Vaccines so far are as effective as naturally acquired immunity. The body doesn't seen to care where the message came from. But even if somehow the body could distinguish some difference the fact is many of us wouldn't survive the natural process.
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This is true for the classical vaccines, but not necessarily for artificially introduced mRNAs. Did you know that up to 40% of the mRNA molecules are truncated (not full length) and therefore may be transcribed to shortened proteins with possibly other conformation and thus other epitopes?