Orthogonal approaches to AAV vector characterization: Validating quantitative TEM for partially filled particles

Adeno-associated viruses (AAVs) have emerged as a leading vector for gene therapy due to their non-pathogenic nature and ability to deliver therapeutic genes effectively. However, the presence of empty and partially filled capsids in AAV preparations can significantly impact therapeutic efficacy, and therefore, robust quality control methods for accurate characterization are required. This study presents quantitative electron microscopy (QuTEM) as a platform-validated method for distinguishing full, partial, and empty AAV capsids based on their internal density. We compared this enhanced TEM method with analytical ultracentrifugation (AUC), mass photometry (MP), and SEC-HPLC (size exclusion chromatography-high-performance liquid chromatography), to assess their effectiveness in characterizing AAV vector content. AAV vectors were produced using both self-complementary (scAAV) and single-stranded (ssAAV) transgenes, and their encapsidation efficiency was evaluated. Results demonstrated that QuTEM provided a reliable quantification of AAV populations, yielding a high concordance with MP and AUC data. Notably, QuTEM exhibited superior granularity by directly visualizing the viral capsids in their native state, preserving structural integrity. These features position the QuTEM analytical method as a potential gold standard for AAV characterization. Additionally, these findings emphasize the importance of integrated analytical approaches in optimizing AAV production and characterization, ensuring its consistency and efficacy for gene therapy applications.