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Second, if the file was infected would Calibre pick that up when converting the format?
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Your anti-virus should alert you the second the file is placed on your computer. That said, no way I'd buy ebooks from anyone on eBay. It's a safe bet the book or books are pirated, and malware on the files could certainly be a side issue. It isn't worth the risk.
There are plenty of legitimate ways to buy ebooks.