Deep-sequencing-guided library screening and profiling of AAV capsids in the primate retina

Intravitreal (IVT) administration of adeno-associated virus (AAV) vectors is considered a promising strategy for retinal gene therapy. Random peptide-display-based directed evolution has yielded novel AAV capsids with potent retinal bioactivity. However, recent reports on safety risks following IVT AAV administration indicate that significant opportunities remain to further refine AAV vector technology. Here, we performed iterative in vivo NGS-guided screening of AAV2 peptide-display libraries in both mice and non-human primates (NHPs), integrating barcoded functional analytics, and single-nuclei RNA sequencing to identify retina-tropic AAV variants. The top-performing capsid in mice, AAV2-GAYPKSP robustly drove eGFP expression in a human retina-on-chip model but failed to drive gene expression in the NHP retina following IVT delivery. In NHPs, a barcoded evaluation of 70 retina-tropic variants revealed a complex correlation between viral genome enrichment and transgene transcriptional output, providing insights that enhance the mechanistic interpretation and methodological design of AAV library selection strategies. Nonetheless, several NHP variants, including AAV2-I.1 and AAV2-I.12, demonstrated broad retinal transduction and potent expression, outperforming benchmarks AAV2 and AAV2-7m8. Single-nucleus RNA sequencing confirmed broad cell-type tropism of the top performing variants. Collectively, these findings expand the AAV toolkit for retinal gene therapy and underscore the importance of optimized screening methodologies in vector discovery.