Characterization of Difficult-to-Remove Host Cell Proteins in Adeno-Associated Virus Downstream Processing

A scalable, serotype-agnostic, and fully chromatographic downstream platform was developed for purification of adeno-associated virus (AAV) based on affinity (AC), ion-exchange (AEX), and multi-modal (MMC) chromatography. Quantitative proteomic profiling across each purification stage was performed using sequential window acquisition of all theoretical fragment ion mass spectra (SWATH-MS) to characterize residual host cell protein (HCP) retention for four AAV serotypes (AAV2, -5, -8, and -9) produced with suspension HEK293 cells. The downstream process showed cumulative vector genome (VG) yields ranging from 44.6 – 69.2% with full capsid enrichments ranging from 2.62 – 5.93-fold across all AAV samples. 880, 99, and 21 HCPs were identified in all AAV samples after AC, AEX, and MMC, respectively. The characterization of HCP retention described here advances the understanding of process-related impurity clearance in scalable AAV downstream systems, with implications for both purification process design and AAV interactions with host cell factors.