I know, same thing happened to @fierito, a friend of mine.

She should start modifying all the comments the virus made, telling what happened and apologizing. For example something like this: https://steemit.com/technology/@heero83/how-to-keep-your-pc-protected-from-viruses-and-your-software-updated-part-ii#@fierito/re-how-to-keep-your-pc-protected-from-viruses-and-your-software-updated-part-ii-100

If she can't change the comments, try with busy.org, steemit is having problems today.

Then she could try to contact with the people that flagged her, and ask them to retire the flag. Start with @spaminator , its vote is very powerfull.

Maybe post an article explaining what happened, something like https://steemit.com/steem/@fierito/sorry-to-every-one

Contact steemcleaners as well to let them know about it. Not sure maybe you can go to #help channel in steem.chat too if they can do something about her reputation since it went down to 0...

And be pacient, it's not difficult to recover the reputation (it's exponential, it's very easy at first and much more dificult with 50 or more), she'll be able to do it with a few posts (she'll have to use voting bots, because at first her posts will be greyed).

Good luck!