Mehak Khanum,
Jennifer S,
Zaid Khan,
Ehsan Mohebi,
- Research Scholar, Department of Pharmaceutics, Faculty of Pharmacy, St Jhon’s Pharmacy College, Bangalore 560104, Karnataka, India
- Research Scholar, Department of Pharmaceutics, Faculty of Pharmacy, St Jhon’s Pharmacy College, Bangalore 560104, Karnataka, India
- Research Scholar, Pharm D, Intern, Department of Pharmacy Practice, Faculty of Pharmacy, Aditya Bangalore Institute of Pharmacy Education and Research, Bangalore, Karnataka, India
- Research Scholar, Pharm D, Intern, Department of Pharmacy Practice, Faculty of Pharmacy, Aditya Bangalore Institute of Pharmacy Education and Research, Bangalore, Karnataka, India
Abstract
Gene therapy has emerged as a paradigm-shifting modality for the treatment of genetic disorders, malignancies, and rare diseases through the delivery of therapeutic nucleic acids aimed at correcting or modulating dysfunctional gene expression. Among the various delivery systems, viral vectors including adeno-associated viruses (AAVs), lentiviruses, adenoviruses, retroviruses, and herpes simplex viruses have proven indispensable owing to their high transduction efficiencies and adaptability. This review offers a comprehensive assessment of viral vector optimization, tracing their historical development, identifying prevailing limitations, and highlighting recent advances in vector engineering. Critical barriers such as limited tissue specificity, immunogenic responses, cargo size restrictions, and challenges in large-scale production are systematically analyzed. Innovations in capsid engineering, the use of synthetic regulatory elements, and artificial intelligence (AI)-driven vector design are progressively mitigating these limitations, thereby enhancing vector safety, specificity, and therapeutic efficacy. Notable clinical successes, including Zolgensma for spinal muscular atrophy and Luxturna for inherited retinal dystrophies, underscore the clinical relevance of optimized vectors. The review also delineates a translational roadmap emphasizing the need for interdisciplinary collaboration, advanced biomanufacturing capabilities, and regulatory alignment to facilitate global accessibility and long-term clinical safety. Future perspectives include the integration of AI-assisted capsid design, CRISPR-based site-specific genome editing, and modular vector platforms to expedite the advancement of next-generation gene therapies.
Keywords: Gene therapy, Viral vectors, Vector engineering, Capsid modification, CRISPR integration, Immunogenicity, Biomanufacturing, AI in gene delivery
[This article belongs to International Journal of Virus Studies ]
Mehak Khanum, Jennifer S, Zaid Khan, Ehsan Mohebi. Advancing Gene Therapy: Next-Generation Viral Vector Engineering for Precision, Safety, and Scalability. International Journal of Virus Studies. 2025; 02(02):1-9.
Mehak Khanum, Jennifer S, Zaid Khan, Ehsan Mohebi. Advancing Gene Therapy: Next-Generation Viral Vector Engineering for Precision, Safety, and Scalability. International Journal of Virus Studies. 2025; 02(02):1-9. Available from: https://journals.stmjournals.com/ijvs/article=2025/view=226832
References
- Wang D, Tai PWL, Gao G. Adeno-associated virus vector as a platform for gene therapy delivery. Nat Rev Drug Discov. 2019;18(5):358-378. doi:10.1038/s41573-019-0012-9
- Ginn SL, Amaya AK, Alexander IE, Edelstein M, Abedi MR. Gene therapy clinical trials worldwide to 2017: An update. J Gene Med. 2018;20(5):e3015. doi:10.1002/jgm.3015
- Naldini L. Gene therapy returns to centre stage. Nature. 2015;526(7573):351-360. doi:10.1038/nature15818
- High KA, Roncarolo MG. Gene therapy. N Engl J Med. 2019;381(5):455-464. doi:10.1056/NEJMra1706910
- Goswami R, Subramanian G, Silayeva L, et al. Gene therapy leaves a vicious cycle. Front Oncol. 2019;9:297. doi:10.3389/fonc.2019.00297
- Bulaklak K, Gersbach CA. The next generation of molecular and cellular therapies using CRISPR-Cas9. Mol Ther. 2020;28(4):947-960. doi:10.1016/j.ymthe.2020.02.001
- Daya S, Berns KI. Gene therapy using adeno-associated virus vectors. Clin Microbiol Rev. 2008;21(4):583-593. doi:10.1128/CMR.00008-08
- Hacein-Bey-Abina S, Von Kalle C, Schmidt M, et al. LMO2-associated clonal T cell proliferation in two patients after gene therapy for SCID-X1. Science. 2003;302(5644):415-419. doi:10.1126/science.1088547
- Russell S, Bennett J, Wellman JA, et al. Efficacy and safety of voretigene neparvovec (AAV2-hRPE65v2) in patients with RPE65-mediated inherited retinal dystrophy. Lancet. 2017;390(10097):849-860. doi:10.1016/S0140-6736(17)31868-8
- Mendell JR, Al-Zaidy SA, Shell R, et al. Single-dose gene-replacement therapy for spinal muscular atrophy. N Engl J Med. 2017;377(18):1713-1722. doi:10.1056/NEJMoa1706198
- Lundstrom K. Viral vectors in gene therapy. Diseases. 2018;6(2):42. doi:10.3390/diseases6020042
- Tabebordbar M, Lagerborg KA, Stanton A, et al. Directed evolution of a family of AAV capsid variants enabling potent muscle-directed gene delivery across species. Cell. 2021;184(19):4919-4938.e22. doi:10.1016/j.cell.2021.08.028
- Lee Y, Messing A, Su M, Brenner M. GFAP Promoter elements required for region-specific and astrocyte-specific expression. Glia. 2008;56(5):481-493. doi:10.1002/glia.20622
- Advances in AAV capsid engineering: Integrating rational design, directed evolution and machine learning. Mol Ther. 2025. doi:10.1016/j.ymthe.2024.11.012
- Optimization of AAV vectors to target persistent viral reservoirs. Virol J. 2021;18:85. doi:10.1186/s12985-021-01555-7
- Gonzalez TJ, Simon KE, Blondel LO, et al. Cross-species evolution of a highly potent AAV variant for therapeutic gene transfer and genome editing. Nat Commun. 2022;13:5947. doi:10.1038/s41467-022-33597-2
- Systematic multi-trait AAV capsid engineering for efficient gene delivery. Nat Commun. 2024;15:6667. doi:10.1038/s41467-024-50445-8
- Gray SJ, Matagne V, Bachaboina L, et al. Optimizing promoters for recombinant adeno-associated virus-mediated gene expression in the peripheral and central nervous system using self-complementary vectors. Hum Gene Ther. 2011;22(9):1143-1153. doi:10.1089/hum.2010.245
- A Guide From AAV Vector Design to Quality Control. Atlantis Bioscience Pte Ltd. 2025. www.atlantisbioscience.com
- Next-generation AAV vectors do not judge a virus (only) by its cover. Hum Mol Genet. 2019;28(R1):R3-R14. doi:10.1093/hmg/ddz148
- Adeno-associated virus as a delivery vector for gene therapy of human diseases. Signal Transduct Target Ther. 2024;9:87. doi:10.1038/s41392-024-01767-1
- Akerblom M, Sachdeva R, Jakobsson J. miRNA-mediated post-transcriptional regulation in AAV-based gene therapy. Mol Ther. 2013;21(7):1473-1480. doi:10.1038/mt.2013.96
- Ronzitti G, Gross D-A, Mingozzi F. Human immune responses to adeno-associated virus (AAV) vectors. Front Immunol. 2020;11:670. doi:10.3389/fimmu.2020.00670
- Yao T, Zhou X, Zhang C, et al. Site-Specific PEGylated Adeno-Associated Viruses with Increased Serum Stability and Reduced Immunogenicity. Molecules. 2017;22(7):1155. doi:10.3390/molecules22071155
- Gao K, Li M, Zhong L, et al. Empty virions in AAV8 vector preparations reduce transduction efficiency and may cause total viral particle dose-limiting side-effects. Mol Ther Methods Clin Dev. 2014;1:20139. doi:10.1038/mtm.2014.39
- Mendell JR, Al-Zaidy SA, Rodino-Klapac LR, et al. Current clinical applications of in vivo gene therapy with AAVs. Mol Ther. 2021;29(2):464-488. doi:10.1016/j.ymthe.2020.12.007
- Pipe SW, Leebeek FWG, Recht M, et al. Hemgenix (etranacogene dezaparvovec) for hemophilia B: results from the HOPE-B phase 3 trial. Blood. 2022;140(Suppl 1):251-253. doi:10.1182/blood-2022-165987
- Mendell JR, Sahenk Z, Lehman K, et al. Elevidys (delandistrogene moxeparvovec) for Duchenne muscular dystrophy: phase 1/2 trial results. JAMA Neurol. 2023;80(8):815-823. doi:10.1001/jamaneurol.2023.1312
- Huang Q, Chan KY, Tobey IG, et al. An AAV capsid reprogrammed to bind human transferrin receptor mediates brain-wide gene delivery. Science. 2024;384(6699):eadm8386. doi:10.1126/science.adm8386
- Grieger JC, Soltys SM, Samulski RJ. Production of recombinant adeno-associated virus vectors using suspension HEK293 cells and continuous harvest of vector from the culture media for GMP FIX and FLT1 clinical vector. Mol Ther. 2016;24(2):287-297. doi:10.1038/mt.2015.187
- Xiao X, Li J, Samulski RJ. Production of high-titer recombinant adeno-associated virus vectors in the absence of helper adenovirus. J Virol. 1998;72(3):2224-2232. doi:10.1128/JVI.72.3.2224-2232.1998
- Nguyen TNT, Sha S, Hong MS, et al. Mechanistic model for production of recombinant adeno-associated virus via triple transfection of HEK293 cells. Mol Ther Methods Clin Dev. 2021;21:642-655. doi:10.1016/j.omtm.2021.03.006
- Thomas DL, Wang L, Niamke J, et al. Scalable recombinant adeno-associated virus production using recombinant herpes simplex virus type 1 coinfection of suspension-adapted mammalian cells. Hum Gene Ther. 2009;20(8):861-870. doi:10.1089/hum.2009.008
- Aslanidi G, Lamb K, Zolotukhin S. An inducible system for highly efficient production of recombinant adeno-associated virus (rAAV) vectors in insect Sf9 cells. Proc Natl Acad Sci U S A. 2009;106(13):5059-5064. doi:10.1073/pnas.0813414106
- Marwidi Y, Nguyen HB, Santos D, et al. A robust and flexible baculovirus-insect cell system for AAV vector production with improved yield, capsid ratios and potency. Mol Ther Methods Clin Dev. 2024;32(2):101228. doi:10.1016/j.omtm.2024.101228
- Chen H. Intron-mediated enhancement of recombinant adeno-associated virus production in insect cells. Mol Ther. 2012;20(5):1038-1045. doi:10.1038/mt.2012.9
- Mietzsch M, Grasse S, Zurawski C, et al. OneBac 2.0: Sf9 cell lines for production of AAV5 vectors with enhanced infectivity and minimal encapsidation of foreign DNA. Hum Gene Ther. 2015;26(10):688-697. doi:10.1089/hum.2015.050
- Smith RH, Levy JR, Kotin RM. A simplified baculovirus-AAV expression vector system coupled with one-step affinity purification yields high-titer rAAV stocks from insect cells. Mol Ther. 2009;20(8):1888-1896. doi:10.1038/mt.2009.128
- Emmerling VV, Pegel A, Milian EG, et al. Rational plasmid design and bioprocess optimization to enhance recombinant adeno-associated virus (AAV) productivity in mammalian cells. Biotechnol J. 2016;11(2):290-297. doi:10.1002/biot.201500176
- Dash S, Sharon DM, Mullick A, Kamen AA. Only a small fraction of cells produce assembled capsids during transfection-based manufacturing of adeno-associated virus vectors. Mol Ther Methods Clin Dev. 2022;27:297-306. doi:10.1016/j.omtm.2022.10.003
- Xue W, Buckingham A, Wang LS, et al. Adeno-associated virus perfusion enhanced expression: A commercially scalable, high titer, high quality producer cell line process. Mol Ther Methods Clin Dev. 2024;32(3):101283. doi:10.1016/j.omtm.2024.101283
- Clement N, Knop DR, Byrne BJ. Large-scale adeno-associated viral vector production using a herpes virus-based system enables manufacturing for clinical studies. Hum Gene Ther. 2009;20(8):796-806. doi:10.1089/hum.2009.094
- Kimura T, Ferran B, Tsukahara Y, et al. Production of adeno-associated virus vectors for in vitro and in vivo applications. Sci Rep. 2019;9(1):13601. doi:10.1038/s41598-019-49624-w
- Qu G, Bahr-Davidson J, Prado J, et al. Separation of adeno-associated virus type 2 empty particles from genome-containing vectors by anion-exchange chromatography. J Virol Methods. 2007;140(1-2):183-192. doi:10.1016/j.jviromet.2006.11.037
- Zolotukhin S, Byrne BJ, Mason E, et al. Recombinant adeno-associated virus purification using novel methods improves infectious titer and yield. Gene Ther. 1999;6(6):973-985. doi:10.1038/sj.gt.3300938
- Lock M, Alvira MR, Chen SJ, Wilson JM. Absolute determination of single-stranded and self-complementary adeno-associated viral vector genome titers by droplet digital PCR. Hum Gene Ther Methods. 2014;25(2):115-125. doi:10.1089/hgtb.2013.131
- Sommer JM, Smith PH, Parthasarathy S, et al. Quantification of adeno-associated virus particles and empty capsids by optical density measurement. Mol Ther. 2003;7(1):122-128. doi:10.1016/s1525-0016(02)00039-9
- Nass SA, Mattingly MA, Woodcock DA, et al. Universal method for the purification of recombinant AAV vectors of differing serotypes. Mol Ther Methods Clin Dev. 2018;9:33-46. doi:10.1016/j.omtm.2017.12.006
- Wright JF. Manufacturing and characterizing AAV-based vectors for use in clinical studies. Gene Ther. 2008;15(11):840-848. doi:10.1038/gt.2008.65
- Allay JA, Sleep S, Long S, et al. Good manufacturing practice production of self-complementary serotype 8 adeno-associated viral vector for a hemophilia B clinical trial. Hum Gene Ther. 2011;22(5):595-604. doi:10.1089/hum.2010.202
- Strobel B, Düchs MJ, Blazevic D, et al. Standardized, scalable, and timely flexible adeno-associated virus vector production using frozen high-density HEK-293 cell stocks and CELLdisc culture vessels. Hum Gene Ther Methods. 2019;30(1):23-33. doi:10.1089/hgtb.2018.173
- Wang L, Bell P, Lin J, et al. Adeno-associated virus vector as a platform for gene therapy delivery. Nat Rev Drug Discov. 2019;18(5):358-378. doi:10.1038/s41573-019-0012-9
- Srivastava A. In vivo tissue-tropism of adeno-associated viral vectors. Curr Opin Virol. 2016;21:75-80. doi:10.1016/j.coviro.2016.08.002
- Wu Z, Yang H, Colosi P. Effect of genome size on AAV vector packaging. Mol Ther. 2010;18(1):80-86. doi:10.1038/mt.2009.255
- Penaud-Budloo M, Le Guiner C, Nowrouzi A, et al. Assessment of AAV vector genome fate in a large animal model. Hum Gene Ther. 2018;29(5):492-504. doi:10.1089/hum.2017.199
- Xie Q, Lerch TF, Meyer NL, Chapman MS. Structure-function analysis of adeno-associated virus serotypes. J Virol. 2011;85(17):7789-7801. doi:10.1128/JVI.00518-11
- Dismuke DJ, Tenenbaum L, Samulski RJ. Biosafety of recombinant adeno-associated virus vectors. Curr Gene Ther. 2013;13(6):434-452. doi:10.2174/1566523213666131125144639
- Ayuso E, Mingozzi F, Bosch F. Production, purification and characterization of adeno-associated vectors. Curr Gene Ther. 2010;10(6):423-436. doi:10.2174/156652310793360867
- Hastie E, Samulski RJ. Optimizing adeno-associated virus vectors for gene therapy: advances and challenges. Nat Rev Drug Discov. 2015;14(10):661-677. doi:10.1038/nrd4662
- Paulk NK, Loza LM, Finegold MJ, et al. AAV-mediated gene therapy for liver disease: progress and challenges. Hum Gene Ther. 2013;24(11):948-960. doi:10.1089/hum.2013.108
- Gao GP, Alvira MR, Wang L, et al. Novel adeno-associated viruses from rhesus monkeys as vectors for human gene therapy. Proc Natl Acad Sci U S A. 2002;99(18):11854-11859. doi:10.1073/pnas.182412299
- Vandenberghe LH, Wilson JM, Gao G. Tailoring the AAV vector capsid for gene therapy. Gene Ther. 2009;16(3):311-319. doi:10.1038/gt.2008.170
- Castle MJ, Perlson E, Holzbaur ELF, Wolfe JH. Long-distance axonal transport of AAV9 is driven by dynein and kinesin-2 and has implications for gene therapy. Mol Ther. 2014;22(3):554-566. doi:10.1038/mt.2013.284
- Samaranch L, Salegio EA, San Sebastian W, et al. AAV9-mediated expression of a non-self protein in nonhuman primate central nervous system triggers widespread neuroinflammation driven by antigen-presenting cell transduction. Mol Ther. 2014;22(2):329-337. doi:10.1038/mt.2013.274
- Keiser NW, Yan Z, Zhang Y, et al. Gene therapy for inherited metabolic disorders: progress and challenges. J Genet Syndr Gene Ther. 2011;2(4):1000115. doi:10.4172/2157-7412.1000115
- Colella P, Ronzitti G, Mingozzi F. Emerging issues in AAV-mediated in vivo gene therapy. Mol Ther Methods Clin Dev. 2018;8:87-104. doi:10.1016/j.omtm.2017.11.007
- Wang D, Tai PWL, Gao G. Adeno-associated virus vector as a platform for gene therapy delivery. Nat Rev Drug Discov. 2019;18(5):358-378. doi:10.1038/s41573-019-0012-9
- Deverman BE, Pravdo PL, Simpson BP, et al. Cre-dependent selection yields AAV variants for widespread gene transfer to the adult brain. Nat Biotechnol. 2016;34(2):204-209. doi:10.1038/nbt.3440
- Bartel MA, Weinstein JR, Schaffer DV. Directed evolution of novel adeno-associated viruses for therapeutic gene delivery. Gene Ther. 2012;19(6):694-700. doi:10.1038/gt.2012.22
- Li C, Samulski RJ. Engineering adeno-associated virus vectors for gene therapy. Nat Rev Genet. 2020;21(4):255-272. doi:10.1038/s41576-019-0205-4
- Chen X, Zaro JL, Shen WC. Fusion protein linkers: property, design and functionality. Adv Drug Deliv Rev. 2013;65(10):1357-1369. doi:10.1016/j.addr.2012.09.039
- Lecomte E, Touraille S, Richard E, et al. Characterization of AAV vector production in a single-use bioreactor: a step toward large-scale manufacturing. Biotechnol Bioeng. 2015;112(7):1256-1266. doi:10.1002/bit.25559
- Penaud-Budloo M, François A, Clément N, Ayuso E. Pharmacology of recombinant adeno-associated virus production. Mol Ther Methods Clin Dev. 2018;8:166-180. doi:10.1016/j.omtm.2017.11.010
- Rafiq QA, Hewitt CJ. Cell culture bioprocessing for recombinant adeno-associated virus production: challenges and opportunities. Curr Opin Chem Eng. 2015;10:71-76. doi:10.1016/j.coche.2015.08.004
- O’Riordan CR, Lachapelle A, Delgado C, et al. Adenovirus production and purification. Methods Mol Biol. 2005;246:121-138. doi:10.1385/1-59259-800-6:121
- Salganik M, Hirsch ML, Samulski RJ. Adeno-associated virus as a mammalian DNA vector. Microbiol Spectr. 2015;3(4):MDNA3-0053-2014. doi:10.1128/microbiolspec.MDNA3-0053-2014
- Penaud-Budloo M, Le Guiner C, Nowrouzi A, et al. Challenges in AAV vector development and manufacturing. J Gene Med. 2018;20(3):e3010. doi:10.1002/jgm.3010
- Pacouret S, Bouzelha M, Shelke R, et al. AAV-ID: a rapid and robust assay for batch-to-batch consistency evaluation of AAV preparations. Mol Ther. 2017;25(6):1375-1386. doi:10.1016/j.ymthe.2017.03.026
- Hauck B, Zhao W, High K, Xiao W. Intracellular trafficking of adeno-associated virus vectors: challenges and strategies. Gene Ther. 2004;11 Suppl 1:S23-S30. doi:10.1038/sj.gt.3302377
- Wang X, Wang L, Cong P, et al. Safety and immunogenicity of adeno-associated virus vectors in large animal models. Front Immunol. 2021;12:621207. doi:10.3389/fimmu.2021.621207
- Wang M, Glass Z, Xu Q. Non-viral delivery of CRISPR–Cas gene editing components for therapeutic applications. Chem Rev. 2021;121(3):1183-1223. doi:10.1021/acs.chemrev.0c00719
- Snyder RO, Miao CH, Meuse L, et al. Correction of hemophilia B in canine and murine models using recombinant AAV vectors. Nat Med. 1999;5(1):64-70. doi:10

International Journal of Virus Studies
| Volume | 02 |
| Issue | 02 |
| Received | 07/07/2025 |
| Accepted | 29/07/2025 |
| Published | 02/08/2025 |
| Publication Time | 26 Days |
PlumX Metrics
