Preparative choline-based anion-exchange chromatography for enrichment of full adeno-associated virus capsids

Recombinant adeno-associated virus (AAV) vectors have emerged as powerful gene delivery tools for the treatment of genetic disorders. However, the production of high-quality AAV vectors still poses significant challenges. In upstream manufacturing, AAV genome packaging typically results in a diverse pool of empty and partially filled capsids, as well as the desired functional virions. Non-functional AAV capsids are considered product-related impurities and pose a risk of adverse immunological reactions. Here, we describe a novel anion-exchange (AEX) chromatography process for the purification of full capsids using a choline-Cl salt gradient in an AEX column packed with quaternary ammonium-type ligand resin. Choline-Cl is a simple, non-toxic salt with a quaternary ammonium structure that presumably competes with the resin ligand for AAV binding with an ion-pairing mechanism. This significantly improves the separation of functional viral vectors from empty capsids as compared to other common methods. During process optimization, the linear gradient was replaced by a series of elution steps specific to serotype AAV8. Following an AAV8 affinity capture, we achieved nearly 90 % full AAV8 separation in a single AEX polishing run as determined by A₂₆₀/A₂₈₀ ratio, analytical AEX chromatography, and size exclusion chromatography multi-angle light scattering (SEC-MALS). This level of full AAV content is comparable to that of commercially sourced AAV samples purified with gradient ultracentrifugation and is considered acceptable for FDA-recommended regulatory standards. The novel choline-based full capsid enrichment strategy described herein can support the development and manufacture of pure, safe, and potent AAV-based gene therapy products.