Real-World AAV Empty-Full Capsid Analysis with ddPCR Technology: Insights from Matica Biotechnology

Measuring the ratio of empty to full capsids serves as a critical quality attribute (CQA) for adeno-associated virus (AAV) products and directly impacts therapeutic potency, safety, and regulatory approval. Drawing on their deep understanding of viral vector production and analytical development, experts from Matica Biotechnology —  a Texas-based viral vector contract development and manufacturing organization (CDMO) — share insights that help you optimize AAV characterization. In this article, you’ll explore the challenges of AAV production, understand trade-offs between orthogonal methods, and discover how technologies like Droplet Digital PCR (ddPCR) enable you to develop faster, more flexible gene therapy manufacturing strategies.

In this interview, we speak with two experts from the Analytical Development department at Matica Bio: Dan Mitchell, Senior Director and Head of Analytical Development and Quality Control, and Gustavo Rivas, Analytical Scientist. They reveal insights into their approach to AAV analytics, discuss common challenges in vector characterization, and explain how they use the Vericheck ddPCR Empty-Full Capsid Kit from Bio-Rad to streamline workflows and boost efficiency.

Dan Mitchell
Senior Director and Head of Analytical Development and Quality Control
Matica Biotechnology, Inc.

Q: Could you tell us a bit about your role at Matica Biotechnology? 

Daniel: I’m the Senior Director and Head of Analytical Development and Quality Control at Matica Bio. I joined the company in its earliest days, back in 2020, before we even had labs or infrastructure. Over the past five years, I’ve built the entire analytical function from scratch and contributed extensively to the QC (quality control) function. This includes method development, transfer, qualification, and validation, as well as compendial workflows, environmental monitoring, and material release. Today, I oversee both Analytical Development and QC, leading everything from method creation to GMP (good manufacturing practice) release testing.

Gustavo Rivas

Analytical Scientist

Matica Biotechnology, Inc.

Gustavo: I’m an Analytical Scientist within the Analytical Development team. I’ve been at Matica Bio for about two and a half years. Our team handles a wide range of responsibilities. We support process development with in-process sample testing, collaborate with QC on method development and transfers, and work closely with clients, especially when they require novel assays or are working with viral vectors we haven’t tackled before. It’s a highly collaborative, cross-functional environment, and our team covers early-stage development through GMP readiness.

Q: How do your roles support Matica Bio’s broader manufacturing capabilities, especially when it comes to supporting GMP production of viral vectors?

Daniel: We offer comprehensive, end-to-end services for cell and gene therapy manufacturing. Most client projects start on the development side and progress through to GMP. Depending on where the client is in their development journey, we support both full development and tech transfers. Our GMP facility includes bioreactor capacity at three scales: 50 L, 200 L, and 500 L. We’ve worked with a wide array of viral vectors — AAV, lentivirus, HSV (herpes simplex virus), vaccinia, adenovirus, and others — and we support everything from manufacturing to final fill, with robust in-house capabilities for compendial and safety release testing. For anything we don’t have in-house, we partner with qualified external labs.

Gustavo: On top of that, we’ve developed a network of partnerships, especially for upstream needs like plasmid production. We don’t just outsource; we’re actively involved in decision-making, from plasmid design to project-specific analytical controls. We tailor our platforms and strategies based on the unique needs of each client and each vector.

Q: When it comes to AAV manufacturing, how does your team approach measuring empty-to-full capsid ratios, and what are some challenges with the different analytical methods?

Gustavo: At the moment, we use a range of orthogonal methods to analyze empty-full capsid ratios. These include our proprietary anion exchange chromatography (AEX) method, capsid ELISA (enzyme-linked immunosorbent assay), and Droplet Digital PCR. Each provides different insights: AEX gives us separation between empty and full particles, ELISA quantifies total capsids, and the ddPCR assay quantifies genome titer. However, each method comes with specific considerations. For example, AEX requires a relatively pure, concentrated sample, which limits its use early in the process. Capsid ELISA is useful, but doesn’t tell you what’s inside the capsid. A ddPCR assay alone gives genome data but not capsid content. Sometimes you need to run two or three methods to get a full answer.

Daniel: Choosing the right method for the sample and the question you’re trying to answer is always a balancing act. For example, AUC (analytical ultracentrifugation) is traditionally considered the gold standard for this type of analysis because it gives the clearest picture of empty, full, and intermediate capsids — but it’s slow, resource-intensive, and not always practical. The AEX method is powerful, but also limited by sample concentration. Capsid ELISA tells you nothing about genome content. So using multiple methods together helps us cross-validate findings and build a comprehensive picture.

Q: Given those trade-offs, what is the biggest challenge you face when analyzing empty-to-full capsid ratios?

Daniel: One of the biggest issues we’re facing is sample variability. In-process samples differ greatly in concentration and purity, and that variability impacts which methods you can use and how reliable the results will be. We’ve built many of our workflows using both empty and full commercial AAV variants across different serotypes, which we’ve characterized extensively. That gives us a baseline, but when you’re working with test articles or process intermediates, the complexity increases. So much of the challenge is choosing and optimizing the right method for the sample type.

Q: With those challenges in mind, what motivated you to explore Bio-Rad’s Vericheck ddPCR Empty-Full Capsid Kit, and how does it compare to the methods you’re currently using?

Gustavo: ddPCR technology is our go-to method for quantifying AAV genomic titer. When we looked at Bio-Rad’s Vericheck ddPCR Empty-Full Capsid Kit, we saw it as an opportunity to bring complementary speed and flexibility into our workflow. Since we already had a well-characterized AAV8 sample, it was a perfect candidate to compare the kit’s performance directly against our published AEX method (Schrecke et al. 2024).

The workflow and assay setup for the Vericheck Kit is very similar to a standard ddPCR method, with a few added steps — including an antibody incubation and ligation step before droplet generation. However, if you compare it to running a separate ELISA and ddPCR assay for a full empty-full analysis, the Vericheck Kit is actually faster. For a single analyst, running all the traditional methods might take two days; with the Vericheck Kit, you could perform a full empty-full analysis in just one day.

In terms of findings, the percentage of full capsids measured by the Vericheck Kit closely mirrored our findings using AEX. Another advantage of the Vericheck Kit is that it also demonstrated specificity and reproducibility, even across different sample types. In a fast-paced manufacturing environment, methods with quicker turnaround are a huge advantage. Bio-Rad’s Vericheck Kit offers a streamlined workflow that could be used as an orthogonal method to support AAV vector characterization.

[Interviewer]: Thank you both for sharing your insights. As gene therapies scale, conversations like this reinforce the importance of integrating innovative, fit-for-purpose technologies — like the Vericheck ddPCR Empty-Full Capsid Kit — into workflows that balance precision, efficiency, and adaptability. We look forward to seeing how Matica Bio continues to lead in this dynamic space.

Accelerate your AAV capsid analysis with the Vericheck ddPCR Kit — see how it works or explore ordering details now.

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