Using nanopore sequencing to test mRNA vaccine quality.

Aim

The speed and effectiveness of mRNA vaccines has been demonstrated by the Moderna and Pfizer COVID-19 vaccines. With funding from NCRIS and UQ, we have established the BASE facility, which supports the research and manufacture of mRNA vaccines. The success of mRNA vaccines to COVID-19 has been realised by advances in the scale and purity of manufacture that ensure efficient translation and the stimulation of strong acquired immunity. Therefore, rigorous quality control of manufacture is key to the performance of mRNA vaccines.

Quality control must ensure mRNA purity and yield, as well as the incorporation of modified nucleotides and 5’ caps that have proven essential components of the Moderna and Pfizer COVID-19 vaccines. However, currently, there is currently no public analytical tests to measure the quality of mRNA vaccine manufacturing.

Our project will use direct RNA sequencing to perform a rapid, rigorous quality-control test of mRNA vaccine quality.

Our test will analyse whether:

1. mRNAs are of the correct length and sequence,
2. modified nucleotides are correctly incorporated, and
3. the 5’ cap is present.

Brief project outline

We aim to establish a test that uses direct RNA sequencing to confirm the quality of mRNA vaccines, including the correct incorporation of modified nucleotides and 5’ caps. To develop the test, we will first train an Oxford Nanopore Technology (ONT) base-calling algorithm on synthetic control mRNA vaccines that include modified nucleotides. We will then validate the sensitivity and specificity of our test, and establish a standardised protocol and software package. Finally, our test will be incorporated within the mRNA manufacturing process at the BASE facility, ensuring that the mRNA therapeutics are of the high quality required for preclinical investigations.

Genomics-based innovative aspect of proposal

We aim to develop a new quality test for mRNAs manufactured by the BASE facility at UQ. This test will represent a new capability for UQ. Additionally, our test requires new capabilities to be established to train the ONT base caller to recognise modified nucleotides, such as those incorporated within the Moderna and Pfizer vaccines. We aim to trial different bioinformatics analysis tools as part of our project, and train and validate our software on a range of IVT mRNAs that incorporate modified or unmodified nucleotides. We intend to gain new capabilities in ONT base caller training, so that further modified nucleotides can be incorporated into the mRNA production workflow.

Broad applicability of the technique

We anticipate that the results of our experiment will interest a broad variety of researchers within and external to UQ. We predict that the development of a pipeline to evaluate the quality of new mRNA vaccines will be of great interest to numerous UQ research groups working in infectious diseases, cancer biology and pharmacology. As our test will be integrated into the BASE mRNA production workflow, our research outcomes will impact all researchers that use our mRNA production service. BASE is actively collaborating with numerous UQ, Australian and international researchers, and expects to significantly expand operations in 2022. We anticipate that providing Queensland researchers with high-quality, synthetic mRNAs at a reasonable cost will spur further development of the new technology and position UQ as a world leader in mRNA therapeutic research.

Additionally, in silico methods, scripts, constructs and some of the sequence data used to train the ONT base callers to detect the modified bases will be made freely available in all cases where they are not covered by contractual confidentiality requirements. Interested researchers are expected to span broad clinical biology interests, and we plan to promote our research through seminar presentations on campus to maximise the outcomes of our research.