The application is sending a copy of your files to our cloud. So if they are infected, they will remain infected. However, we encrypt and compress all files, so if one file is infected, it won't infect the rest of your files that are stored on our backup servers. I suggest running anti-virus scan before the online backup runs. And if you ever need to recover files from our cloud, you can recover them, then run a virus-scan before you open them. You an also select a previous version before the backup took place, and roll back to then.
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