2019;15(8):e1007991. https://doi.org/10.1371/journal.ppat.1007991.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Pollack RA, Jones RB, Pertea M, Bruner KM, Martin AR, Thomas AS, et al. Defective HIV-1 proviruses are expressed and can be recognized by cytotoxic T lymphocytes, which shape the proviral landscape. Cell Host Microbe. 2017;21(4):494-506.e4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Anderson EM, Simonetti FR, Gorelick RJ, Hill S, Gouzoulis MA, Bell J, et al. Dynamic shifts in the HIV proviral landscape during long term combination antiretroviral therapy: implications for persistence and control of HIV infections. Viruses. 2020;12(2):136.

    Article  CAS  PubMed Central  Google Scholar 

  26. Liu R, Catalano AA, Ho Y-C. Measuring the size and decay dynamics of the HIV-1 latent reservoir. Cell Rep Med. 2021;2(4):100249.

    Article  PubMed  PubMed Central  Google Scholar 

  27. Peluso MJ, Bacchetti P, Ritter KD, Beg S, Lai J, Martin JN, et al. Differential decay of intact and defective proviral DNA in HIV-1-infected individuals on suppressive antiretroviral therapy. JCI Insight. 2020;5(4):e132997.

    Article  PubMed Central  Google Scholar 

  28. Antar AAR, Jenike KM, Jang S, Rigau DN, Reeves DB, Hoh R, et al. Longitudinal study reveals HIV-1–infected CD4+ T cell dynamics during long-term antiretroviral therapy. J Clin Invest. 2020;130(7):3543.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Einkauf KB, Osborn MR, Gao C, Sun W, Sun X, Lian X, et al. Parallel analysis of transcription, integration, and sequence of single HIV-1 proviruses. Cell. 2022;185(2):266-282.e15.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Abrahams MR, Joseph SB, Garrett N, Tyers L, Moeser M, Archin N, et al. The replication-competent HIV-1 latent reservoir is primarily established near the time of therapy initiation. Sci Transl Med. 2019;11(513):eaaw5589.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Brodin J, Zanini F, Thebo L, Lanz C, Bratt G, Neher RA, et al. Establishment and stability of the latent HIV-1 DNA reservoir. Elife. 2016;5(November2016):e18889.

    Article  PubMed  PubMed Central  Google Scholar 

  32. White JA, Simonetti FR, Beg S, McMyn NF, Dai W, Bachmann N, et al. Complex decay dynamics of HIV virions, intact and defective proviruses, and 2LTR circles following initiation of antiretroviral therapy. Proc Natl Acad Sci USA. 2022;119(6):e2120326119.

    Article  CAS  PubMed  Google Scholar 

  33. Lian X, Gao C, Sun X, Jiang C, Einkauf KB, Seiger KW, et al. Signatures of immune selection in intact and defective proviruses distinguish HIV-1 elite controllers. Sci Transl Med. 2021;13(624):eabl4097. https://doi.org/10.1126/scitranslmed.abl4097.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Hartana CA, Yu XG. Immunological effector mechanisms in HIV-1 elite controllers. Curr Opin HIV AIDS. 2021;16(5):243–8.

    CAS  PubMed  Google Scholar 

  35. Pardons M, Fromentin R, Pagliuzza A, Routy JP, Chomont N. Latency reversing agents induce differential responses in distinct memory CD4 T cell subsets in individuals on antiretroviral therapy. Cell Rep. 2019;29(9):2783.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Kulpa DA, Talla A, Brehm JH, Ribeiro SP, Yuan S, Bebin-Blackwell A-G, et al. Differentiation into an effector memory phenotype potentiates HIV-1 latency reversal in CD4 + T cells. J Virol. 2019;93(24):e00969-19. https://doi.org/10.1128/JVI.00969-19.

    Article  PubMed  PubMed Central  Google Scholar 

  37. Kwon KJ, Timmons AE, Sengupta S, Simonetti FR, Zhang H, Hoh R, et al. Different human resting memory CD4+ T cell subsets show similar low inducibility of latent HIV-1 proviruses. Sci Transl Med. 2020;12(528):6795. https://doi.org/10.1126/scitranslmed.aax6795.

    Article  CAS  Google Scholar 

  38. Battivelli E, Dahabieh MS, Abdel-Mohsen M, Svensson JP, Da Silva IT, Cohn LB, et al. Distinct chromatin functional states correlate with HIV latency reactivation in infected primary CD4+ T cells. Elife. 2018;7:e34655.

    Article  PubMed  PubMed Central  Google Scholar 

  39. Lenasi T, Contreras X, Peterlin BM. Transcriptional interference antagonizes proviral gene expression to promote HIV latency. Cell Host Microbe. 2008;4(2):123–33.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Lelek M, Casartelli N, Pellin D, Rizzi E, Souque P, Severgnini M, et al. Chromatin organization at the nuclear pore favours HIV replication. Nat Commun. 2015;6(1):1–12.

    Article  Google Scholar 

  41. Tantale K, Garcia-Oliver E, Robert MC, L’Hostis A, Yang Y, Tsanov N, et al. Stochastic pausing at latent HIV-1 promoters generates transcriptional bursting. Nat Commun. 2021;12(1):1–20.

    Article  Google Scholar 

  42. Singh A, Razooky B, Cox CD, Simpson ML, Weinberger LS. Transcriptional bursting from the HIV-1 promoter is a significant source of stochastic noise in HIV-1 gene expression. Biophys J. 2010;98(8):L32.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Cole B, Lambrechts L, Gantner P, Noppe Y, Bonine N, Witkowski W, et al. In-depth single-cell analysis of translation-competent HIV-1 reservoirs identifies cellular sources of plasma viremia. Nat Commun. 2021;12(1):1–13.

    Article  Google Scholar 

  44. Hiener B, Horsburgh BA, Eden JS, Barton K, Schlub TE, Lee E, et al. Identification of genetically intact HIV-1 proviruses in specific CD4+ T cells from effectively treated participants. Cell Rep. 2017;21(3):813–22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Wagner TA, McLaughlin S, Garg K, Cheung CYK, Larsen BB, Styrchak S, et al. Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection. Science (80−). 2014;345(6196):570–3. https://doi.org/10.1126/science.1256304.

    Article  CAS  Google Scholar 

  46. Simonetti FR, Zhang H, Soroosh GP, Duan J, Rhodehouse K, Hill AL, et al. Antigen-driven clonal selection shapes the persistence of HIV-1–infected CD4+ T cells in vivo. J Clin Invest. 2021;131(3):e145254.

    Article  CAS  PubMed Central  Google Scholar 

  47. Liu R, Simonetti FR, Ho YC. The forces driving clonal expansion of the HIV-1 latent reservoir. Virol J. 2020;17(1):4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Pinzone MR, VanBelzen DJ, Weissman S, Bertuccio MP, Cannon L, Venanzi-Rullo E, et al. Longitudinal HIV sequencing reveals reservoir expression leading to decay which is obscured by clonal expansion. Nat Commun. 2019;10(1):1–12.

    Article  Google Scholar 

  49. Preston BD, Poiesz BJ, Loeb LA. Fidelity of HIV-1 reverse transcriptase. Science (80−). 1988;242(4882):1168–71. https://doi.org/10.1126/science.2460924.

    Article  CAS  Google Scholar 

  50. Cuevas JM, Geller R, Garijo R, López-Aldeguer J, Sanjuán R. Extremely high mutation rate of HIV-1 in vivo. PLoS Biol. 2015;13(9):e1002251.

    Article  PubMed  PubMed Central  Google Scholar 

  51. Masuda T, Sato Y, Huang YL, Koi S, Takahata T, Hasegawa A, et al. Fate of HIV-1 cDNA intermediates during reverse transcription is dictated by transcription initiation site of virus genomic RNA. Sci Rep. 2015;5(1):17680.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Peliska JA, Benkovic SJ. Mechanism of DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase. Science (80−). 1992;258(5085):1112–8.

    Article  CAS  Google Scholar 

  53. Chen Y, Balakrishnan M, Roques BP, Fay PJ, Bambara RA. Mechanism of minus strand strong stop transfer in HIV-1 reverse transcription. J Biol Chem. 2003;278(10):8006–17.

    Article  CAS  PubMed  Google Scholar 

  54. Imamichi H, Dewar RL, Adelsberger JW, Rehm CA, O’Doherty U, Paxinos EE, et al. Defective HIV-1 proviruses produce novel protein-coding RNA species in HIV-infected patients on combination antiretroviral therapy. Proc Natl Acad Sci USA. 2016;113(31):8783.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Song H, Giorgi EE, Ganusov VV, Cai F, Athreya G, Yoon H, et al. Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection. Nat Commun. 2018;9(1):1–15.

    Article  Google Scholar 

  56. Morris A, Marsden M, Halcrow K, Hughes ES, Brettle RP, Bell JE, et al. Mosaic structure of the human immunodeficiency virus type 1 genome infecting lymphoid cells and the brain: evidence for frequent in vivo recombination events in the evolution of regional populations. J Virol. 1999;73(10):8720–31. https://doi.org/10.1128/JVI.73.10.8720-8731.1999.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Inoue M, Hoxie JA, Reddy MVR, Srinivasan A, Reddy EP. Mechanisms associated with the generation of biologically active human immunodeficiency virus type 1 particles from defective proviruses. Proc Natl Acad Sci. 1991;88(6):2278–82.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Wei H, Yu D, Geng X, He Y. Defective HIV-1 envelope gene promotes the evolution of the infectious strain through recombination in vitro. BMC Infect Dis. 2020;20(1):1–10. https://doi.org/10.1186/s12879-020-05288-w.

    Article  CAS  Google Scholar 

  59. Sharma S, Patnaik SK, Taggart RT, Baysal BE. The double-domain cytidine deaminase APOBEC3G is a cellular site-specific RNA editing enzyme. Sci Rep. 2016;6(1):1–12.

    Article  Google Scholar 

  60. Chiu YL, Soros VB, Kreisberg JF, Stopak K, Yonemoto W, Greene WC. Cellular APOBEC3G restricts HIV-1 infection in resting CD4+ T cells. Nature. 2005;435(7038):108–14.

    Article  CAS  PubMed  Google Scholar 

  61. Mangeat B, Turelli P, Caron G, Friedli M, Perrin L, Trono D. Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts. Nature. 2003;424(6944):99–103.

    Article  CAS  PubMed  Google Scholar 

  62. Harris RS, Bishop KN, Sheehy AM, Craig HM, Petersen-Mahrt SK, Watt IN, et al. DNA deamination mediates innate immunity to retroviral infection. Cell. 2003;113(6):803–9.

    Article  CAS  PubMed  Google Scholar 

  63. Salamango DJ, Harris RS. Dual functionality of HIV-1 Vif in APOBEC3 counteraction and cell cycle arrest. Front Microbiol. 2020;11:622012.

    Article  PubMed  Google Scholar 

  64. Laguette N, Sobhian B, Casartelli N, Ringeard M, Chable-Bessia C, Ségéral E, et al. SAMHD1 is the dendritic- and myeloid-cell-specific HIV-1 restriction factor counteracted by Vpx. Nature. 2011;474(7353):654–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Lahouassa H, Daddacha W, Hofmann H, Ayinde D, Logue EC, Dragin L, et al. SAMHD1 restricts the replication of human immunodeficiency virus type 1 by depleting the intracellular pool of deoxynucleoside triphosphates. Nat Immunol. 2012;13(3):223–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Goldstone DC, Ennis-Adeniran V, Hedden JJ, Groom HCT, Rice GI, Christodoulou E, et al. HIV-1 restriction factor SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase. Nature. 2011;480(7377):379–82.

    Article  CAS  PubMed  Google Scholar 

  67. Hrecka K, Hao C, Gierszewska M, Swanson SK, Kesik-Brodacka M, Srivastava S, et al. Vpx relieves inhibition of HIV-1 infection of macrophages mediated by the SAMHD1 protein. Nature. 2011;474(7353):658–61.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Dutilleul A, Rodari A, Van Lint C. Depicting HIV-1 transcriptional mechanisms: a summary of what we know. Viruses. 2020;12(12):1385.

    Article  CAS  PubMed Central  Google Scholar 

  69. Mbonye U, Karn J. The molecular basis for human immunodeficiency virus latency. Annu Rev Virol. 2017;4(1):261–85.

    Article  CAS  PubMed  Google Scholar 

  70. Shukla A, Ramirez NGP, D’Orso I. HIV-1 proviral transcription and latency in the new era. Viruses. 2020;12(5):555.

    Article  CAS  PubMed Central  Google Scholar 

  71. Bacon CW, D’Orso I. CDK9: a signaling hub for transcriptional control. Transcription. 2019;10(2):57.

    Article  CAS  PubMed  Google Scholar 

  72. Lu H, Li Z, Xue Y, Zhou Q. Viral-host interactions that control HIV-1 transcriptional elongation. Chem Rev. 2013;113(11):8567.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Rice AP. The HIV-1 Tat protein: mechanism of action and target for HIV-1 cure strategies. Curr Pharm Des. 2017;23(28):4098.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Günthard HF, Havlir DV, Fiscus S, Zhang ZQ, Eron J, Mellors J, et al. Residual human immunodeficiency virus (HIV) Type 1 RNA and DNA in Lymph Nodes and HIV RNA in genital secretions and in cerebrospinal fluid after suppression of viremia for 2 years. J Infect Dis. 2001;183(9):1318–27.

    Article  PubMed  Google Scholar 

  75. Ishizaka A, Sato H, Nakamura H, Koga M, Kikuchi T, Hosoya N, et al. Short intracellular HIV-1 transcripts as biomarkers of residual immune activation in patients on antiretroviral therapy. J Virol. 2016;90(12):5665.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Dornadula G, Zhang H, VanUitert B, Stern J, Livornese L, Ingerman MJ, et al. Residual HIV-1 RNA in blood plasma of patients taking suppressive highly active antiretroviral therapy. JAMA. 1999;282(17):1627–32.

    Article  CAS  PubMed  Google Scholar 

  77. Fischer M, Huldrych F, Günthard HF, Opravil M, Joos B, Huber W, et al. Residual HIV-RNA levels persist for up to 2.5 years in peripheral blood mononuclear cells of patients on potent antiretroviral therapy. 2004;16(12):1135–40. https://doi.org/10.1089/088922200414974. https://home.liebertpub.com/aid. Accessed 21 Feb 2022.

  78. Wiegand A, Spindler J, Hong FF, Shaoc W, Cyktor JC, Cillo AR, et al. Single-cell analysis of HIV-1 transcriptional activity reveals expression of proviruses in expanded clones during ART. Proc Natl Acad Sci USA. 2017;114(18):E3659–68. https://doi.org/10.1073/pnas.1617961114.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Sertznig H, Hillebrand F, Erkelenz S, Schaal H, Widera M. Behind the scenes of HIV-1 replication: alternative splicing as the dependency factor on the quiet. Virology. 2018;516:176–88.

    Article  CAS  PubMed  Google Scholar 

  80. Mancarella A, Procopio FA, Achsel T, De Crignis E, Foley BT, Corradin G, et al. Detection of antisense protein (ASP) RNA transcripts in individuals infected with human immunodeficiency virus type 1 (HIV-1). J Gen Virol. 2019;100(5):863–76.

    Article  CAS  PubMed  Google Scholar 

  81. Landry S, Halin M, Lefort S, Audet B, Vaquero C, Mesnard JM, et al. Detection, characterization and regulation of antisense transcripts in HIV-1. Retrovirology. 2007;4(1):1–16. https://doi.org/10.1186/1742-4690-4-71.

    Article  CAS  Google Scholar 

  82. Cassana E, Arigon-Chifolleaua AM, Mesnard JM, Gross A, Gascuel O. Concomitant emergence of the AntiSense Protein gene of HIV-1 and of the pandemic. Proc Natl Acad Sci USA. 2016;113(41):11537–42.

    Article  Google Scholar 

  83. Peng BJ, Carlson JM, Liu MKP, Gao F, Goonetilleke N, McMichael AJ, et al. Antisense-derived HIV-1 cryptic epitopes are not major drivers of viral evolution during the acute phase of infection. J Virol. 2018. https://doi.org/10.1128/JVI.00711-18.

    Article  PubMed  PubMed Central  Google Scholar 

  84. Lochelt M, Muranyi W, Flugel RM. Human foamy virus genome possesses an internal, Bel-1-dependent and functional promoter. Proc Natl Acad Sci USA. 1993;90:7317–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Löchelt M, Flügel RM, Aboud M. The human foamy virus internal promoter directs the expression of the functional Bel 1 transactivator and Bet protein early after infection. J Virol. 1994;68:638–45.

    Article  PubMed  PubMed Central  Google Scholar 

  86. Arrigo S, Yun M, Beemon K. cis-acting regulatory elements within gag genes of avian retroviruses. Mol Cell Biol. 1987;7:388–97.

    CAS  PubMed  PubMed Central  Google Scholar 

  87. Verdin E, Becker N, Bex F, Droogmans L, Burny A. Identification and characterization of an enhancer in the coding region of the genome of human immunodeficiency virus type 1. Proc Natl Acad Sci USA. 1990;87:4874–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Van Lint C, Ghysdael J, Paras P Jr, Burny A, Verdin E. A transcriptional regulatory element is associated with a nuclease-hypersensitive site in the pol gene of human immunodeficiency virus type 1. J Virol. 1994;68(4):2632.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Cochrane AW, Jones KS, Beidas S, Dillon PJ, Skalka AM, Rosen CA. Identification and characterization of intragenic sequences which repress human immunodeficiency virus structural gene expression. J Virol. 1991;65(10):5305.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Olsen HS, Cochrane AW, Rosen C. Interaction of cellular factors with intragenic Cis-acting repressive sequences within the HIV genome. Virology. 1992;191(2):709–15.

    Article  CAS  PubMed  Google Scholar 

  91. Amendt BA, Hesslein D, Chang L-J, Stoltzfus CM. Presence of negative and positive cis-acting RNA splicing elements within and flanking the first tat coding exon of human immunodeficiency virus type 1. Mol Cell Biol. 1994;14(6):3960–70. https://doi.org/10.1128/mcb.14.6.3960-3970.1994.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Verdin E. DNase I-hypersensitive sites are associated with both long terminal repeats and with the intragenic enhancer of integrated human immunodeficiency virus type 1. J Virol. 1991;65(12):6790.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Kint S, Trypsteen W, De Spiegelaere W, Malatinkova E, Kinloch-De Loes S, De Meyer T, et al. Underestimated effect of intragenic HIV-1 DNA methylation on viral transcription in infected individuals. Clin Epigenet. 2020;12(1):1–11. https://doi.org/10.1186/s13148-020-00829-1.

    Article  CAS  Google Scholar 

  94. Verdin E, Becker N, Bex F, Droogmans L, Burny A. Identification and characterization of an enhancer in the coding region of the genome of human immunodeficiency virus type 1. Proc Natl Acad Sci USA. 1990;87(12):4874.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Kuniholm J, Armstrong E, Bernabe B, Coote C, Berenson A, Patalano SD, Olson A, et al. Intragenic proviral elements support transcription of defective HIV-1 proviruses. PLoS Pathog. 2021;17(12):e1009982. https://doi.org/10.1371/journal.ppat.1009982.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Champiat S, Raposo RAS, Maness NJ, Lehman JL, Purtell SE, Hasenkrug AM, et al. Influence of HAART on alternative reading frame immune responses over the course of HIV-1 infection. PLoS ONE. 2012;7(6):e39311.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Cardinaud S, Moris A, Février M, Rohrlich PS, Weiss L, Langlade-Demoyen P, et al. Identification of cryptic MHC I-restricted epitopes encoded by HIV-1 alternative reading frames. J Exp Med. 2004;199(8):1053–63.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Imamichi H, Smith M, Adelsberger JW, Izumi T, Scrimieri F, Sherman BT, et al. Defective HIV-1 proviruses produce viral proteins. Proc Natl Acad Sci USA. 2020;117(7):3704.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Affram Y, Zapata JC, Gholizadeh Z, Tolbert WD, Zhou W, Iglesias-Ussel MD, et al. The HIV-1 antisense protein ASP is a transmembrane protein of the cell surface and an integral protein of the viral envelope. J Virol. 2019;93(21):e00574-19. https://doi.org/10.1128/JVI.00574-19.

    Article  PubMed  PubMed Central  Google Scholar 

  100. Wang T, Green LA, Gupta SK, Amet T, Byrd DJ, Yu Q, et al. Intracellular Nef detected in peripheral blood mononuclear cells from HIV patients. AIDS Res Hum Retrovir. 2015;31(2):217.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Baxter AE, Niessl J, Fromentin R, Richard J, Porichis F, Charlebois R, et al. Single-cell characterization of viral translation-competent reservoirs in HIV-infected individuals. Cell Host Microbe. 2016;20(3):368–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Pardons M, Baxter AE, Massanella M, Pagliuzza A, Fromentin R, Dufour C, et al. Single-cell characterization and quantification of translation-competent viral reservoirs in treated and untreated HIV infection. PLoS Pathog. 2019;15(2):e1007619.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Schubert U, Antón LC, Gibbs J, Norbury CC, Yewdell JW, Bennink JR. Rapid degradation of a large fraction of newly synthesized proteins by proteasomes. Nature. 2000;404(6779):770–4.

    Article  CAS  PubMed  Google Scholar 

  104. Vanhée-Brossollet C, Thoreau H, Serpente N, D’Auriol L, Lévy JP, Vaquero C. A natural antisense RNA derived from the HIV-1 env gene encodes a protein which is recognized by circulating antibodies of HIV+ individuals. Virology. 1995;206(1):196–202.

    Article  PubMed  Google Scholar 

  105. Bansal A, Mann T, Sterrett S, Peng BJ, Bet A, Carlson JM, et al. Enhanced recognition of HIV-1 cryptic epitopes restricted by HLA-Class I alleles associated with a favorable clinical outcome. J Acquir Immune Defic Syndr. 2015;70(1):1.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Jiang C, Lian X, Gao C, Sun X, Einkauf KB, Chevalier JM, et al. Distinct viral reservoirs in individuals with spontaneous control of HIV-1. Nature. 2020;585(7824):261–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Huang SH, Ren Y, Thomas AS, Chan D, Mueller S, Ward AR, et al. Latent HIV reservoirs exhibit inherent resistance to elimination by CD8+ T cells. J Clin Invest. 2018;128(2):876–89.

    Article  PubMed  PubMed Central  Google Scholar 

  108. Bansal A, Carlson J, Yan J, Akinsiku OT, Schaefer M, Sabbaj S, et al. CD8 T cell response and evolutionary pressure to HIV-1 cryptic epitopes derived from antisense transcription. J Exp Med. 2010;207(1):51–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Berger CT, Llano A, Carlson JM, Brumme ZL, Brockman MA, Cedeño S, et al. Immune screening identifies novel T cell targets encoded by antisense reading frames of HIV-1. J Virol. 2015;89(7):4015–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Hoffmann M, Pantazis N, Martin GE, Hickling S, Hurst J, Meyerowitz J, et al. Exhaustion of activated CD8 T cells predicts disease progression in primary HIV-1 infection. PLoS Pathog. 2016;12(7):e1005661.

    Article  PubMed  PubMed Central  Google Scholar 

  111. Kostense S, Vandenberghe K, Joling J, Van Baarle D, Nanlohy N, Manting E, et al. Persistent numbers of tetramer+ CD8+ T cells, but loss of interferon-γ+ HIV-specific T cells during progression to AIDS. Blood. 2002;99(7):2505–11. https://ashpublications.org/blood/article/99/7/2505/106719/Persistent-numbers-of-tetramer-CD8-T-cells-but. Accessed 31 Jan 2022.

  112. Tauriainen J, Scharf L, Frederiksen J, Naji A, Ljunggren HG, Sönnerborg A, et al. Perturbed CD8+ T cell TIGIT/CD226/PVR axis despite early initiation of antiretroviral treatment in HIV infected individuals. Sci Rep. 2017;7(1):1–14.

    Article  Google Scholar 

  113. Sakhdari A, Mujib S, Vali B, Yue FY, MacParland S, Clayton K, et al. Tim-3 negatively regulates cytotoxicity in exhausted CD8+ T cells in HIV infection. PLoS ONE. 2012;7(7):e40146.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Appay V, Nixon DF, Donahoe SM, Gillespie GMA, Dong T, King A, et al. HIV-specific Cd8+ T cells produce antiviral cytokines but are impaired in cytolytic function. J Exp Med. 2000;192(1):63–76.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Day CL, Kaufmann DE, Kiepiela P, Brown JA, Moodley ES, Reddy S, et al. PD-1 expression on HIV-specific T cells is associated with T-cell exhaustion and disease progression. Nature. 2006;443(7109):350–4.

    Article  CAS  PubMed  Google Scholar 

  116. Trautmann L, Mbitikon-Kobo FM, Goulet JP, Peretz Y, Shi Y, Van Grevenynghe J, et al. Profound metabolic, functional, and cytolytic differences characterize HIV-specific CD8 T cells in primary and chronic HIV infection. Blood. 2012;120(17):3466–77. https://ashpublications.org/blood/article/120/17/3466/30612/Profound-metabolic-functional-and-cytolytic. Accessed 8 Feb 2022.

  117. Lichterfeld M, Kaufmann DE, Yu XG, Mui SK, Addo MM, Johnston MN, et al. Loss of HIV-1-specific CD8+ T cell proliferation after acute HIV-1 infection and restoration by vaccine-induced HIV-1-specific CD4+ T cells. J Exp Med. 2004;200(6):701–12. https://doi.org/10.1084/jem.20041270.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Aubert RD, Kamphorst AO, Sarkar S, Vezys V, Ha SJ, Barber DL, et al. Antigen-specific CD4 T-cell help rescues exhausted CD8 T cells during chronic viral infection. Proc Natl Acad Sci USA. 2011;108(52):21182–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Cardinaud S, Consiglieri G, Bouziat R, Urrutia A, Graff-Dubois S, Fourati S, et al. CTL escape mediated by proteasomal destruction of an HIV-1 cryptic epitope. PLOS Pathog. 2011;7(5):e1002049. https://doi.org/10.1371/journal.ppat.1002049.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Zicari S, Sessa L, Cotugno N, Ruggiero A, Morrocchi E, Concato C, et al. Immune activation, inflammation, and non-AIDS co-morbidities in HIV-infected patients under long-term ART. Viruses. 2019;11:200.

    Article  CAS  PubMed Central  Google Scholar 

  121. Paisible AL, Chang CCH, So-Armah KA, Butt AA, Leaf DA, Budoff M, et al. HIV infection, cardiovascular disease risk factor profile, and risk for acute myocardial infarction. J Acquir Immune Defic Syndr. 2015;68(2):209–16.

    Article  PubMed  Google Scholar 

  122. Višković K, Židovec Lepej S, Gorenec A, Grgić I, Lukas D, Zekan Š, et al. Cardiovascular markers of inflammation and serum lipid levels in HIV-infected patients with undetectable viremia. Sci Rep. 2018;8(1):1–8.

    Article  Google Scholar 

  123. Deeks SG, Tracy R, Douek DC. Systemic effects of inflammation on health during chronic HIV infection. Immunity. 2013;39(4):633.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Simioni S, Cavassini M, Annoni JM, Rimbault Abraham A, Bourquin I, Schiffer V, et al. Cognitive dysfunction in HIV patients despite long-standing suppression of viremia. AIDS. 2010;24(9):1243–50.

    Article  PubMed  Google Scholar 

  125. Babu H, Ambikan AT, Gabriel EE, Akusjärvi SS, Palaniappan AN, Sundaraj V, et al. Systemic inflammation and the increased risk of inflamm-aging and age-associated diseases in people living with HIV on long term suppressive antiretroviral therapy. Front Immunol. 2019;10(1):1965.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Schank M, Zhao J, Moorman JP, Yao ZQ. The impact of HIV- and ART-induced mitochondrial dysfunction in cellular senescence and aging. Cells. 2021;10(1):174.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Sankaran S, George MD, Reay E, Guadalupe M, Flamm J, Prindiville T, et al. Rapid onset of intestinal epithelial barrier dysfunction in primary human immunodeficiency virus infection is driven by an imbalance between immune response and mucosal repair and regeneration. J Virol. 2008;82(1):538–45. https://doi.org/10.1128/JVI.01449-07.

    Article  CAS  PubMed  Google Scholar 

  128. Gross AM, Jaeger PA, Kreisberg JF, Licon K, Jepsen KL, Khosroheidari M, et al. Methylome-wide analysis of chronic HIV infection reveals five-year increase in biological age and epigenetic targeting of HLA. Mol Cell. 2016;62(2):157.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  129. Horvath S, Levine AJ. HIV-1 infection accelerates age according to the epigenetic clock. J Infect Dis. 2015;212(10):1563–73.

    Article  PubMed  PubMed Central  Google Scholar 

  130. Levine AJ, Quach A, Moore DJ, Achim CL, Soontornniyomkij V, Masliah E, et al. Accelerated epigenetic aging in brain is associated with pre-mortem HIV-associated neurocognitive disorders. J Neurovirol. 2016;22(3):366.

    Article  CAS  PubMed  Google Scholar 

  131. Titanji BK, Gwinn M, Marconi VC, Sun YV. Epigenome-wide epidemiologic studies of human immunodeficiency virus infection, treatment, and disease progression. Clin Epigenet. 2022;14(1):1–16. https://doi.org/10.1186/s13148-022-01230-w.

    Article  Google Scholar 

  132. Olson A, Coote C, Snyder-Cappione JE, Lin N, Sagar M. HIV-1 transcription but not intact provirus levels are associated with systemic inflammation. J Infect Dis. 2021;223(11):1934–42.

    Article  CAS  PubMed  Google Scholar 

  133. Berg RK, Melchjorsen J, Rintahaka J, Diget E, Søby S, Horan KA, et al. Genomic HIV RNA induces innate immune responses through RIG-I-dependent sensing of secondary-structured RNA. PLoS ONE. 2012;7(1):e29291.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Akiyama H, Jalloh S, Park S, Lei M, Mostoslavsky G, Gummuluru S. Expression of HIV-1 intron-containing RNA in microglia induces inflammatory responses. J Virol. 2020;95(5):e01386-20. https://doi.org/10.1128/JVI.01386-20.

    Article  Google Scholar 

  135. Akiyama H, Miller CM, Ettinger CR, Belkina AC, Snyder-Cappione JE, Gummuluru S. HIV-1 intron-containing RNA expression induces innate immune activation and T cell dysfunction. Nat Commun. 2018;9(1):1–12.

    Article  CAS  Google Scholar 

  136. Kennedy EM, Bogerd HP, Kornepati AVR, Kang D, Ghoshal D, Marshall JB, et al. Post-transcriptional m6A editing of HIV-1 mRNAs enhances viral gene expression. Cell Host Microbe. 2016;19(5):675.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  137. Nasr N, Alshehri AA, Wright TK, Shahid M, Heiner BM, Harman AN, et al. Mechanism of interferon-stimulated gene induction in HIV-1-infected macrophages. J Virol. 2017;91(20):744–61. https://doi.org/10.1128/JVI.00744-17.

    Article  Google Scholar 

  138. Meås HZ, Haug M, Beckwith MS, Louet C, Ryan L, Hu Z, et al. Sensing of HIV-1 by TLR8 activates human T cells and reverses latency. Nat Commun. 2020;11(1):1–16.

    Article  Google Scholar 

  139. Iwasaki A. Innate immune recognition of HIV-1. Immunity. 2012;37:389–98.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. Sauter D, Kirchhoff F. HIV replication: a game of hide and sense. Curr Opin HIV AIDS. 2016;11(2):173–81.

    Article  CAS  PubMed  Google Scholar 

  141. Schlee M, Hartmann G. Discriminating self from non-self in nucleic acid sensing. Nat Rev Immunol. 2016;16(9):566–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  142. Rodari A, Darcis G, Van Lint CM. The current status of latency reversing agents for HIV-1 remission. Annu Rev Virol. 2021;8(1):491–514.

    Article  PubMed  Google Scholar 

  143. Moranguinho I, Valente ST. Block-and-lock: new horizons for a cure for HIV-1. Viruses. 2020;12(12):1443.

    Article  CAS  PubMed Central  Google Scholar 

  144. Atkins AJ, Allen AG, Dampier W, Haddad EK, Nonnemacher MR, Wigdahl B. HIV-1 cure strategies: why CRISPR? Expert Opin Biol Ther. 2021;21(6):781–93.

    Article  CAS  PubMed  Google Scholar 

  145. Darcis G, Das AT, Berkhout B. Tackling HIV persistence: pharmacological versus CRISPR-based shock strategies. Viruses. 2018;10(4):157.

    Article  PubMed Central  Google Scholar 

  146. Jerome KR. Disruption or excision of provirus as an approach to HIV Cure. AIDS Patient Care STDS. 2016;30(12):551–5.

    Article  PubMed  PubMed Central  Google Scholar 

  147. Shrivastava S, Ray RM, Holguin L, Echavarria L, Grepo N, Scott TA, et al. Exosome-mediated stable epigenetic repression of HIV-1. Nat Commun. 2021;12(1):5541.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  148. Spivak AM, Planelles V. Novel latency reversing agents for HIV-1 cure. http://www.unaids.org/en/. Accessed 21 Jan 2020.

  149. Liu H, Hu PW, Dubrulle J, Stossi F, Nikolai BC, Mancini MA, et al. Identification of celastrol as a novel HIV-1 latency reversal agent by an image-based screen. PLoS ONE. 2021;16(4):e0244771. https://doi.org/10.1371/journal.pone.0244771.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Ebina H, Misawa N, Kanemura Y, Koyanagi Y. Harnessing the CRISPR/Cas9 system to disrupt latent HIV-1 provirus. Sci Rep. 2013;3(1):1–7.

    Article  Google Scholar 

  151. Pache L, Marsden MD, Teriete P, Portillo AJ, Heimann D, Kim JT, et al. Pharmacological activation of non-canonical NF-κB signaling activates latent HIV-1 reservoirs in vivo. Cell Rep Med. 2020;1(3):100037.

    Article  PubMed  PubMed Central  Google Scholar 

  152. Pache L, Dutra MS, Spivak AM, Marlett JM, Murry JP, Hwang Y, et al. BIRC2/cIAP1 is a negative regulator of HIV-1 transcription and can be targeted by Smac mimetics to promote reversal of viral latency. Cell Host Microbe. 2015;18(3):345–53.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Olson A, Basukala B, Lee S, Gagne M, Wong WW, Henderson AJ. Targeted chromatinization and repression of HIV-1 provirus transcription with repurposed CRISPR/Cas9. Viruses. 2020;12(10):1154.

    Article  CAS  PubMed Central  Google Scholar 

  154. Mediouni S, Chinthalapudi K, Ekka MK, Usui I, Jablonski JA, Clementz MA, et al. Didehydro-cortistatin a inhibits HIV-1 by specifically binding to the unstructured basic region of tat. MBio. 2019;10(1):1–19. https://doi.org/10.1128/mBio.02662-18.

    Article  Google Scholar 

  155. Kessing CF, Nixon CC, Li C, Tsai P, Takata H, Mousseau G, et al. In vivo suppression of HIV rebound by didehydro-Cortistatin A, a “block-and-lock” strategy for HIV-1 cure. Cell Rep. 2017;21(3):600.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. Hu W, Kaminski R, Yang F, Zhang Y, Cosentino L, Li F, et al. RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection. Proc Natl Acad Sci. 2014;111(31):11461–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  157. Kaminski R, Bella R, Yin C, Otte J, Ferrante P, Gendelman HE, et al. Excision of HIV-1 DNA by gene editing: a proof-of-concept in vivo study. Gene Ther. 2016;23(8):690–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  158. Dash PK, Kaminski R, Bella R, Su H, Mathews S, Ahooyi TM, et al. Sequential LASER ART and CRISPR treatments eliminate HIV-1 in a subset of infected humanized mice. Nat Commun. 2019;10(1):1–20.

    Article  CAS  Google Scholar 

  159. Wang G, Zhao N, Berkhout B, Das AT. CRISPR-Cas9 can inhibit HIV-1 replication but NHEJ repair facilitates virus escape. Mol Ther. 2016;24(3):522–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  160. Lai M, Maori E, Quaranta P, Matteoli G, Maggi F, Sgarbanti M, et al. CRISPR/Cas9 ablation of integrated HIV-1 accumulates proviral DNA circles with reformed long terminal repeats. J Virol. 2021;95(23):e01358-21. https://doi.org/10.1128/JVI.01358-21.

    Article  PubMed Central  Google Scholar 

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Acknowledgements

We thank members of the Henderson laboratory, Binita Basukala, Jonathan Kilroy, Alex Olsen for discussions and critical feedback.

Funding

This work was in part funded by NIH grants including R01 AI138960, R01 DA1055488 and R61/R33 DA047032 to AJH. J.K. was supported by the Immunology Training Program (NIAID T32 AI007309-31). We also received support from the Providence/Boston CFAR, P30 AI042853.

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  1. Department of Microbiology, Section of Infectious Diseases, Boston University School of Medicine, Boston, MA, 02116, USA

    Jeffrey Kuniholm & Andrew J. Henderson

  2. Department of Medicine, Section of Infectious Diseases, Boston University School of Medicine, Boston, MA, 02116, USA

    Carolyn Coote & Andrew J. Henderson

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  1. Jeffrey Kuniholm
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The manuscript was conceived and written by JK and AJH. CC wrote sections and provided editorial and intellectual feedback. All authors read and approved the final manuscript.

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Correspondence to Andrew J. Henderson.

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Kuniholm, J., Coote, C. & Henderson, A.J. Defective HIV-1 genomes and their potential impact on HIV pathogenesis. Retrovirology 19, 13 (2022). https://doi.org/10.1186/s12977-022-00601-8

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Keywords

Retrovirology

ISSN: 1742-4690

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