VAX-seq: A Glimpse into the Future of mRNA Vaccine Analysis and Quality Assurance

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The advent of messenger ribonucleic acid (mRNA) vaccines has been a game-changer, especially in the context of the COVID-19 pandemic. However, ensuring the quality and purity of these groundbreaking vaccines is paramount. Manufacturing innovations have allowed the production of billions of mRNA vaccine doses, emphasizing the need for rigorous quality control.

The Complexity of Assessing mRNA Vaccine Quality

As mRNA vaccines have taken center stage, assessing their quality has become a critical aspect of ensuring their safety and effectiveness. Traditional methods, while reliable, often lack the speed and efficiency required to meet the demands of large-scale manufacturing.

In a recent study published in Nature Communications, researchers unveiled a promising approach called VAX-seq for analyzing mRNA vaccines. This innovative technique leverages long-read sequencing to comprehensively assess the quality and integrity of mRNA vaccines.

The VAX-seq Method

VAX-seq presents a streamlined procedure for mRNA vaccine analysis, offering a multifaceted examination of critical quality features. The study compared VAX-seq against established industry standards, including chromatography, capillary and agarose electrophoresis, and immunoblotting.

The researchers employed various methodologies, such as Illumina plasmid DNA sequencing, ONT cDNA-PCR sequencing, and Oxford Nanopore direct ribonucleic acid sequencing, to develop a holistic view of mRNA vaccine quality.

Key Quality Features Assessed by VAX-seq

VAX-seq scrutinized several vital aspects of mRNA quality, including:

  1. Sequence Similarity: Ensuring that the mRNA sequence aligns with the intended target.
  2. Integrity: Detecting any signs of fragmentation or degradation.
  3. 3′-Poly(A) Nucleotide Tail Dimension: Measuring the length of the poly(A) tail, a crucial element for mRNA stability and function.
  4. RNA and DNA Contamination: Identifying any impurities that could compromise safety.

To complement VAX-seq, the researchers developed a software toolbox that automates reporting on mRNA quality, streamlining the analysis process.

Testing VAX-seq with eGFP mRNA

The researchers applied VAX-seq to evaluate enhanced green fluorescent protein (eGFP) mRNA, using it as a reference to validate the methodology. The study involved the amplification of a plasmid template in Escherichia coli, which was subsequently purified and linearized. The linearized plasmid DNA template served as the basis for in vitro synthetic mRNA transcription.

VAX-seq combined with complementary deoxyribonucleic acid (cDNA) sequencing facilitated the examination of the isolated mRNA. The technique strategically attached a reverse transcriptase primer to the poly(A) nucleotide tail’s 3′ terminus, allowing precise measurement of tail length.

Unveiling the Strengths of VAX-seq

The study’s findings showcased VAX-seq’s capabilities in detecting sequence variations, assessing integrity, and ensuring purity. Notably, VAX-seq proved effective in identifying impurities originating from plasmid amplification.

The analysis of eGFP mRNA revealed a predominant peak (77%) closely aligned with the predicted length, along with smaller, fragmented mRNA molecules. Compared to short-read sequencing, VAX-seq delivered more consistent and robust results across replicates.

Understanding mRNA Modifications

The study also delved into the impact of mRNA modifications, particularly N1-methylpseudouridine, on mRNA quality. While these modifications were found to have minimal effects on mRNA characteristics and cDNA sequencing, direct ribonucleic acid sequencing revealed a higher error rate.

Interestingly, modified mRNA vaccines exhibited a greater prevalence of truncated-type transcripts, with a significant proportion falling below 500 nucleotides in length. Direct ribonucleic acid sequencing identified base-calling errors related to N1-methylpseudouridine, affecting the messenger RNA length profile.

The Promise of VAX-seq

In conclusion, VAX-seq emerges as a promising long-read sequencing approach for assessing crucial mRNA vaccine quality attributes. Its potential significance lies in its ability to offer a comprehensive evaluation at various stages of mRNA vaccine development and production.

VAX-seq provides a sensitive and quantitative assessment of mRNA features, surpassing traditional analytical techniques in efficiency. Furthermore, its real-time capabilities allow for rapid testing shortly after manufacturing.

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This innovative method also holds promise for identifying off-target ribonucleic acid contaminants and potential vaccine degradation, offering a valuable tool for large-scale quality validation of vaccine batches.

Exploring the Potential of mRNA Vaccines

mRNA vaccines represent a groundbreaking approach to disease prevention. They introduce messenger RNA into cells, instructing them to produce a specific protein that triggers an immune response. This response leads to the production of antibodies, bolstering the body’s defense against future infections.

mRNA vaccines offer several advantages, including rapid development, safety, and versatility in targeting various diseases. While mild side effects like localized pain and fatigue may occur, these vaccines have proven highly effective in combatting diseases such as COVID-19, influenza, and Zika.


Frequently Asked Questions (FAQs)

  1. What is VAX-seq?
    VAX-seq is an innovative long-read sequencing approach used to assess the quality and integrity of mRNA vaccines. It offers a comprehensive evaluation of critical quality features, including sequence similarity, integrity, poly(A) tail dimension, and contamination.
  2. How does VAX-seq compare to traditional methods for assessing mRNA vaccine quality?
    VAX-seq surpasses traditional methods in efficiency and sensitivity. It can detect sequence variations and impurities with greater precision, making it a valuable tool for large-scale vaccine quality validation.
  3. What are the key quality features assessed by VAX-seq?
    VAX-seq examines sequence similarity, integrity, 3′-poly(A) nucleotide tail dimension, and RNA and DNA contamination in mRNA vaccines.
  4. Can VAX-seq be used for quality control of other mRNA-based products besides vaccines?
    Yes, VAX-seq’s versatile approach can be applied to assess the quality of various mRNA-based products, including therapeutics and research reagents.
  5. What are the potential applications of VAX-seq beyond vaccine quality assessment?
    VAX-seq holds promise for identifying off-target ribonucleic acid contaminants and potential degradation in mRNA-based products, making it a valuable tool for research and development in the field of mRNA therapeutics.

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