Exploring Development Options of a Polishing Chromatography Step for AAV7 and AAV8

As impact of adeno-associated virus (AAV) empty capsids on drug product safety and quality remains inconclusive, downstream purification strategy has been focusing on empty capsid removal. Anion-exchange chromatography (AEX) has made significant progress in separating empty from full capsids in recent years. Still, achieving baseline resolution between different AAV subpopulations remains challenging due to subtle charge differences. With a certain AAV construct design, this difficulty is compounded when upstream packaging efficiency is low or when empty and full capsids of a particular serotype have similar electrostatic charge profiles. To improve separation and product purity, secondary interaction mechanisms using multimodal (mix-mode) chromatography are often introduced.In this study, we present a case study on developing a polishing chromatography step to remove empty capsids from AAV7 and AAV8 preparations. To create a challenging feed material for the polishing step, we used small gene-of-interest (GOI) and poorly packaged starting materials. We investigated multiple critical process parameters, including buffer matrix, salt concentration, pH, peak fractionation strategies, and column chemistry (strong AEX vs. mix-mode). Mass photometry (MP) and charge detection mass spectrometry (CDMS) were used to characterize capsid populations. Optimized AEX conditions for AAV8 achieved 80% full capsids by MP and 90% GOI-containing capsids by CDMS. For AAV7, the mix-mode column demonstrated improved resolution compared with the standard AEX gradient method. These results demonstrate that mix-mode chromatography provides an alternative polishing option for serotypes where traditional AEX fails to achieve the desired separation.