The safest way is to backup your data and do a Factory Restore. Then re-download your apps and restore the data previously backed up.
This way the factory shipping image which is compressed in a protected area will be uncompressed during a reboot process. Phone is good as new. Do to this make sure your battery don't run out halfway. This way get rid of everything including ROOTED virus.
Most virus are malware and not so strong as ROOTed virus. However, after long time using and downloading lots of games, it is best to assume you got the strongest ROOTed virus, a clean factory restore will clean up all kinds of shit and get full performance.
Installing anti-virus will slow down your phone and go crazy, especially after installing more than 1 anti-virus, your phone stone like crap. At that stage you can only do Factory Restore.