Using Gene-Editing to Remove HIV from Human Immune Cells and Prevent Reinfection

Human Immunodeficiency Virus (HIV) remains one of the world’s most challenging infectious diseases. Since its discovery, antiretroviral therapy (ART) has transformed HIV from a death sentence into a chronic condition for many. However, ART has limitations: it suppresses viral replication but does not eradicate the virus, latent reservoirs persist, continuous therapy is required, and side effects or drug resistance can emerge. Recent advances in gene-editing technology offer the possibility of completely eliminating HIV genomes integrated into human cells and introducing resistance to reinfection. This article reviews the current state of this research, the promising methods under investigation, the challenges involved, ethical and safety considerations, and future directions.

Background: HIV Persistence and Why It Is Hard to Cure

When HIV infects a person, it not only replicates actively but also integrates its genetic material (proviral DNA) into the host’s genome, especially in CD4⁺ T cells. Some of these cells become latent reservoirs: they carry integrated HIV DNA but do not actively produce virus. These latently infected cells can persist for years even under ART. If ART is stopped, the virus can reactivate from these reservoirs.

Therefore, any cure strategy must both eliminate or inactivate HIV proviral DNA in latently infected cells and prevent new infections (reinfection) of uninfected immune cells.

Gene-Editing Technologies Used Against HIV

Multiple gene-editing approaches are being explored. The most prominent ones include:

CRISPR/Cas9 – Clustered Regularly Interspaced Short Palindromic Repeats with Cas9 nuclease. RNA guide sequences (gRNAs) direct Cas9 to specific DNA sequences to cut. Used both to delete proviral HIV DNA sequences and to disrupt genes in host cells that HIV uses to enter (e.g. CCR5).
Engineered Recombinases – Enzymes modified to recognize particular HIV long terminal repeat (LTR) sequences and excise provirus. Examples include TRE recombinase and develop-ments like Brec1, which target relatively conserved LTR sequences across many HIV strains.
Other nucleases (like ZFNs, TALENs) for editing host genes such as CCR5 and CXCR4. These co-receptors are required for many HIV strains to enter cells. Disabling or mutating them can reduce susceptibility to infection.

Recent Studies: Removing HIV from Immune Cells

Several key studies demonstrate progress:

Elimination of HIV-1 Genomes from Human T-lymphoid Cells (Kaminski et al., 2016): Researchers used CRISPR/Cas9 with guide RNAs targeting the 5′ and 3′ long terminal repeats (LTRs) of integrated HIV‐1 in latently infected human CD4⁺ T cells. They removed the entire proviral sequence between those LTRs. Whole genome sequencing confirmed the excision and showed minimal off-target effects. Furthermore, T cells so edited were resistant to reinfection.
CRISPR/Cas9 Ablation of Integrated HIV-1 Accumulates Mutagenic Damage (Lai et al., 2021): Work showing that applying CRISPR/Cas9 to infected cells can accumulate mutations in HIV proviral DNA, damaging or disabling it.
Editing Host CCR5 Gene (Recent Reviews, 2025): A recent paper focuses on gene editing of CCR5, known from individuals who naturally bear a mutation called CCR5-Δ32, giving resistance to R5-tropic HIV strains. Multiplex strategies (editing CCR5, CXCR4, and HIV LTR sites together) are being considered to block infection more comprehensively.
Emerging Strategies and Reviews: A 2025 review “Breaking Barriers to an HIV-1 Cure” details how CRISPR/Cas9 can excise latent HIV DNA, how combinatorial use of multiple gRNAs enhances efficacy, and ways to reduce off-target effects.

Preventing Reinfection: Editing for Resistance

Eliminating proviral HIV DNA is only part of the solution. Preventing new infections (reinfection) is equally important. Several strategies target host genes or receptors to make immune cells less vulnerable:

CCR5 Editing: CCR5 is a major co-receptor HIV uses to enter CD4⁺ T cells. Persons with homozygous CCR5-Δ32 mutation are largely resistant to R5-tropic HIV. Gene editing technologies (CRISPR, ZFNs) are being used to mimic or introduce CCR5 deletions or disruptions in patient cells.
Multiplex Targeting: Since HIV can switch tropism (i.e. from CCR5 to CXCR4 usage), or use multiple entry co-receptors, editing both CCR5 and CXCR4 is being considered. Also, combining host gene editing with excision of viral DNA strengthens defense.
Combining with Immunotherapy: Gene-edited immune cells (for example, T cells or stem cells with altered CCR5 or other modifications) can be used in adoptive cell therapy. Also, immune-boosting strategies may help clear cells still harboring HIV.

Challenges and Limitations

While the advances are promising, there remain substantial challenges before such approaches can become safe and widely applicable.

Viral Diversity and Escape
HIV mutates rapidly. Many of the gene-editing tools (guide RNAs, recombinase target sites) are designed for specific sequences. Variation among HIV subtypes or even within an individual can lead to escape: the virus may have mismatches that prevent the editing tool from recognizing and cutting.
Latent Reservoirs
Latently infected cells are rare and may be scattered in many tissues (lymph nodes, brain, gut). Reaching all these cells with gene-editing delivery tools is difficult. Also, some provirus in latency may be transcriptionally silent and difficult to detect/edit.
Delivery
Getting gene-editing machinery (Cas9, guide RNAs, recombinases) into the relevant human cells in the body safely and efficiently is a major obstacle. Viral vectors (lentivirus, AAV, etc.) are commonly used in models, but issues include immunogenicity, off-target integration, limited tissue targeting, and reaching enough cells.
Safety: Off-Target Effects and Genotoxicity
Unintended cuts in human DNA (off-target cleavage) can lead to mutations, chromosomal rearrangements, or cancer. Any therapy must have extremely low risk of such effects. Some studies report minimal off-target activity, but more work is needed. Also, long-term effects in humans are not known.
Efficiency
For a cure, editing must occur in essentially all cells carrying proviral HIV, which is demanding. Partial editing may reduce viral load but may not prevent rebound when ART is stopped.
Ethical, Regulatory, and Cost Issues
Editing human genes, particularly in stem cells or in vivo, raises ethical questions. Regulatory oversight is needed. Also, costs and complexity may limit access in low- and middle-income countries where HIV burden is high.

Recent Clinical Advances

A very recent review (2025) on CCR5 gene editing describes not only preclinical work but also early trials, assessing safety and preliminary efficacy. The study underscores that editing CCR5 in hematopoietic stem cells or T cells is feasible.
There is also a first-in-human trial reported of CRISPR delivered via adeno-associated virus (AAV9) designed to target latent HIV proviral DNA (multiplex CRISPR-Cas9). Early results suggest that the intended HIV DNA was targeted, and some clearance in blood seen over six months. However, this is initial, phase 1/2 work, mostly focused on safety and proof of concept rather than full cure.

Theoretical Scenarios: How a Gene-Editing HIV Cure Might Work

Putting the pieces together, a possible therapeutic regimen might include:

Identify and isolate cells carrying latent HIV
Using biomarkers (if available) or broad delivery methods.
Apply gene editing to excise proviral DNA
Use CRISPR/Cas9 or recombinases designed to target highly conserved parts of the HIV genome (for example, LTRs). Possibly use multiplexed guide RNAs to reduce risk of escape.
Simultaneously edit host genes to prevent reinfection
For example, introduce CCR5 knockout or mutation in the same or other immune cells, so that even if free virus remains, infection of new cells is blocked.
Support immune system clearance
Use immunotherapy approaches, e.g. engineered T cells, broadly neutralizing antibodies, etc., to clear residual infected cells and prevent rebound.
Delivery strategies
Use vectors capable of reaching tissues where latent reservoirs are (blood, lymphoid tissue, brain, gut). Ensure minimal immune reaction to delivery system.
Long-term monitoring for safety and efficacy
Monitor for off-target mutagenesis, viability of edited cells, durability of HIV suppression without ART, etc.

Ethical, Social, and Global Considerations

Informed Consent and Human Trials: When editing genes in humans, participants must understand potential risks, including unknown long-term effects. Clinical trials must follow strict regulatory protocols.
Equitable Access: Many regions hardest hit by HIV have limited access to cutting-edge therapies. Ensuring that gene-editing cures (if successful) are affordable and accessible is crucial.
Genetic Diversity: HIV subtypes differ by region; therapies developed based on one subtype may be less effective elsewhere. Also, human genetic diversity (e.g. variations in CCR5, immune genes) may affect outcomes.
Germline vs Somatic Editing: Most therapeutic strategies aim for somatic cell editing (not inheritable). Germline editing is highly controversial and widely considered unethical.

Future Directions

To move toward a viable cure, research should focus on:

Improved delivery systems: Better AAV or other viral/ non-viral vectors that can reach latent reservoir sites safely.
Multiplex targeting: Using multiple guide RNAs or combining gene editing tools to cover conserved HIV regions and co-receptor genes.
Host immune boosting: Combining gene editing with immune therapies (vaccines, broadly neutralizing antibodies, CAR-T cells) to help clear reservoirs.
Personalised approaches: Tailoring editing tools to each patient’s HIV subtype, viral diversity, and the location of latent reservoirs.
Long-term safety studies: Extensive preclinical work in animals, then cautious human trials to ensure no adverse effects.

Conclusion

Gene-editing offers one of the most promising frontiers in the quest for an HIV cure. The ability to excise HIV proviral DNA from infected immune cells and to edit host receptors like CCR5 to prevent reinfection could, in combination, deliver a sterilizing cure (complete viral eradication) or a functional cure (viral control without therapy). Though many challenges remain—viral diversity, delivery, safety, ethical issues—recent studies show real progress. If these obstacles can be overcome, the dream of eradicating HIV from the human body, rather than merely suppressing it, may be achievable.