Codon-Optimization of Wild-Type Adeno-Associated Virus Capsid Sequences Enhances DNA Family Shuffling while Conserving Functionality
Abstract
Adeno-associated virus (AAV) vectors have become one of the most widely used gene transfer tools in human gene therapy. Considerable effort is currently being focused on AAV capsid engineering strategies with the aim of developing novel variants with enhanced tropism for specific human cell types, decreased human seroreactivity, and increased manufacturability. Selection strategies based on directed evolution rely on the generation of highly variable AAV capsid libraries using methods such as DNA-family shuffling, a technique reliant on stretches of high DNA sequence identity between input parental capsid sequences. This identity dependence for reassembly of shuffled capsids is inherently limiting and results in decreased shuffling efficiency as the phylogenetic distance between parental AAV capsids increases. To overcome this limitation, we have developed a novel codon-optimization algorithm that exploits evolutionarily defined codon usage at each amino acid residue in the parental sequences. This method increases average sequence identity between capsids, while enhancing the probability of retaining capsid functionality, and facilitates incorporation of phylogenetically distant serotypes into the DNA-shuffled libraries. This technology will help accelerate the discovery of an increasingly powerful repertoire of AAV capsid variants for cell-type and disease-specific applications.
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BibTeX
@article{cabanescreus2026codonoptimization,
title = {{Codon-Optimization of Wild-Type Adeno-Associated Virus Capsid Sequences Enhances DNA Family Shuffling while Conserving Functionality}},
author = {Marti Cabanes-Creus and Samantha Ginn and Anais Amaya and Sophia Liao and Adrian Westhaus and Claus Hallwirth and Patrick Wilmott and Jason Ward and Kimberley Dilworth and Giorgia Santilli and Arkadiusz Rybicki and Hiroyuki Nakai and Adrian Thrasher and Adrian Filip and Ian Alexander and Leszek Lisowski and Sophia H.Y. Liao},
journal = {Molecular Therapy - Methods and Clinical Development},
year = {2026},
month = sep,
doi = {10.1016/j.omtm.2018.10.016},
url = {https://hal.science/hal-05771956v1},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Codon-Optimization of Wild-Type Adeno-Associated Virus Capsid Sequences Enhances DNA Family Shuffling while Conserving Functionality
AU - Marti Cabanes-Creus
AU - Samantha Ginn
AU - Anais Amaya
AU - Sophia Liao
AU - Adrian Westhaus
AU - Claus Hallwirth
AU - Patrick Wilmott
AU - Jason Ward
AU - Kimberley Dilworth
AU - Giorgia Santilli
AU - Arkadiusz Rybicki
AU - Hiroyuki Nakai
AU - Adrian Thrasher
AU - Adrian Filip
AU - Ian Alexander
AU - Leszek Lisowski
AU - Sophia H.Y. Liao
PY - 2026
DA - 2026/09/30
JO - Molecular Therapy - Methods and Clinical Development
DO - 10.1016/j.omtm.2018.10.016
UR - https://hal.science/hal-05771956v1
AB - Adeno-associated virus (AAV) vectors have become one of the most widely used gene transfer tools in human gene therapy. Considerable effort is currently being focused on AAV capsid engineering strategies with the aim of developing novel variants with enhanced tropism for specific human cell types, decreased human seroreactivity, and increased manufacturability. Selection strategies based on directed evolution rely on the generation of highly variable AAV capsid libraries using methods such as DNA-family shuffling, a technique reliant on stretches of high DNA sequence identity between input parental capsid sequences. This identity dependence for reassembly of shuffled capsids is inherently limiting and results in decreased shuffling efficiency as the phylogenetic distance between parental AAV capsids increases. To overcome this limitation, we have developed a novel codon-optimization algorithm that exploits evolutionarily defined codon usage at each amino acid residue in the parental sequences. This method increases average sequence identity between capsids, while enhancing the probability of retaining capsid functionality, and facilitates incorporation of phylogenetically distant serotypes into the DNA-shuffled libraries. This technology will help accelerate the discovery of an increasingly powerful repertoire of AAV capsid variants for cell-type and disease-specific applications.
SN - 2329-0501
ER -