Search history is saved by the browser in use - it's not cached by google or other search engines.
While it is plausible that the file in which the browser saves a search history could be tampered with, I believe that it's more likely that the user got the virus(es) from inappropriate websites, rather than the other way around.
If you have a content filter such as websense or a firewall that saves recent web history, could you check to see if those websites have been visited while the user was at work?
If it's a laptop and they take it off-site, I would consider clearing the searches and viruses and then check the search history at a future date to see if they've returned, or installing a filter such as OpenDNS or a parental control software to block access to such sites.