Kevin McKernan, David J Speicher, Jessica Rose
Copyright: © 2026 McKernan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Recent work by Achs et al. (2025) claimed to demonstrate no excessive residual DNA in COVID-19 mRNA vaccines using four orthogonal approaches. Since this work is being cited by regulatory authorities to claim DNA levels in mRNA vaccines are within limits, it is imperative that a robust public discussion occur regarding the methods strengths and weaknesses. We present a comprehensive critique identifying critical methodological flaws that systematically bias results toward underestimation of residual DNA contamination. These include: (1) inappropriate plasmid molecular weight calculations producing 1.5–10× underestimation (plasmid equivalents), (2) fragment size bias in primer design favoring detection of non-functional sequences over spike-encoding DNA, (3) thermal degradation of samples during library preparation, (4) analytical detection limits exceeding regulatory thresholds, (5) platform limitations excluding detection of kilobase-length DNA fragments, and (6) failure to account for RNA:DNA hybrid formation protecting spike DNA from degradation. Collectively, these flaws render the study's conclusions invalid for regulatory assessment of residual DNA contamination.