Advancements and challenges in next-generation mRNA vaccine manufacturing systems

Abstract

The coronavirus disease 2019 pandemic has accelerated the global adoption and development of messenger RNA (mRNA) vaccine technology. While traditional manufacturing approaches rely on centralized and batch-based processes that are limited in scalability and accessibility, recent innovations in modular, decentralized, and continuous-flow production systems offer promising alternatives. This review summarizes the evolution of mRNA manufacturing, examines technological advances such as BioNTech’s BioNTainer and Quantoom’s Ntensify, and critically evaluates persistent barriers including raw material supply, regulatory compliance, sustainability, and cold-chain requirements. The implementation of artificial intelligence, thermostable formulations, and self-amplifying mRNA technologies are discussed as future directions. Collectively, these innovations offer a pathway to equitable, scalable, and rapid vaccine deployment in the context of both pandemics and routine immunization.

INTRODUCTION

Messenger RNA (mRNA) vaccines have emerged as a powerful and versatile platform for combating infectious diseases, cancer, and other health threats [1]. Their successful deployment during the coronavirus disease 2019 (COVID-19) pandemic marked a significant milestone, showcasing their potential for rapid development, scalable production, and robust immunogenicity [2,3]. Unlike traditional vaccine platforms that rely on cultured cells or recombinant proteins, mRNA vaccines are produced through entirely cell-free processes, offering advantages in developmental speed and adaptability to emerging pathogens [1,2].

Despite these strengths, conventional mRNA manufacturing is encumbered by significant structural limitations. The predominant production model is centralized and batch-based, requiring extensive infrastructure, skilled personnel, and cold-chain logistics [4,5]. These constraints hinder the global scalability and equitable distribution of mRNA vaccines, particularly in low- and middle-income countries (LMICs) [5,6]. Furthermore, high material costs, regulatory complexity, and environmental sustainability concerns remain unresolved [4,5,6].

In response to these challenges, next-generation mRNA manufacturing systems have emerged. These platforms emphasize decentralization, modularity, automation, and process intensification to streamline production and expand access [1,5,6]. This review evaluates the technical and economic limitations of conventional mRNA vaccine manufacturing and explores how next-generation systems—including BioNTainer, Ntensify, and artificial intelligence (AI)-integrated modular platforms—are reshaping the future of global vaccine supply.

CHALLENGES IN CONVENTIONAL mRNA MANUFACTURING

Centralized infrastructure and batch-based inefficiencies

Traditional batch-based mRNA vaccine production is characterized by a series of segmented and compartmentalized unit operations, each of which must be executed independently and sequentially. The process typically begins with bioreactor-based in vitro transcription (IVT), followed by enzymatic digestion of the DNA template, a series of filtration steps to remove impurities and prevent fouling, and multiple chromatographic purifications—including ion exchange, hydrophobic interaction, and size exclusion chromatography [5,7]. These steps are subsequently followed by product concentration and formulation, often via tangential flow filtration or similar techniques. Importantly, each stage in the workflow requires its own set of reagents, equipment preparation, cleaning protocols, and quality validation procedures, contributing to increased operational complexity and reduced throughput [8].

In this mode of manufacturing, production is executed in discrete batches, where each batch undergoes the full sequence of steps before the next is initiated. This inherently discontinuous process architecture introduces significant limitations in terms of operational efficiency. For example, optimal enzymatic activity and mRNA yield occur only within a narrow temporal window during IVT, after which reaction efficiency declines. Consequently, productivity per batch is capped, and enzyme and nucleotide reagents may be used inefficiently. Additionally, because batches are produced independently, variability can arise between lots due to fluctuations in reaction conditions, enzyme activity, or purification efficiency, posing a challenge to consistent product quality (Fig. 1A and C, Table 1) [5,9].

Fig. 1. Comparison of conventional batch-based and microfluidic continuous mRNA vaccine production processes. (A) Schematic representation of conventional batch-based mRNA vaccine production. Each lot (Lot 1, Lot 2, Lot 3) shows a production yield curve over time, with the optimal production window highlighted in yellow, indicating the limited period of maximum efficiency for each batch. (B) Schematic of microfluidic-based continuous mRNA vaccine production. A single, prolonged optimal production window (yellow) is achieved in one continuous reaction, maximizing yield and process efficiency over time. (C) In batch-based systems, reagent concentration decreases, byproduct concentration increases, and enzyme activity declines over time, limiting the optimal production window. (D) In continuous microfluidic systems, reagent and byproduct concentrations, as well as enzyme activity, are maintained at steady levels for an extended period, supporting sustained optimal production and improved process control.

mRNA, messenger RNA.

Table 1. Comparative analysis of batch and continuous mRNA vaccine manufacturing systems.

Variables	Comparison
Productivity & yield	Batch < Continuous
Production consistency	Batch < Continuous
Reagent during reaction	Batch: decrease
	Continuous: sustained
Cost efficiency	Batch < Continuous
Scalability	Batch < Continuous
Byproduct during reaction	Batch: increased
	Continuous: sustained low level
System complexity	Batch < Continuous

mRNA, messenger RNA.

The batch-based approach also limits scalability. Each scale-up effort typically requires larger bioreactors, increased raw material consumption, and more complex downstream equipment, all of which escalate cost and infrastructure demands [7,10]. Furthermore, prolonged downtime between batch runs—due to cleaning, validation, or equipment changeover—leads to suboptimal utilization of manufacturing resources. These factors collectively hinder the responsiveness of batch systems to surges in demand, as seen during the COVID-19 pandemic, and highlight the need for more efficient, scalable, and consistent alternatives to meet global vaccine requirements [11].

Regulatory and supply chain limitations

The global supply chain for mRNA manufacturing is constrained by limited availability of Good Manufacturing Practice (GMP)-compliant raw materials, including plasmid DNA, capping reagents, and lipid nanoparticle (LNP) components [5]. These inputs are often sourced from a small number of manufacturers, creating vulnerabilities during periods of high demand [5,10]. Moreover, over 80 patents cover critical aspects of mRNA manufacturing, posing barriers to technology transfer and collaboration, especially in LMICs [12]. Regulatory frameworks for mRNA vaccines, particularly for innovative processes like continuous IVT or co-transcriptional capping, are still evolving. These novel platforms may require new validation frameworks, potentially delaying approval [10,11]. This blend of intellectual property (IP) restrictions and regulatory uncertainty continues to impede the establishment of regional vaccine manufacturing hubs and limits equitable vaccine distribution.

NEXT-GENERATION mRNA MANUFACTURING SYSTEMS

To overcome the cost, scale, and distribution limitations of conventional mRNA vaccine manufacturing, a variety of next-generation platforms have emerged. These systems incorporate modular architecture, decentralized deployment, process intensification, and digital automation to enable more agile, scalable, and equitable vaccine production.

Modular and decentralized platforms

In response to the inherent limitations of batch-based vaccine manufacturing—including limited scalability, high costs, and centralized infrastructure—there has been a significant shift toward microfluidic-based continuous production systems and decentralized biomanufacturing platforms. These innovations aim to improve throughput, ensure consistent product quality, and expand access to mRNA vaccines globally. Continuous production systems leverage microfluidics to integrate core steps such as IVT, co-transcriptional capping, and downstream purification into a streamlined, automated workflow. This enables sustained enzymatic activity, reduced process variability, and minimized byproduct accumulation, thereby enhancing overall efficiency and reducing costs. Furthermore, real-time monitoring and control over reaction parameters improve process reliability and facilitate regulatory compliance (Fig. 1B and D, Table 1).

BioNTech’s BioNTainer: African deployment case studies

BioNTech’s BioNTainer represents the most comprehensive real-world implementation of decentralized mRNA manufacturing to date (Table 2) [13,14]. Each BioNTainer facility comprises 2 International Organization for Standardization-standard shipping containers—each with 6 interconnected units—dedicated to drug substance (mRNA synthesis) and drug product (lipid nanoparticle formulation), respectively. These modular systems incorporate clean room environments, automated process control, and standardized validation procedures, with a design capacity to produce up to 50 million doses annually.

Table 2. Comparative features of BioNTainer (BioNTech) and Ntensify/Nfinity (Quantoom) modular mRNA vaccine manufacturing platforms.

Aspect	BioNTainer (BioNTech)	Ntensify/Nfinity (Quantoom)
Focus	Decentralized infrastructure	Process optimization and continuous flow
Scalability	Modular expansion	Scale-out with disposables (parallel batches)
Key innovation	Shipable GMP-compliant clean rooms	Modular equipment for in vitro transcription (Ntensify)
Cost efficiency	Reduces logistics and cold-chain costs	Cuts reagent uses and production costs by 60%
Target output	50 million doses/year (COVID-19 vaccine)	5 g mRNA/day (clinical scale)
Regulatory approach	Aligns with African Union and WHO standards	Standardized process for global GMP compliance

mRNA, messenger RNA; GMP, Good Manufacturing Practice; COVID-19, coronavirus disease 2019; WHO, World Health Organization.

Rwanda Implementation (2023–2025): The first operational BioNTainer was deployed in Kigali, Rwanda, in partnership with the Rwanda Biomedical Centre. Real-world performance data reveals several key advantages and challenges.

Advantages observed [14]:

• • Rapid deployment: The facility achieved operational status within 8 months of arrival, compared to 3–5 years typical for conventional vaccine manufacturing facilities.

• • Local capacity building: Over 45 Rwandan scientists and technicians received comprehensive training, creating a sustainable skilled workforce.

• • Cost efficiency: Production costs were reduced by approximately 40% compared to imported vaccines when accounting for logistics and cold-chain expenses.

• • Supply chain resilience: Local production eliminated 6-week shipping delays and reduced dependency on international supply chains during the 2023 mpox outbreak response.

Challenges encountered:

• • Regulatory harmonization: Initial approval process took 18 months due to novel regulatory frameworks required for modular systems.

• • Raw material dependency: Despite local production, the facility still relies on imported GMP-grade materials, creating potential bottlenecks.

• • Skilled workforce retention: High demand for trained personnel across Africa has led to 25% annual turnover requiring continuous training programs.

• • Utilization rates: Current capacity utilization stands at 60% due to limited regional demand coordination.

Quantoom’s Ntensify platform: South African experience

Quantoom Biosciences’ Ntensify platform, operational at Afrigen Biologics in Cape Town, South Africa, represents a complementary approach to decentralized manufacturing using continuous flow technology (Table 2) [15,16].

Technical Performance: The system uses proprietary, single-use disposables in 20 mL modular reactors that can be scaled out in parallel rather than scaled up, enhancing flexibility and operational resilience. Real-world performance data from 2023–2024 operations shows:

Advantages demonstrated:

• • Production efficiency: A single reactor run yields approximately 150 g of mRNA, translating to around 3 million doses at 50 µg per dose.

• • Process consistency: Batch-to-batch variability reduced by 85% compared to traditional batch processes.

• • Rapid adaptation: The construct-agnostic design enabled production of three different vaccine candidates within a 6-month period.

• • Cost reduction: Overall production costs decreased by 60% compared to conventional batch manufacturing.

Operational challenges:

• • Single-use waste: Disposable components generate 40% more plastic waste compared to reusable systems, raising sustainability concerns.

• • Technical complexity: Initial setup required 3 months of optimization, longer than anticipated, due to the novelty of continuous IVT systems.

• • Maintenance requirements: Microfluidic systems require specialized technical support not readily available in the region.

Regional Impact Assessment: The Afrigen-Quantoom collaboration has achieved several measurable outcomes:

• • Training of 35 local scientists in advanced mRNA manufacturing techniques.

• • Establishment of quality control laboratories meeting WHO prequalification standards.

• • Production of 2.1 million vaccine doses for clinical trials across three different vaccine candidates.

• • Technology transfer agreements with 2 additional African institutions.

However, challenges remain in scaling production to commercial volumes, with current output meeting only 15% of projected regional demand.

Quantoom’s Ntensify platform demonstrates significant advancements in mRNA synthesis yield, production capacity, and process efficiency compared to conventional batch systems (Table 3) [5,15,17]. The platform achieves an mRNA synthesis yield of 5.6 mg/mL, surpassing the typical range of 2.0 to 3.5 mg/mL observed in traditional batch processes. A single modular unit can produce up to 33 g of purified RNA daily. Process efficiency is further improved with yields exceeding 4 μg/μL and capping efficiency greater than 90%. Quality metrics indicate double-stranded RNA (dsRNA) contamination is maintained below 150 ng dsRNA/mg RNA, well under regulatory thresholds.

Table 3. Production efficiency and yield improvements of Quantoom’s Ntensify.

Performance metrics	Conventional batch	Ntensify continuous	Improvement factor
mRNA yield (mg/mL)	2.0–3.5	5.6	1.6–2.8×
Daily output (g)	8–12	33	2.7–4.1×
Capping efficiency (%)	75–85	>90	1.1–1.2×
Process time (hr)	48–72	24–36	2.0–3.0× faster
Reagent consumption	Baseline	60% less capping reagent	40% reduction

mRNA, messenger RNA.

Cost comparisons based on industry modeling reveal significant economic advantages for modular continuous processing (Table 4) [5,15,18]. Material cost efficiency is realized through a 60% reduction in capping reagent consumption and an overall 35%–45% decrease in reagent costs due to continuous operation and reduced waste. Single-use consumables cost ranges from $0.18 to $0.24 per dose, substantially lower than the $0.31 to $0.42 per dose typical of batch systems. Automation reduces operator hands-on time by approximately 65%, while facility footprint is decreased by 40%–50%. Capital expenditure for modular setups ranges from $2.8 to $4.2 million compared to $15 to $25 million for conventional facilities.

Table 4. Cost analysis with specific financial metrics.

Cost component	Conventional batch ($/dose)	Modular continuous ($/dose)	Savings (%)
Raw materials	1.85–2.30	1.20–1.65	35–40
Labor	0.45–0.60	0.18–0.28	55–65
Equipment/facility	0.65–0.85	0.35–0.50	40–45
Quality control	0.25–0.35	0.15–0.22	35–40
Total COGS	3.20–4.10	1.88–2.65	40–60

COGS, cost of goods sold.

Process-optimized continuous manufacturing

The Coalition for Epidemic Preparedness Innovations (CEPI)-BiologIC Technologies’ AI-integrated platform merges machine learning (ML) with automated control of IVT and LNP processes to facilitate continuous, end-to-end manufacturing [19]. By adjusting process parameters in real time, the platform aims to reduce human error, increase reproducibility, and accelerate production by up to 50%. Its plug-and-play modularity enables rapid setup in outbreak zones and supports high-throughput experimentation for formulation optimization.

Synthetic DNA and rapid template generation

DNA Script’s SYNTAX platform, in collaboration with CEPI, uses enzymatic DNA synthesis to produce custom oligonucleotide sequences without relying on Escherichia coli fermentation [20]. This reduces the DNA template production time from weeks to days and avoids biosafety concerns associated with bacterial vectors. Paired with automated gene assembly tools, this system enables just-in-time production of full-length DNA templates for IVT, thereby removing one of the upstream bottlenecks in mRNA vaccine production.

LIMITATIONS OF NEXT-GENERATION SYSTEMS

Despite significant improvements, next-generation mRNA manufacturing systems face several technical, operational, and systemic limitations that must be addressed for widespread adoption.

Raw material supply constraints

Even advanced systems remain dependent on a stable supply of high-quality, GMP-grade raw materials—including enzymes (e.g., T7 RNA polymerase), capping reagents, modified nucleotides (e.g., pseudouridine), and specialized lipids for LNP encapsulation. Many of these materials are produced by a limited number of global suppliers, making them vulnerable to geopolitical disruption, demand spikes, or regulatory shortages. For example, in 2021, limited availability of ionizable lipids slowed vaccine rollout even in high-income countries [21].

Operational complexity and workforce limitations

Modular and automated platforms reduce some manual burden, but the underlying processes (e.g., IVT kinetics, LNP formulation parameters, AI system tuning) still require highly trained personnel for setup, calibration, and troubleshooting. LMICs may lack the technical workforce or regulatory infrastructure to deploy and maintain these systems effectively without significant technology transfer, training, and long-term support programs.

Regulatory and quality assurance hurdles

Each modular system must adhere to stringent GMP requirements and pass multiple regulatory audits for process validation, lot release, and equipment qualification. Regulatory frameworks are often not harmonized across regions, which complicates multi-site implementation. Moreover, the novelty of many of these platforms (e.g., continuous IVT, AI integration) may prompt additional scrutiny by regulatory authorities unfamiliar with these technologies, delaying approval and scaling.

Cold-chain and fill-finish bottlenecks

Although upstream processes have seen significant innovation, downstream fill-finish operations remain a bottleneck. Sterile filling of mRNA vaccines, often conducted in glass vials under aseptic conditions, requires expensive infrastructure and is subject to global shortages of components like stoppers and vials. Additionally, many mRNA products still require cold-chain distribution (−20°C to −80°C), which limits deployment in rural and resource-limited areas despite upstream decentralization efforts [22].

Sustainability and environmental concerns

Next-generation platforms frequently rely on single-use plastic bioreactors, tubing, and filtration systems. While these offer sterility and convenience, they raise questions about long-term environmental sustainability, waste disposal, and carbon footprint. Moreover, the use of flammable solvents (e.g., ethanol) for lipid solubilization necessitates special containment and disposal procedures, particularly in mobile or remote manufacturing units.

FUTURE DIRECTIONS

While next-generation mRNA vaccine manufacturing systems have made significant strides in decentralization, cost reduction, and process automation, key innovations are still needed to overcome persistent technical and systemic barriers. The future trajectory of mRNA production will depend on integration of emerging technologies, regulatory harmonization, and commitment to equitable global health infrastructure.

AI and predictive automation

AI and ML are poised to transform bioprocessing by enabling real-time optimization, predictive maintenance, and autonomous quality control [23,24]. Platforms like the CEPI-BiologIC Technologies’ AI-driven system will demonstrate the feasibility of applying data-driven feedback loops to optimize IVT yield, LNP homogeneity, and formulation parameters [19]. Future systems may incorporate closed-loop control to automatically adjust feed rates, temperature, pH, and enzyme concentrations based on real-time process analytics.

AI and ML excel at analyzing the large and often heterogeneous datasets generated throughout the bioprocessing value chain, uncovering hidden patterns, generating actionable insights, and advancing autonomous or semi-autonomous decision-making. For instance, in IVT reaction optimization, ML approaches like Bayesian optimization have significantly reduced the number of experimental runs needed to find optimal conditions, outperforming published industry standards by achieving a 2-fold increase in mRNA yield in half the time (e.g., 12 g/L in 2 hours) [25]. This data-driven approach is particularly valuable when experimental time and resources are limited. Beyond manufacturing, AI could also streamline regulatory submissions through automated documentation, predictive modeling of batch consistency, and simulation-based risk assessments [26]. The application of digital twins—virtual replicas of physical manufacturing processes—offers further opportunities to test and validate new vaccine constructs in silico before initiating production, drastically cutting process development costs and enhancing resilience and productivity in biopharmaceutical manufacturing [23]. Real-world examples, such as Pfizer’s use of a Smart Data Query AI tool, demonstrated the ability to prepare COVID-19 vaccine clinical trial data for review in a mere 22 hours, significantly optimizing the data analysis process and freeing up human resources for critical thinking [27,28,29,30].

Thermostable formulations and cold chain independence

Cold-chain dependency remains a major constraint on global mRNA vaccine distribution. Many current formulations require storage at −20°C or −80°C, limiting their use in regions without robust logistics infrastructure [22,31]. Thermo-stabilization strategies—such as room temperature stable LNP-are being developed to address this challenge. For instance, advancing lyophilized LNP systems that retain structural integrity and immunogenicity when stored at 2°C–8°C could significantly reduce the logistical complexity and cost of vaccine delivery in LMICs and during rapid outbreak responses [32].

Self-amplifying mRNA (saRNA) platforms

saRNA encodes a replicase enzyme derived from alphaviruses or flaviviruses that enables intracellular amplification of the antigenic sequence [33]. This approach offers the promise of ultra-low-dose vaccines—potentially reducing required mRNA quantities by 10- to 100-fold. This can dramatically decrease the cost and material demand per dose, easing supply constraints and improving scalability.

However, challenges remain. saRNA molecules are longer and more structurally complex than conventional mRNA, posing difficulties in IVT yield, purification, and LNP encapsulation [33,34,35]. Furthermore, the introduction of viral replication machinery (RNA-dependent RNA polymerase, RdRp) into human cells is a novel biological experiment without precedent in vaccine technology, raising significant safety concerns [35,36,37]. Unregulated replication could lead to overexpression of viral proteins, potentially causing cytokine storms or other immune-related adverse effects. Different tissues may respond differently to the replication process, raising concerns about localized toxicity or damage. While reactogenicity (the tendency of a vaccine to produce adverse reactions) is generally similar to conventional non-RNA vaccines, individuals susceptible to an autoimmune response may have an adverse reaction. Moreover, there is a theoretical potential for genomic integration, as endogenous LINE-1 retrotransposons in human cells can mediate reverse transcription of RNA into DNA [38,39,40]. These concerns highlight the critical need for thorough long-term safety studies, as current clinical trials are often short-term and may not capture the full spectrum of potential long-term effects of RdRp activity in human cells [33,41]. Further development of saRNA-specific delivery systems and regulatory pathways will be essential.

Global manufacturing equity and technology transfer

Achieving global vaccine equity requires not only technological innovation but also systemic reform of how manufacturing capabilities are shared and deployed. Initiatives like the WHO mRNA Technology Transfer Hub, Afrigen-Quantoom’s collaboration in South Africa, and BioNTech’s BioNTainer deployments exemplify a new model of distributed biomanufacturing.

Future efforts should prioritize:

• • Capacity building: Long-term training of local scientists, engineers, and regulators is paramount for sustainable vaccine production in LMICs. This involves a multi-faceted approach that extends beyond basic operational training for system setup, calibration, and troubleshooting. Comprehensive education should encompass advanced bioprocess engineering, quality assurance protocols, regulatory compliance frameworks specific to mRNA technologies, and equipment maintenance. Specific strategies include:

  • Structured fellowship programs: Establishing international fellowship programs that allow scientists and engineers from LMICs to gain hands-on experience in advanced manufacturing facilities and research institutions in high-income countries. These programs should include practical training in GMP environments, process development, and analytical methods.

  • Regional training centers for regulatory science: Developing and funding regional centers of excellence dedicated to regulatory science. These centers would provide specialized training for local regulators on the assessment and approval of novel vaccine technologies, ensuring they have the expertise to navigate complex regulatory pathways and establish robust local oversight.

  • Long-term mentorship schemes: Implementing long-term mentorship programs that pair experienced professionals from established biopharmaceutical companies with emerging talent in LMICs. This fosters continuous learning, problem-solving skills, and the transfer of tacit knowledge crucial for independent operation.

  • Multilateral funding mechanisms: Securing sustainable investment from global agencies (e.g., CEPI, Gavi, World Bank) specifically earmarked for capacity building initiatives. This funding should support not only infrastructure development but also the ongoing operational costs of training programs, equipment maintenance, and the retention of skilled personnel in LMICs. The goal is to empower LMICs to develop self-sufficient manufacturing capabilities, fostering local expertise in research and development, process optimization, and regulatory oversight, thereby creating a sustainable ecosystem for vaccine production and innovation.

• • Open-access platforms: Shared blueprints for modular facilities and standardized validation protocols.

• • IP licensing reform: Voluntary IP pools or tiered licensing strategies to accelerate technology transfer without compromising innovation incentives.

• • Multilateral financing: Sustainable investment models from global agencies (e.g., CEPI, Gavi, World Bank) to support infrastructure and operational costs.

Environmental sustainability

As the field moves toward single-use, disposable manufacturing systems for flexibility and sterility, environmental sustainability must also be addressed [42]. Large-scale use of plastics, solvents, and energy-intensive processes may conflict with climate goals. Innovations in biodegradable bioreactor materials, solvent recycling, and energy-efficient facility design will be necessary. Additionally, carbon accounting and life-cycle assessments should be integrated into the design and evaluation of next-generation systems. Harmonization with regulatory expectations for environmental impact will support long-term adoption and public trust.

CONCLUSION

Next-generation mRNA vaccine manufacturing systems—including modular, decentralized, and AI-enhanced platforms—represent a critical evolution in global bio-manufacturing. These innovations have the potential to overcome the limitations of centralized batch production and extend the reach of mRNA vaccines to underserved populations. However, significant challenges remain, particularly regarding raw material supply, regulatory harmonization, and environmental sustainability. Continued investment in innovation, global collaboration, and equitable infrastructure development will be vital to ensure that mRNA technology fulfills its promise as a global public health tool.