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Abstract SARS‐CoV‐2 causes individualized symptoms. Many reasons have been given. We propose that an individual's epitranscriptomic system could be responsible as well. The viral RNA genome can be subject to epitranscriptomic modifications, which can be different for different individuals, and thus epitranscriptomics can affect many events including RNA replication differently. In this context, we studied the effects of modifications including pseudouridine (Ψ), 5‐methylcytosine (m⁵C),N6‐methyladenosine (m⁶A),N1‐methyladenosine (m¹A) andN3‐methylcytosine (m³C) on the activity of SARS‐CoV‐2 replication complex (SC2RC). We found that Ψ, m⁵C, m⁶A and m³C had little effect, whereas m¹A inhibited the enzyme. Both m¹A and m³C disrupt canonical base pairing, but they had different effects. The fact that m¹A inhibits SC2RC implies that the modification can be difficult to detect. This fact also implies that individuals with upregulated m¹A including cancer, obesity and diabetes patients might have milder symptoms. However, this contradicts clinical observations. Relevant discussions are provided.