mRNA technologies have rapidly advanced over the past decade, fueled by breakthroughs in RNA modification chemistry, delivery systems, and large-scale manufacturing. The success of mRNA vaccines during the COVID-19 pandemic showcased the platform’s speed, flexibility, and clinical potential—placing mRNA squarely at the center of next-generation therapeutics.

Unlike DNA-based drugs, mRNA does not integrate into the genome and is naturally degraded through normal metabolic pathways. It does not need to enter the nucleus to function, and its in vitro transcription (IVT) manufacturing process allows fast, sequence-specific design. These advantages make mRNA uniquely suited for precision medicine, from vaccines to protein replacement and personalized immuno-oncology therapies.

Today, mRNA vaccines and therapeutics are being explored across a wide range of indications—including cancer immunotherapy, infectious disease prevention, metabolic disorders, and cardiovascular disease. As the market grows, so does the importance of robust, regulatory-aligned quality and safety control strategies throughout the entire mRNA development and manufacturing lifecycle.

Regulatory Landscape: Evolving Standards for mRNA Quality Control

Although mRNA vaccine manufacturing appears relatively straightforward, its regulatory framework is new and rapidly evolving. Agencies worldwide—including the U.S. FDA, USP, EMA, WHO, and China’s CDE—have introduced guidelines addressing identity, purity, impurities, potency, and manufacturing controls for mRNA products.

Table 1. Key Global Guidelines and Pharmacopoeial Requirements

Year	Document	Agency
2024	Analytical Procedures for Quality of mRNA Vaccines and Therapeutics (Draft, 3rd Edition)	USP
2023	Analytical Procedures for mRNA Vaccine Quality (2nd Edition Draft)	USP
2022	Analytical Procedures for mRNA Vaccine Quality (Draft)	USP
2021	Q&A for Comirnaty (COVID-19 Vaccine mRNA)	FDA
2021	Quality, Safety and Efficacy of mRNA Vaccines: Regulatory Considerations	WHO
2021	Development Support and Evaluation Procedures for COVID-19 Vaccines	EMA
2020	China’s mRNA vaccine R&D and CMC technical guidelines	CDE

The most recent (2024) USP draft introduces several notable updates:

• Every batch of plasmid DNA used for IVT must be tested before release
• More detailed requirements for host cell residual RNA testing and acceptance criteria
• New purity requirements for process-related impurities—including residual T7 RNA polymerase

(the first time a single-enzyme impurity is specifically highlighted for mRNA drug QC)

These updates reflect the industry's need to strengthen analytical rigor as mRNA platforms expand beyond pandemic-driven vaccine development into broader therapeutic applications.

Quality Control Across the mRNA Manufacturing Workflow

Each stage introduces potential impurities—host cell DNA, host cell proteins, enzyme residues, dsRNA by-products, endotoxin, and more. Effective QC strategies ensure that mRNA products meet safety, potency, and purity expectations for clinical and commercial use.

Figure 1. Quality control products of Yeasen in the mRNA drug research and development and production process.

Yeasen Integrated Quality Control Solutions for mRNA Vaccines and Therapeutics

To support developers navigating this complex landscape, Yeasen offers a comprehensive portfolio of quality and safety control kits covering early-stage plasmid template testing, in-process IVT monitoring, and final product release analytics.

Table2. Product Qualifications & Performance

Category	Feature	Description
Product Qualifications	IND Filing Support	Several products have been successfully included in IND submissions and approved by China CDE and the U.S. FDA.
	Regulatory Compliance	Fully validated according to ChP, USP, and ICH Q2(R1) guidelines; performance meets both domestic and international regulatory standards.
	Audit Support	Manufactured under an ISO 13485–compliant quality system with complete audit-ready documentation.
	Quality Assurance	All raw materials are independently developed; enzyme formulations (e.g., qPCR Mix) are produced in an ultra-clean enzyme manufacturing facility.
Product Performance	High Sensitivity	Lower limit of quantification (LLOQ) reaches fg/µL for nucleic-acid assays and pg/mL for enzyme/protein assays.
	High Precision	Excellent within-batch repeatability and minimal batch-to-batch variation.
	High Accuracy	Spike-in recovery rates maintained within 70–130%.
	High Specificity	Strong specificity with no interference from exogenous DNA, RNA, or proteins.
	Strong Anti-Interference	Internal controls included to rule out sample inhibition, matrix interference, or reaction setup errors.

Host Cell Residual Nucleic Acid Detection

Residual host cell DNA and RNA are critical quality control parameters in biopharmaceutical production due to potential risks of immunogenicity, infectivity, and tumorigenicity. Regulatory agencies such as the NMPA (China), FDA (U.S.), EMA (Europe), and ICH guidelines (Q5A/Q6B) all require that residual host cell nucleic acids be minimized and quantitatively monitored.

Residual host cell DNA is a critical safety attribute. Regulatory limits include:

• China Pharmacopeia (ChP 2020): <100 pg/dose for cell-based products; <10 ng/dose for microbial systems (E. coli, yeast)
• European Pharmacopeia (EP 10.0): Typically <10 ng/dose
• FDA: <100 pg/dose for most biologics; Up to <10 ng/dose for high-dose biologics (e.g., mAbs)

qPCR is now the preferred global standard due to its sensitivity and specificity.

Features

• Regulatory Compliance: Fully validated according to ChP, USP, and ICH guidelines.
• Quality Assurance: Enzymes and master mixes are manufactured in an ultra-clean enzyme production facility to ensure superior product quality.
• Audit-Ready: Stable performance with controlled batch-to-batch variation and comprehensive audit documentation available.
• High Sensitivity: LLOQ as low as fg/μL, enabling precise detection of trace nucleic acids.
• Strong Specificity: Highly specific assays unaffected by other exogenous genomic DNA.

Highlight Product- E. coli Host Cell Residual DNA Detection   (Cat#41308)

• Good linearity

Figure 1. Standard curve and amplification plot of E. coli DNA, showing excellent linearity.

• Limit of Quantification (LOQ): ≤ 3 fg/μL
  

Figure 2. Detection limit as low as 3 fg/μL: qPCR detection results for 3 fg/μL E. coli D

Host Cell Protein (HCP) Residual Testing

Residual host cell proteins (HCPs) are a class of unavoidable impurities generated during the manufacturing of biopharmaceuticals, including monoclonal antibodies, cell and gene therapies, and vaccines. The presence of HCPs may reduce the efficacy of therapeutic products and potentially cause adverse toxicological or immunogenic reactions. Therefore, regulatory guidelines worldwide strictly require that HCP levels in biopharmaceuticals be controlled within acceptable limits.

HCP impurities can trigger immunogenicity or impact product stability. Regulatory expectations include:

• CHO-derived biologics: <500 ppm
• E. coli-derived biologics: <100 ppm
• USP <1132>: HCP levels typically below assay detection limits

Both the Chinese Pharmacopoeia (ChP) and the United States Pharmacopeia (USP) recommend the use of ELISA for HCP detection. Due to its simplicity, speed, and high-throughput capability, ELISA has become the gold standard for HCP testing in the industry. Yeasen Biotechnology has independently developed a series of HCP ELISA kits—covering CHO, E. coli, and HEK293 host systems—that enable rapid and efficient detection of residual HCPs in samples.

Features

• Regulatory Compliance – Fully validated in accordance with regulatory requirements such as ChP, USP, and ICH guidelines.
• Quality Assurance – All critical reagents, including detection antibodies and reference standards, are independently developed and manufactured in-house, ensuring high quality and full traceability.
• Audit Support – Stable production processes with low lot-to-lot variability and comprehensive documentation available for regulatory audits.
• High Sensitivity – Limit of Quantification (LLOQ) reaching ng/mL levels.
• High Specificity – Excellent specificity with minimal interference from other foreign proteins.

Highlight Product- E. coli HCP Residue ELISA Detection Kit   (36712ES)

• Detection Range: 3.125–200 ng/mL, R² = 0.999.

For all tested concentrations, the coefficient of variation (CV) is ≤ 5%.

Table 3. Standard curve

Standard Concentration (ng/mL)	Measured Mean (ng/mL)	Recovery (%)	CV (%)
200	196.600	98.3%	2.1%
100	102.782	102.8%	1.8%
50	48.470	96.9%	0.9%
25	25.160	100.6%	3.6%
12.5	13.719	109.8%	1.9%
6.25	7.223	115.6%	4.2%
3.125	3.711	118.8%	2.4%
0	—	—	—

Residual Enzyme Testing for mRNA Synthesis

During large-scale production of mRNA vaccines, key process enzymes—including T7 RNA Polymerase, Inorganic Pyrophosphatase, Vaccinia Capping Enzyme, and RNase Inhibitor—are essential for in vitro transcription, pyrophosphate removal, 5' cap formation, and RNA protection, respectively.

However, the use of these enzymes introduces process-related impurities in the form of residual enzyme proteins. To ensure product safety and quality, it is critical to monitor their levels using enzyme-specific ELISA kits throughout the manufacturing process.

Only when the residual enzyme concentrations fall below predefined acceptance thresholds can the purified mRNA intermediate be released for subsequent production steps.These process-related impurities must be quantified to ensure product purity and enable lot release.

 Figure 3. ELISA experimental procedure for detecting residual key enzymes in mRNA synthesis by Yisheng Biotechnology.

Highlight Product-Double-stranded RNA (dsRNA) ELISA kit (36717ES)

• Specificity – Impact of dsRNA Length and Sequence

dsRNAs of different lengths and sequences were tested using each of the four standard types included in the kit.

Results: The assay values are largely unaffected by dsRNA sequence or length.

Figure 4. Testing Results for dsRNAs of Different Lengths and Sequences

• Sensitivity

Limit of Detection (LOD): The LOD is defined as the concentration corresponding to the mean of 24 blank (zero standard) OD values plus two times the standard deviation (Mean + 2SD), interpolated from the standard curve.

Table 4. Limit of Detection

dsRNA Standard Type	Blank Mean (OD)	Blank SD (OD)	Mean + 2SD (OD)	LOD (pg/μL)
Unmodified	0.016	0.00048	0.01696	≤0.001
pUTP-Modified	0.016	0.00072	0.01744	≤0.001
N1-Me-pUTP-Modified	0.034	0.00119	0.03638	≤0.001
5-OMe-UTP-Modified	0.115	0.00290	0.1208	≤0.01

Related Products

Category	Catalog No.	Product Name	Specification
Sample Pre-processing Kits	18461ES	Magnetic Residual DNA Sample Preparation Kit (Bottle)	25T / 100T
	18469ES	Magnetic Sample Preparation Kit (Bottled, Fast Version)	25T / 100T
Host Cell Residual DNA Detection Kits	41308ES	E.coli Host Cell DNA Residue Detection Kit (2G)	50T / 100T
	41323ES	Plasmid DNA Residue Detection Kit	50T / 100T
DNA Fragment Analysis Kits	41337ES	E.coli Host Cell Residual DNA Size Analysis Kit	4×50T / 4×100T
Residual RNA Detection Kits	41318ES	E.coli Host Cell RNA Residue Detection Kit	50T / 100T
Host Cell Protein (HCP) ELISA Detection	36712ES	E.coli HCP ELISA Kit	48T / 96T
	36721ES	E.coli HCP ELISA Kit (Plasmid)	48T / 96T
Process Enzyme Residual Detection	36705ES	T7 RNA Polymerase ELISA Kit	48T / 96T
	36706ES	Inorganic Pyrophosphatase ELISA Kit	48T / 96T
	36707ES	Murine RNase Inhibitor ELISA Kit	48T / 96T
	36709ES	Vaccinia Capping Enzyme ELISA Kit	48T / 96T
	36717ES	Double-stranded RNA (dsRNA) ELISA Kit	48T / 96T
	41309ES	RNase Viability Assay Kit (Fluorescent Labeling)	1×96T / 5×96T
	41322ES	DNase Viability Assay Kit (Fluorescent Labeling)	48T / 192T