How Can Rapid mRNA Quantification Enhance Multivalent Vaccine Development?

Advances in mRNA quantification are paving the way for improved vaccine analytics — a critical component as the industry shifts toward multivalent mRNA vaccines.

With these vaccines designed to target multiple pathogens or strains simultaneously, the need for universal assays that can rapidly confirm the identity and quantity of several mRNA constructs in one test has never been more urgent.

Emerging evidence indicates that a multivalent mRNA vaccine encoding hemagglutinin antigens from all known influenza virus subtypes can elicit broad, cross-reactive antibody responses in animal models, demonstrating the potential of mRNA platforms to overcome challenges posed by antigenically variable viruses. These vaccines can be engineered to address antigenic variability and stimulate a wide-ranging immune response. Collectively, these insights underscore the imperative for rapid, robust mRNA quantification methods.

In this Xtalks Spotlight interview, Dr. Erica Dawson, Chief Research and Development Officer at InDevR, shared her insights on the current landscape of mRNA analytics and the potential breakthroughs that could support the future of multivalent vaccine development.

With 18 years of experience in managing cross-functional research and development teams, Dr. Dawson has played a key role in advancing InDevR’s technologies, including leading the company through its first 510(k) clearance in 2019.

Dr. Dawson’s expertise is particularly valuable as the industry grapples with the complexities of rapidly quantifying multiple mRNA constructs.

The Current State of mRNA Analytics

“There isn’t a lot of emphasis right now being put on new method development specifically for application to multivalent mRNA vaccines. And I think this is surprising given just how many multivalent mRNA vaccines are currently in clinical development,” begins Dr. Dawson.

Despite a surge in multivalent vaccine candidates — ranging from combination influenza and coronavirus vaccines to seasonal influenza and respiratory syncytial virus (RSV) formulations — many current analytical methods, such as mass spectrometry and sequencing-based approaches, face significant challenges. These methods often require extensive sample preparation, complex bioinformatics or specialized lab environments, making them less ideal for quality control and release testing, where multiple mRNA constructs are already mixed.

While RT-PCR methods can handle some level of multiplexing, they do require specialized, contamination-free environments.

“So while there certainly have been advancements in mRNA analytics, there hasn’t been a whole lot of advancement with an eye towards the increasing amount of multiplex vaccines that are in the clinical pipeline,” said Dr. Dawson.

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Speed Matters: The Benefits of Rapid mRNA Quantification

Time is a critical factor in vaccine development, and rapid mRNA quantification plays a vital role in reducing development timelines.

“Often, samples end up sitting in a queue prior to analysis, sometimes up to weeks before they actually get analyzed,” explained Dr. Dawson. “And by definition, that waiting delays any actionable information received from those analytics that could help inform the bioprocess, which ultimately then can delay the development time,” she added.

Rapid assays that can deliver same-day results are highly attractive to pharma companies, as they eliminate lengthy sample queues often seen with centralized or outsourced testing. This speed not only accelerates the overall development process but also provides immediate actionable insights for bioprocess adjustments.

Moreover, ensuring reproducibility between different sites is increasingly important given the global nature of vaccine manufacturing. The ability to quantify and confirm identity in real-time enhances efficiency in both bioprocess and quality control laboratories.

Universal Quantification for Influenza mRNA Vaccines

An example of a significant technical challenge in the field is the universal quantification of influenza hemagglutinin (HA) mRNA constructs, a need for upcoming mRNA-based seasonal vaccines.

Dr. Dawson reflected upon the time InDevR, supported by funding from NIIMBL (the National Institute for Innovation in Manufacturing Biopharmaceuticals), developed an identity and quantification universal assay for all HA mRNA constructs in seasonal influenza vaccines: “The key challenges here are the nature of influenza, right?” she noted.

In achieving universal quantification, one of the challenges stems from the continual antigenic drift of the influenza virus, which requires constant updates to the vaccine composition, and therefore it’s mRNA sequences.

Additionally, manufacturers often use proprietary codon optimization schemes, meaning that even mRNA constructs for the same protein may differ significantly at the nucleotide level.

To overcome these obstacles, InDevR focused on meticulous sequence design and the optimization of hybridization conditions.

“In terms of sequence design, we did amino acid sequence alignments of all the recent influenza vaccine strains for each component in the vaccine. And then we assessed that amino acid space for areas of sequence similarity for related viruses. We also had to focus on trying to determine which stretches of those amino acids were going to be less subject to codon optimization,” outlined Dr. Dawson.

She further elaborated on the complexity, saying, “We have these three challenges of being specific against the other vaccine components and then being generally universal to viruses as they mutate over time for a specific component, and to be robust against those different codon optimization strategies.” Since nucleic acid hybridization is highly sensitive to salt conditions and additives, optimizing both specificity and reactivity was critical.

This approach ensured that the assay could balance specificity with sensitivity, even when faced with diverse construct sequences.

The result was a prepackaged, off-the-shelf reagent kit that provided reliable quantification for a wide variety of influenza mRNA vaccine constructs.

Collaborative Insights with Pfizer

Dr. Dawson also highlighted the benefits of custom assay development, sharing her experience collaborating with Pfizer.

Although the work with Pfizer was more straightforward — given the focus on a specific vaccine formulation — it underscored a broader industry need: the transition from high information content methods like sequencing to streamlined, routine identity testing.

“I think what we learned from Pfizer was that the timeline for developing a custom assay from start to finish was quite rapid — on the order of just several months — allowing us to develop and validate a fully off-the-shelf assay for identity and quantity for a multivalent mRNA vaccine,” surmised Dr. Dawson.

The Future of mRNA Analytics

Looking ahead, Dr. Dawson emphasized the need for analytical methods that are truly fit for purpose in multivalent vaccine development. “A lot of the current methodologies that are used to analyze mRNA constructs end up falling apart as you add additional constructs into the mix,” she said.

While sequencing is invaluable early in development to confirm the integrity of an entire mRNA sequence, it may be excessive for routine in-process and final identity testing. Dr. Dawson argued that using sequencing in these scenarios is akin to “using a sledgehammer to crack a nut.”

As multivalent mRNA vaccines become more common, fit-for-purpose analytics will be essential to maintaining efficiency, ensuring quality and delivering effective vaccines to the public faster.

“My hope moving forward is that there’s going to be increased acceptance both by the manufacturers and by the regulators for in-process and QC testing applications that may provide a bit lower information [such as InDevR’s VaxArray platform] but have the benefits of being provided in a prepackaged off-the-shelf kit that enables good reproducibility and standardization across sites.”

Dr. Dawson’s insights underline key metrics for successful mRNA analytics: rapid, providing actionable information and without the need for complicated upfront sample pre-processing.

Through our interview, she captured a sentiment universal to the industry’s desire for a practical, efficient solution that can reliably inform vaccine production without the need for overly complex methods.

This article was created in collaboration with the sponsoring company and the Xtalks editorial team.