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The answer is yes and no.
Many AV scanners can see inside files that have some simple
encryption, such as some versions of Word DOC files that store the
macros in an unencrypted state. Some can even see through some other
forms of simple encryption.
However, it is safer to assume that all encrypted files will not be scanned
properly for viruses. The vast majority of encryption processes are not
covered by AV scanners (and that is, in a way, a reassuring fact for
those who use encryption).
To properly scan any file, the scanner must have access to the contents
in as pure a state as possible. That is just one justification for running a
real-time scanner set on detection upon write/create. When a file is
decrypted, a temporary or permanent copy is created on the local hard
disk, and the real-time scanner would then scan it.
For more information on this topic, visit these other SearchSecurity resources:
News & Analysis: Scanning encrypted e-mail a tricky proposition
Best Web Links: Encryption
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