MADCAP: isolation of novel nAb-naïve AAV capsids from metagenomic data
- 1Genomic Medicine Unit, Sanofi, Waltham, Massachusetts, USA
Abstract
Gene therapy using adeno-associated virus (AAV) vectors offers promising treatment for genetic disorders, but significant limitations restrict clinical application. Current AAV serotypes exhibit strong liver tropism and require high doses for extra-hepatic targeting, and pre-existing antibodies (NAbs) exclude up to 50% of potential patients. Evolutionarily distant isolates can evade neutralization but typically transduce human tissues poorly and require extensive engineering. We developed MADCAP (Metagenomic AAV Discovery and Capsid Annotation Pipeline) to systematically mine metagenomic data for functional, clinically relevant AAV capsids. We hypothesized that these sources might contain capsids that do not circulate widely in humans, can transduce human cells, and avoid neutralization. We screened 4.2 million metagenomic samples and identified 139 novel AAV capsid isolates which were tested for viral capsid assembly, viability, neutralization evasion, and tissue transduction in non-human primates. While natural serotypes (AAV1, AAV2, AAV9) were neutralized at low dilutions of pooled human immunoglobulin (IVIG), 68% of tested MADCAP capsids exhibited minimal to undetectable neutralization even at supra-physiological IVIG concentrations. Systemically delivered MADCAP capsids effectively transduced multiple clinically relevant tissues in non-human primates. Two capsids, MC46 and MC55, demonstrated improved CNS tropism compared to AAV9 while maintaining comparable production yields. In passive transfer studies, MC46 retained full transduction efficiency in the presence of human antibodies, while AAV9 transduction was completely lost. This work establishes metagenomic mining as a powerful tool for accelerating AAV capsid discovery, identifying isolates with favorable tissue tropisms and resistance to broadly neutralizing antibodies.
IMPORTANCE: This work provides proof of concept that potentially clinically relevant AAVs can be isolated from metagenomic data. Our findings lay the groundwork for accelerated discovery of AAV capsids which could potentially increase the accessibility and effectiveness of AAV gene therapy.
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BibTeX
@article{lyashenko2026madcap,
title = {{MADCAP: isolation of novel nAb-naïve AAV capsids from metagenomic data}},
author = {Eugenia Lyashenko and Tess Torregrosa and Alexandra B. Ysasi and Jason Wu and Jie Bu and Margaret Hennessy and Youngji Na and Michael J. Ryan and Mehmet Takar and Rachna Manek and Joshua A. Hull and Edith L. Pfister and Christian Mueller and Sourav R. Choudhury},
journal = {Journal of Virology},
year = {2026},
month = sep,
doi = {10.1128/jvi.00630-26},
url = {https://doi.org/10.1128/jvi.00630-26},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - MADCAP: isolation of novel nAb-naïve AAV capsids from metagenomic data
AU - Eugenia Lyashenko
AU - Tess Torregrosa
AU - Alexandra B. Ysasi
AU - Jason Wu
AU - Jie Bu
AU - Margaret Hennessy
AU - Youngji Na
AU - Michael J. Ryan
AU - Mehmet Takar
AU - Rachna Manek
AU - Joshua A. Hull
AU - Edith L. Pfister
AU - Christian Mueller
AU - Sourav R. Choudhury
PY - 2026
DA - 2026/09/09
JO - Journal of Virology
DO - 10.1128/jvi.00630-26
UR - https://doi.org/10.1128/jvi.00630-26
AB - Gene therapy using adeno-associated virus (AAV) vectors offers promising treatment for genetic disorders, but significant limitations restrict clinical application. Current AAV serotypes exhibit strong liver tropism and require high doses for extra-hepatic targeting, and pre-existing antibodies (NAbs) exclude up to 50% of potential patients. Evolutionarily distant isolates can evade neutralization but typically transduce human tissues poorly and require extensive engineering. We developed MADCAP (Metagenomic AAV Discovery and Capsid Annotation Pipeline) to systematically mine metagenomic data for functional, clinically relevant AAV capsids. We hypothesized that these sources might contain capsids that do not circulate widely in humans, can transduce human cells, and avoid neutralization. We screened 4.2 million metagenomic samples and identified 139 novel AAV capsid isolates which were tested for viral capsid assembly, viability, neutralization evasion, and tissue transduction in non-human primates. While natural serotypes (AAV1, AAV2, AAV9) were neutralized at low dilutions of pooled human immunoglobulin (IVIG), 68% of tested MADCAP capsids exhibited minimal to undetectable neutralization even at supra-physiological IVIG concentrations. Systemically delivered MADCAP capsids effectively transduced multiple clinically relevant tissues in non-human primates. Two capsids, MC46 and MC55, demonstrated improved CNS tropism compared to AAV9 while maintaining comparable production yields. In passive transfer studies, MC46 retained full transduction efficiency in the presence of human antibodies, while AAV9 transduction was completely lost. This work establishes metagenomic mining as a powerful tool for accelerating AAV capsid discovery, identifying isolates with favorable tissue tropisms and resistance to broadly neutralizing antibodies. IMPORTANCE: This work provides proof of concept that potentially clinically relevant AAVs can be isolated from metagenomic data. Our findings lay the groundwork for accelerated discovery of AAV capsids which could potentially increase the accessibility and effectiveness of AAV gene therapy.
SN - 0022-538X
SN - 1098-5514
ER -