More than four decades after the first cases of AIDS were identified, HIV remains one of humanity's most formidable viral adversaries. Antiretroviral therapy (ART) has transformed HIV from a death sentence into a manageable chronic condition, but it is not a cure. The virus hides inside the very cells that are meant to protect us, weaving its genetic code into our DNA and waiting. For the roughly 39 million people living with HIV worldwide, that means a lifetime of daily medication, ongoing side effects, persistent stigma, and the ever-present risk that the virus could rebound if treatment is interrupted.
Now, gene editing technologies — most prominently CRISPR-Cas9 — are opening a fundamentally different path. Instead of suppressing the virus, researchers are asking: what if we could cut HIV's DNA out of infected cells entirely? And what if we could make human immune cells resistant to infection in the first place? These are not hypothetical questions. Clinical trials are underway, and the results so far suggest that a true, functional cure for HIV may be within reach.
How HIV Hides: The Problem of the Provirus
To understand why HIV is so difficult to cure, you need to understand how it operates at the molecular level.
HIV is a retrovirus, a class of viruses that carries its genetic information as RNA rather than DNA. When HIV infects a CD4+ T cell — a critical component of the human immune system — it uses an enzyme called reverse transcriptase to convert its RNA genome into double-stranded DNA. Another viral enzyme, integrase, then stitches this DNA copy directly into the host cell's chromosomes. This integrated viral DNA is called a provirus.
Once the provirus is embedded in the host genome, it becomes essentially indistinguishable from the cell's own genetic material. The cell's own machinery reads it, copies it, and passes it on to daughter cells when the cell divides. In some cells, particularly long-lived memory CD4+ T cells, the provirus can remain silent for years or even decades. These cells form what researchers call the latent reservoir — a hidden cache of HIV-infected cells that are invisible to the immune system and untouched by antiretroviral drugs.
This is the crux of the problem. ART works by blocking various stages of the viral life cycle: entry, reverse transcription, integration, and the production of new viral particles. It is remarkably effective at preventing active viral replication, driving viral loads in the blood down to undetectable levels. But ART cannot reach proviral DNA that is already integrated into the genome of resting cells. If a patient stops taking antiretrovirals, the latent reservoir reactivates, and the virus rebounds — typically within weeks.
The latent reservoir is estimated to contain between one and sixty million cells carrying replication-competent proviral DNA. It is established within the first days of infection and has a half-life estimated at 44 months, meaning that even with perfect ART adherence, it would take more than 70 years for the reservoir to decay naturally. In practical terms, ART alone cannot cure HIV.
Antiretrovirals: A Triumph That Falls Short
The development of combination antiretroviral therapy in the mid-1990s was one of the great achievements of modern medicine. Before ART, an HIV diagnosis was effectively a terminal one. Today, people who begin treatment early and adhere to their regimen can expect a near-normal lifespan.
Modern ART regimens typically combine two or three drugs from different classes, targeting multiple steps in the viral life cycle simultaneously. This multi-drug approach prevents the virus from developing resistance to any single agent. Current regimens are simpler than ever — many patients take a single pill once daily — and side effects have been substantially reduced compared to earlier-generation drugs. Long-acting injectable formulations, administered every one to two months, have further improved convenience.
Yet ART has significant limitations:
- Lifelong commitment: Treatment must continue indefinitely. Missing doses can allow the virus to rebound and potentially develop drug resistance.
- Chronic side effects: Even modern ART is associated with increased risks of cardiovascular disease, kidney dysfunction, bone density loss, and metabolic complications over decades of use.
- Cost and access: While generic antiretrovirals have dramatically reduced costs in low-income countries, treatment still requires functioning healthcare infrastructure, regular monitoring, and sustained supply chains. Globally, roughly 14% of people living with HIV still lack access to treatment.
- Stigma and psychological burden: The requirement for daily medication serves as a constant reminder of HIV status, and the need for ongoing medical appointments can create disclosure challenges and psychological strain.
- The reservoir persists: Most critically, ART does not eliminate the latent reservoir. The virus remains embedded in the genome, waiting.
For all these reasons, the search for a true cure — one that either eliminates HIV from the body or permanently controls it without ongoing medication — has remained a central goal of HIV research.
The Berlin and London Patients: Proof That a Cure Is Possible
The most compelling evidence that HIV can be cured comes from two extraordinary cases that share a common thread: the CCR5 gene.
CCR5 (C-C chemokine receptor type 5) is a protein found on the surface of CD4+ T cells and other immune cells. It serves as a co-receptor that most strains of HIV use to enter and infect cells. Think of it as a door handle — without CCR5, the most common strains of HIV (called R5-tropic viruses) cannot get in.
A naturally occurring mutation called CCR5-delta32 produces a truncated, nonfunctional version of the CCR5 protein. People who inherit two copies of this mutation (one from each parent) are largely resistant to R5-tropic HIV infection. This mutation is found in approximately 1% of people of Northern European descent, likely selected for by historical plague epidemics, and is essentially absent in most other populations.
Timothy Ray Brown — The Berlin Patient. In 2007, Timothy Ray Brown, an American living in Berlin, was HIV-positive and being treated with ART when he developed acute myeloid leukemia. His oncologist, Dr. Gero Hutter, made a bold decision: to treat the leukemia with a bone marrow transplant from a donor who was homozygous for the CCR5-delta32 mutation. The idea was to simultaneously treat the cancer and replace Brown's immune system with HIV-resistant cells.
The procedure was brutal. Brown underwent total body irradiation and two separate transplants after his leukemia relapsed. But when he recovered, something remarkable had happened: HIV was undetectable in his body, even without antiretroviral therapy. Brown remained HIV-free for the rest of his life until his death from leukemia recurrence in 2020. He was the first person ever confirmed to be cured of HIV.
Adam Castillejo — The London Patient. In 2019, a second case was reported. Adam Castillejo, who had been living with HIV since 2003, also developed a blood cancer (Hodgkin lymphoma) and received a bone marrow transplant from a CCR5-delta32 homozygous donor. Like Brown, he achieved sustained HIV remission off ART. By 2020, his case was confirmed as a cure, and he went public with his identity to give hope to others.
Several additional cases have since been reported, including the Dusseldorf patient, the New York patient (who received CCR5-delta32 cord blood stem cells), and the City of Hope patient. Each reinforces the same conclusion: replacing the immune system with CCR5-negative cells can lead to HIV cure.
However, bone marrow transplantation is not a scalable cure strategy. The procedure carries a mortality risk of 10-20%, requires a matched donor with the rare CCR5-delta32 mutation, and involves intensive chemotherapy conditioning. It is only justified when the patient also has a life-threatening blood cancer. For the tens of millions of people living with HIV who are otherwise healthy, this approach is not an option.
The question became: could gene editing replicate the biology of the Berlin and London patients without the danger of a transplant?
CRISPR Approaches to Curing HIV
Gene editing technologies offer two fundamentally different strategies for curing HIV, and researchers are pursuing both.
Strategy 1: CCR5 Knockout — Making Cells Resistant
The first strategy draws directly from the lesson of the Berlin and London patients. If cells without functional CCR5 are resistant to HIV, why not use gene editing to disable CCR5 in a patient's own cells?
The approach works like this: CD4+ T cells or hematopoietic stem cells are collected from an HIV-positive patient. In the laboratory, CRISPR-Cas9 (or another gene editing tool) is used to disrupt the CCR5 gene, mimicking the natural CCR5-delta32 mutation. The edited cells are then infused back into the patient. Over time, these HIV-resistant cells would have a survival advantage over unedited cells, because the virus would selectively destroy unedited CD4+ T cells while leaving the CCR5-knockout cells intact. Gradually, the edited cells would come to dominate the immune system.
This approach has several attractive features. It does not require identifying and targeting every last cell in the latent reservoir. Even if some HIV remains, it would have nowhere to go — the new immune cells would be resistant to infection. It is conceptually simple and builds on proven biology.
But there are also significant challenges. Editing hematopoietic stem cells ex vivo requires the same kind of myeloablative conditioning (chemotherapy to destroy the existing bone marrow) used in transplants, which carries serious risks. Editing only circulating T cells avoids this problem but provides only temporary protection, since T cells have a limited lifespan and are not self-renewing.
Additionally, some HIV strains use a different co-receptor called CXCR4 instead of CCR5. Knocking out CCR5 alone would not protect against these X4-tropic viruses, which tend to emerge in later stages of HIV infection. A patient cured of R5-tropic HIV could potentially still be vulnerable to X4-tropic strains.
Strategy 2: Proviral DNA Excision — Cutting HIV Out
The second strategy is more ambitious and, if successful, more definitive: using CRISPR to directly excise the proviral HIV DNA from the genomes of infected cells. Rather than making new cells resistant, this approach aims to eliminate the virus from cells where it has already taken up residence.
This is the approach championed by Excision BioTherapeutics, whose lead candidate, EBT-101, represents the most advanced clinical program of its kind.
The concept was pioneered by Dr. Kamel Khalili and his team at Temple University. They designed a CRISPR-based system that uses two guide RNAs simultaneously: one targeting the 5' long terminal repeat (LTR) of the HIV provirus and the other targeting the 3' LTR. The LTRs are repetitive sequences that flank the integrated viral genome and are essential for viral gene expression and replication. By cutting at both LTRs simultaneously, the entire proviral DNA sequence between them — roughly 9,700 base pairs — is excised from the host chromosome. The cell's DNA repair machinery then joins the loose ends, effectively removing HIV from that cell's genome permanently.
This dual-guide RNA approach is critical. If only one cut were made, the virus might still be able to function or could be repaired by the cell. Two simultaneous cuts ensure that the entire proviral sequence is physically removed and cannot be reconstituted.
In preclinical studies, this approach successfully eliminated HIV proviral DNA from humanized mice and from non-human primate models infected with SIV (simian immunodeficiency virus, the primate equivalent of HIV). The results were striking: in some animals, no replication-competent virus could be detected after treatment, even in tissues known to harbor latent reservoirs.
Excision BioTherapeutics and EBT-101
Excision BioTherapeutics, founded in 2015 and headquartered in San Francisco, was created specifically to translate Dr. Khalili's work into a clinical therapy. The company's lead product, EBT-101, is the first CRISPR-based gene editing therapy designed to cure HIV to enter human clinical trials.
EBT-101 is delivered using an adeno-associated virus (AAV) vector — specifically AAV9, which has the ability to cross the blood-brain barrier and reach tissues throughout the body, including the central nervous system, lymph nodes, gut-associated lymphoid tissue, and other sites where latent HIV reservoirs are known to hide. This is a crucial advantage over ex vivo approaches, which only edit cells that have been removed from the body.
The therapy is designed as a single intravenous infusion. Once administered, the AAV9 vector delivers the CRISPR-Cas9 machinery and the two guide RNAs to cells throughout the body. In HIV-infected cells, the system identifies the proviral LTR sequences and excises the integrated viral DNA.
The Phase 1/2 Clinical Trial
In 2022, Excision launched a Phase 1/2 clinical trial (ClinicalTrials.gov identifier NCT05144386) to evaluate the safety and efficacy of EBT-101 in people living with HIV who are virally suppressed on ART. The trial, conducted at several sites in the United States, enrolled adults who had been on stable ART for at least two years with consistently undetectable viral loads.
The trial uses a dose-escalation design, starting with low doses to establish safety before moving to higher, potentially more efficacious doses. The primary endpoints focus on safety and tolerability, with secondary endpoints examining changes in the size of the latent HIV reservoir and the potential for ART interruption.
Early results, presented at scientific conferences, have been cautiously encouraging. The treatment appeared to be well-tolerated at the initial dose levels, with no serious adverse events attributed to the therapy. Importantly, there were signals suggesting reduction in proviral DNA levels in some participants, though the data remain preliminary and the trial is ongoing.
The most meaningful test will come when participants undergo an analytical treatment interruption (ATI) — a carefully monitored pause in ART to see whether the virus rebounds. If EBT-101 has successfully eliminated enough of the latent reservoir, viral load should remain undetectable even without antiretroviral drugs. This would represent a functional cure.
Challenges and Open Questions
Despite the promise, EBT-101 and the proviral excision approach face substantial challenges:
Reaching all latent cells. The latent reservoir is scattered across many tissues and cell types throughout the body. The AAV9 vector has broad tissue tropism, but it is unclear whether it can reach every last reservoir cell. Even a tiny number of surviving proviral copies could potentially reignite infection upon ART interruption.
Off-target editing. CRISPR-Cas9 can occasionally cut at genomic sites that resemble but are not identical to the intended target — so-called off-target effects. In the context of HIV treatment, where the therapy is being delivered systemically to billions of cells, even a very low off-target rate could theoretically cause unintended mutations in critical genes. This risk is particularly concerning in hematopoietic and immune cells, where certain off-target mutations could potentially contribute to malignancy. Extensive off-target analysis using whole-genome sequencing and other methods is a major component of the safety evaluation.
Immune response to AAV and Cas9. AAV vectors can trigger immune responses, particularly in people who have pre-existing antibodies to AAV from natural exposure. The Cas9 protein, derived from bacteria, can also provoke an immune reaction. These responses could reduce the therapy's effectiveness or cause adverse effects. Additionally, AAV-mediated delivery typically results in transient expression, which may limit the window during which editing occurs.
HIV sequence diversity. HIV is notorious for its high mutation rate and genetic diversity, both between patients and within a single patient's viral population. The guide RNAs in EBT-101 target conserved regions of the LTRs, but some proviral copies may have mutations in these regions that prevent efficient cutting. Incomplete excision would leave behind the very variants most likely to escape the therapy.
Durability and re-infection. Even if EBT-101 successfully eliminates all proviral DNA, the cured individual would still be susceptible to new HIV infection. Unlike the CCR5 knockout approach, proviral excision does not confer ongoing resistance. Post-cure prevention strategies, including PrEP or behavioral interventions, would need to be part of the long-term plan.
Other Gene Editing Approaches
Excision BioTherapeutics is not the only group pursuing gene editing as an HIV cure strategy. Several other approaches deserve attention.
Sangamo Therapeutics: Zinc Finger Nuclease CCR5 Knockout
Before CRISPR entered the picture, Sangamo Therapeutics was already exploring gene editing for HIV using zinc finger nucleases (ZFNs) — an earlier generation of programmable DNA-cutting enzymes. Sangamo's approach, SB-728, involved editing a patient's own CD4+ T cells ex vivo to disrupt the CCR5 gene, then reinfusing the modified cells.
Phase 1 and Phase 2 clinical trials, some conducted in collaboration with the University of Pennsylvania, showed that the approach was feasible and safe. Edited T cells engrafted successfully, persisted in the body, and showed a survival advantage over unedited cells when ART was interrupted. In some patients, the edited cell population expanded significantly during treatment interruption as unedited cells were depleted by the virus.
However, the results were not sufficient for a functional cure. The proportion of CCR5-edited cells was too low to provide complete protection, and the virus eventually rebounded in most participants when ART was stopped. The trials did, however, provide critical proof-of-concept that gene-edited immune cells could be safely administered to people with HIV and could confer a measurable biological advantage.
Sangamo's work laid important groundwork, but the field has largely shifted toward CRISPR-based approaches, which are more efficient, easier to design, and less expensive to manufacture than zinc finger nucleases.
Base Editing and Prime Editing
Newer gene editing technologies, including base editing and prime editing, offer the potential for more precise modifications without creating double-strand DNA breaks. Base editors can change a single DNA letter (for example, converting a C to a T) without cutting both strands of the DNA helix, which reduces the risk of unwanted insertions, deletions, or chromosomal rearrangements.
Researchers at several institutions are exploring whether base editing could be used to disable CCR5 or to introduce specific mutations that render the proviral DNA nonfunctional. These approaches are still in early preclinical stages for HIV, but they represent a potentially safer alternative to traditional CRISPR-Cas9 cutting.
In Vivo Delivery via Lipid Nanoparticles
One of the major limitations of ex vivo gene editing is that it only modifies cells that can be removed from and returned to the body. For HIV, this means that editing cannot reach the full extent of the latent reservoir across all tissues. Several research groups are developing in vivo delivery systems using lipid nanoparticles (LNPs) — the same technology used in mRNA COVID-19 vaccines — to deliver CRISPR components directly to specific cell types in the body.
The challenge is targeting. LNPs naturally accumulate in the liver, which is not where most latent HIV resides. Engineering LNPs to specifically target CD4+ T cells, macrophages, and other reservoir cells in lymph nodes, the gut, and the central nervous system remains an active area of research. If solved, LNP delivery could provide a redosable, non-viral alternative to AAV vectors.
Ethical Considerations
The application of gene editing to HIV raises several important ethical questions that the field must address as clinical programs advance.
Equity and access. Gene therapies are expensive to develop and manufacture. If a CRISPR-based HIV cure reaches the market, it will almost certainly carry a high price tag initially. The global burden of HIV falls disproportionately on low- and middle-income countries, particularly in sub-Saharan Africa, where roughly two-thirds of all people with HIV live. A cure that is only available to wealthy patients in high-income countries would represent a profound ethical failure. Early planning for equitable global access, including technology transfer, regional manufacturing, and tiered pricing, is essential.
Informed consent and risk communication. Participants in HIV gene editing trials are, by definition, people who are already managing their condition effectively with ART. They are being asked to accept the risks of an experimental therapy — including unknown long-term consequences of gene editing — when they have a safe and effective existing treatment. The informed consent process must be exceptionally thorough, ensuring participants understand both the potential benefits and the uncertainties.
Germline considerations. All current HIV gene editing approaches target somatic cells (body cells that are not passed to offspring), not germline cells (eggs, sperm, or embryos). This is a critical ethical boundary. The infamous 2018 case of He Jiankui, who used CRISPR to edit the CCR5 gene in human embryos, was universally condemned by the scientific community. The resulting children, Lulu and Nana, carry edits whose long-term consequences are unknown. Somatic cell gene editing for HIV does not raise the same concerns, but the field must remain vigilant against any attempts to apply these technologies to the germline.
Long-term monitoring. Gene editing introduces permanent changes to cellular DNA. Unlike a drug that can be discontinued if problems arise, an edit cannot easily be reversed. Long-term follow-up of trial participants — potentially for decades — is necessary to monitor for delayed adverse effects, including the theoretical risk of oncogenesis from off-target editing. Regulatory frameworks and funding mechanisms for such long-term surveillance are still being developed.
The cure imperative and its limits. There is a risk that the pursuit of a gene editing cure could divert attention and resources from proven prevention strategies (PrEP, condoms, harm reduction) and from efforts to expand ART access to the millions who still lack it. A cure is a worthy goal, but it must not come at the expense of the interventions that are saving lives today.
Future Outlook
The convergence of gene editing technology, improved delivery systems, and deepening understanding of HIV biology has created genuine momentum toward a cure. Several developments to watch in the coming years:
EBT-101 data maturation. The most important near-term milestone is the completion of Excision's Phase 1/2 trial and, crucially, the results of analytical treatment interruptions. If even a subset of participants achieves sustained HIV remission off ART, it would represent a landmark proof-of-concept and almost certainly trigger larger, pivotal trials.
Combination approaches. Many researchers believe that the most effective cure strategy will combine multiple modalities: gene editing to reduce the latent reservoir, immune-based therapies (such as broadly neutralizing antibodies or therapeutic vaccines) to control any residual virus, and possibly CCR5 modification to prevent reinfection. These "kick and kill" or "block and lock" strategies, enhanced by gene editing, are being explored in several academic and industry programs.
Next-generation editing tools. As base editing, prime editing, and other precision tools mature, they may offer safer and more efficient alternatives to conventional CRISPR-Cas9 for HIV applications. The ability to make precise modifications without double-strand breaks could substantially reduce off-target risk.
Improved delivery. Advances in LNP engineering, viral vector design, and cell-specific targeting will be critical for reaching the full latent reservoir. The development of CD4+ T cell-targeted LNPs, in particular, could be transformative for the field.
Regulatory pathways. Regulators at the FDA and EMA are actively developing frameworks for evaluating gene editing therapies, informed by the precedent set by Casgevy and other approved gene therapies. Clear and predictable regulatory pathways will be important for encouraging continued investment in HIV cure research.
Global collaboration. Organizations including the International AIDS Society, amfAR, and the NIH-funded Martin Delaney Collaboratories are working to coordinate global HIV cure research, establish shared standards, and ensure that advances benefit patients worldwide. The involvement of researchers and communities in heavily affected regions, particularly in Africa, is essential for both ethical and scientific reasons.
The Bottom Line
For more than 40 years, HIV has exploited one of the most elegant tricks in biology: writing its code into our own genome and hiding there, invisible and untouchable. Antiretroviral therapy blunted the virus's lethality but accepted its persistence. The Berlin and London patients proved that persistence could be broken.
CRISPR gene editing — particularly the proviral excision approach being tested by Excision BioTherapeutics — represents the first technology with the potential to directly erase HIV from the human genome at scale. It is still early. The clinical data are preliminary, the challenges are real, and the path from promising trial to approved cure will be long. But the scientific foundation is solid, the tools are increasingly powerful, and the first human data are accumulating.
We are not yet at the point where a doctor can offer an HIV-positive patient a single infusion and declare them cured. But we may be closer to that moment than at any point in the history of the epidemic. For the 39 million people living with HIV worldwide, and for the communities that have borne the weight of this virus for generations, that possibility matters enormously.
Sources and Further Reading
- Khalili, K., et al. (2017). "CRISPR/Cas9 Elimination of HIV-1 from Infected T Cells and Humanized Mice." Proceedings of the National Academy of Sciences, 114(49), 12967-12972.
- Excision BioTherapeutics. (2023). "EBT-101: A CRISPR-Based Therapeutic for HIV." Company pipeline overview. excisionbio.com
- ClinicalTrials.gov. NCT05144386. "EBT-101 in Aviremic HIV-1 Infected Adults on Stable Antiretroviral Therapy."
- Hutter, G., et al. (2009). "Long-Term Control of HIV by CCR5 Delta32/Delta32 Stem-Cell Transplantation." New England Journal of Medicine, 360(7), 692-698.
- Gupta, R.K., et al. (2019). "HIV-1 Remission Following CCR5-Delta32/Delta32 Haematopoietic Stem-Cell Transplantation." Nature, 568, 244-248.
- Tebas, P., et al. (2014). "Gene Editing of CCR5 in Autologous CD4 T Cells of Persons Infected with HIV." New England Journal of Medicine, 370(10), 901-910.
- UNAIDS. (2025). "Global HIV & AIDS Statistics." unaids.org
- Deeks, S.G., et al. (2021). "Research Priorities for an HIV Cure: International AIDS Society Global Scientific Strategy 2021." Nature Medicine, 27, 2085-2098.
- Mancuso, P., et al. (2020). "CRISPR Based Editing of SIV Proviral DNA in ART Treated Non-Human Primates." Nature Communications, 11, 6065.
- International AIDS Society. (2024). "Towards an HIV Cure: Global Scientific Strategy." iasociety.org
