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# Assemblies-of-putative-SARS-CoV2-spike-encoding-mRNA-sequences-for-vaccines-BNT-162b2-and-mRNA-1273
##version 0.2Beta 03/30/21: (update intended to (i) clarify the clinical and research importance of sequence information and strand topology measurements, and (ii) clarify that the mRNA sequence is not a recipe to produce vaccine)##
##version 0.21Beta 04/14/21: (updates intended to (i) clarify the clinical and research importance of sequence information and strand topology measurements, and (ii) clarify that the mRNA sequence is not a recipe to produce vaccine)##
Dae-Eun Jeong, Matthew McCoy, Karen Artiles, Orkan Ilbay, Andrew Fire*, Kari Nadeau, Helen Park, Brooke Betts, Scott Boyd, Ramona Hoh, and Massa Shoura*
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RNA preparations lacking dsRNA are desirable in generating vaccine formulations as these will minimize an otherwise dramatic biological (and nonspecific) response that vertebrates have to double stranded character in RNA (https://www.nature.com/articles/nrd.2017.243). Numerous recent advances have resulted in approaches to minimize dsRNA (e.g. https://pubmed.ncbi.nlm.nih.gov/30933724/, https://pubmed.ncbi.nlm.nih.gov/31900329/); nonetheless measurement remains a continued necessity. In the sequence data that we analyzed, we found that the vast majority of reads were from the expected sense strand. In addition, the minority of antisense reads appeared different from sense reads in lacking the characteristic extensions expected from the template switching protocol. Examining only the reads with an evident template switch (as an indicator for strand-of-origin), we observed that both vaccines overwhelmingly yielded sense reads (>99.99%). Independent sequencing assays and other experimental measurements are ongoing and will be needed to determine whether this template-switched sense read fraction in the SmarterSeq protocol indeed represents actual dsRNA content in the original material.
This work provides an initial assessment of two RNAs that are now a part of the human ecosystem and that are likely to appear in numerous other high throughput RNA-seq studies in which a fraction of the individuals may have previously been vaccinated.
Despite the transience of RNA from any individual inoculation, these mRNA vaccines and their derivatives will likely continue to be manufactured and administered as key tools for taming the ongoing COVID pandemic. In such context, this work provides an initial assessment of two RNAs that are now a part of the human ecosystem and that are likely to appear in numerous other high throughput RNA-seq studies in which a fraction of the individuals may have previously been vaccinated.
ProtoAcknowledgements: We thank our colleagues here for their help and suggestions (Nimit Jain, Emily Greenwald, Nelson Hall, Lamia Wahba, William Wang, Amisha Kumar, Sameer Sundrani, David Lipman, Marc Salit), and additionally acknowledge numerous colleagues who have discussed and educated us (directly and indirectly) in areas of RNA synthesis enzymology, vaccine design, and software engineering.