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 the purification of adeno-associated virus (AAV) based on affinity chromatography (AC), anion-exchange chromatography (AEX), and multi-modal polishing chromatography (MMC). 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 to 69.2% with full capsid enrichments ranging from 2.62- to 5.93-fold across all AAV samples. A total of 880, 99, and 21 HCPs were identified in all AAV samples after AC, AEX, and MMC, respectively. Vector-mediated mechanisms of retention are proposed (i.e., capsid or genome association) based on enrichment in protein- and nucleic acid-binding properties of difficult-to-remove HCPs, little clearance across multiple modes of separation, and divergence of HCP profiles for AAV-containing samples vs. null lysate material. 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.