Impact of downstream purification process and AAV serotype on protein-impurity clearance

Host cell proteins (HCPs) are process-related impurities in recombinant adeno-associated virus (rAAV) gene therapy products and are monitored as critical quality attributes. We assessed residual proteins to evaluate the impact of serotype and downstream processing, as well as to benchmark the performance of orthogonal analytical methods. Four AAV serotypes-AAV8, C8-R5#704, AAV9, and LICA1-encoding the same GFP transgene were produced under an identical upstream protocol; in-process and drug substance (DS) samples were analyzed by commercial, in-house ELISAs and liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods. Purification efficiently reduced the HCP burden, and no serotype-specific HCP signature was evidenced. In contrast, the purification design was the primary driver of the residual profile: a dual-step chromatography (affinity followed by mixed mode) reduced the number of detectable HCPs by half and decreased their relative abundance compared with single-step affinity capture. Several proteins persisted across batches and purification processes, suggesting protein-capsid interactions that may limit clearance. Furthermore, plasmid-derived proteins-including AAV replicase (Rep) isoforms and adenoviral proteins-were detected in DS following single-step purification and were largely removed by the second chromatographic step. These findings highlight the importance of orthogonal analytical methods for comprehensive impurity profiling and support risk-based process optimization to minimize residual proteins and ensure consistent, safe rAAV products.