Global Profiling of m6A-Associated DRACH Motifs in 9.3 Million SARS-CoV-2 Genomes Uncovers Progressive Loss of Host RNA Modification Signatures

N6-methyladenosine (m6A) is a common host-imposed RNA modification that influences viral replication and immune detection [1, 4, 9]. In SARS-CoV-2, m6A is deposited primarily at DRACH motifs (D = A/G/U, R = A/G, H = A/C/U) sequence signatures that can mark viral RNA for host surveillance [2, 7, 12]. Here, we analyze 9.36 million high-quality SARS-CoV-2 genomes collected between early 2020 and early 2025, mapping over 6.25 billion DRACH motifs to chart the evolution of these epitranscriptomic targets at unprecedented scale. We find a statistically significant decline in DRACH density from an average of 670.2 motifs per genome in 2020 to 664.5 in 2025 (p < 0.001) driven largely by reductions in the most prevalent motifs, AAACA, TAACA, and TGACA. This erosion coincides with the rise of immune-evasive variants like Omicron, suggesting SARS-CoV-2 may be shedding m6A sites to reduce “molecular visibility” to host defenses [10, 13, 18, 22]. Our dataset, DRACHscape, offers a foundational resource for studying RNA modification-driven viral adaptation and host-pathogen conflict [3, 14, 24].