Side-by-side comparison of lentivirus vs AAV specifically for HDR applications

Precise genome editing using homology-directed repair (HDR) requires efficient delivery of a donor template into target cells. Viral vectors are commonly used to introduce HDR donor DNA, with lentivirus and adeno-associated virus (AAV) being two widely utilized systems. Although both vectors can deliver donor templates, they differ significantly in genome structure, integration behavior, packaging capacity, and overall suitability for HDR-based genome engineering.

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Key Differences Relevant to HDR

Feature	Lentivirus	AAV
Genome type	Single-stranded RNA (reverse transcribed to dsDNA)	Single-stranded DNA
Integration	Integrates into host genome	Mostly episomal; minimal integration
HDR donor delivery	Possible but less commonly used	Widely used for HDR donor templates
Packaging capacity	~8–10 kb	~4.7 kb
Efficiency for precise editing	Lower HDR bias due to integration	High efficiency donor delivery for HDR
Safety profile	Risk of insertional mutagenesis	Low integration risk
Typical use in gene editing	Stable gene expression or CRISPR component delivery	HDR donor template delivery

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Why AAV is Often Preferred for HDR

AAV vectors are widely considered the gold standard for delivering HDR donor templates in genome editing workflows. Their single-stranded DNA genome closely mimics natural HDR substrates, enabling efficient homologous recombination when a double-strand break is introduced by tools such as CRISPR-Cas9.

Additional advantages include:

• High nuclear delivery efficiency
• Minimal random genomic integration
• Efficient HDR in both dividing and some non-dividing cells
• Low cytotoxicity and strong safety profile

Because of these features, AAV donors are frequently used in therapeutic genome editing and knock-in studies.

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When Lentivirus May Be Useful

Although lentivirus is not typically used as the HDR donor itself, it plays an important role in delivering genome editing machinery, such as:

• Cas9 expression constructs
• gRNA libraries
• Base editor or CRISPR effector systems

In many experimental workflows, researchers combine lentiviral delivery of CRISPR components with AAV-mediated HDR donor delivery to achieve efficient genome editing.

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Practical Strategy

A commonly used HDR workflow includes:

1. Lentivirus delivery of Cas9 and gRNA
2. AAV delivery of the HDR donor template
3. CRISPR-induced double-strand break
4. HDR-mediated precise genome insertion or correction

This hybrid strategy leverages the stable expression capability of lentivirus and the high HDR compatibility of AAV.

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Summary

While both lentivirus and AAV are powerful gene delivery systems, their roles in HDR-based genome editing are distinct:

• AAV is typically the preferred vector for HDR donor template delivery due to its DNA genome and high recombination efficiency.
• Lentivirus is better suited for stable delivery of genome editing tools, including Cas9 and guide RNAs.

Combining these platforms can provide a robust and efficient approach for precise genome engineering in research and therapeutic development.