There are no OS X viruses currently in circulation. A Trojan does not slow your computer.
Fact: People say "slow" for any of four meanings...
-- Safari is slow loading web pages (Test your connection speed at the link below. Should be 500 or higher. Fix a low speed by paying for a wider bandwidth account with your Internet service company).
-- Youtube HD videos stall and start again. (Fix this also with a wider bandwidth account). This is not really slowness, but is a dropping of video frames -- the movie just stops for a second, and then starts again. Slow video, on the other hand, is called "Slow motion" and means people look like they are floating through the air when they jump.
-- Word or other font-using app is slow to launch (Fix by troubleshooting, or reducing the number of, fonts).
-- The third or fourth big app you try to launch is slow to open (Fix by buying/installing more RAM).
-- All kinds of slowness is happening. For this, read on...
Fact: Computer systems run "overall" slower than optimum for these four reasons...
-- Bad RAM, although you would expect other glitches besides just slowness. Test RAM with Rember, link below. Replace RAM that tests bad-- Did I need to mention that? Haha!
-- The HDD file system has minor corruption. (Fix it using Disk Utility).
-- The HDD is full (Needs at least 10% available space. Fix it by trashing large documents you downloaded and EMPTY THE TRASH -- many people forget to do this).
-- The user account has too many or too big Login Items. (Fix it by removing Login Items).
Myth: "Having lots of files on the HDD slows the computer." This is utter nonsense, as only system and user login files load into RAM. The documents just hanging out on the HDD are not affecting the system's speed at all. Those 10,000 songs on the HDD do not play every time you start up the system. They just sit and wait.
Myth: "Gremlins accumulate like dust bunnies in the file system and start to block the air or Qi or whatever, thus slowing the computer." Hogwash. Windows can have some malware issues, but OS X does not get slowed by viruses, since there are no actual OS X viruses currently in circulation.
Myth: "Cache, cookies, and history slows OS X." This is my biggest pet peeve. Cache has the explicit job of speeding the system. Cookies and history are simple database text files and have no effect on anything except keeping track of logins or where you've been surfing. Only font cache can sometimes become corrupt, and you clear that quite easily by starting once in Safe Boot.
Myth: "Fragmentation slows OS X." Anyone who has used a Mac for ten years or more (me? 15 years) knows that Mac OS has never had any problem with fragmentation. Only Final Cut Pro has some issues with dropped frames when dealing with many huge (10 GB or larger) video files during rendering to a fragmented drive volume. That's why all pro video editors use a huge external HDD (or several), copy from one HDD to another, erase that first HDD, and never render to the system volume. That nips fragmentation in the bud. For us non-pro video editors, it just doesn't matter. Even if you run a defrag app, it finds such a tiny amount of fragmentation as to amaze you, and no speed improvement comes from it.
Truth: Erasing the HDD and installing the OS fresh will fix three of the four reasons above, but it is unnecessary. Do the fixes listed for these four issues above. There are exactly two reasons to erase a computer's startup drive:
-- The file system has problems that cannot be repaired by Disk Utility.
-- The startup drive is full, and you don't know how or don't want to take the time to delete stuff.
There are a couple of very rare issues that can cause HDD space to disappear mysteriously in OS X, but don't think about it until you attend to the four likely suspects above.