Check to see if the anti-virus software you are using has a command line interface where you can specify (through parameters) which file you want to check. They use the [man]exec()[/man] function to run the software.
If your anti-virus doesn't have this facility, then I can only suggest that you use one that at least has a real-time scanning facility. This should pick up on viruses as it scans through your files. Any anti-vrus package that is worth its salt should have this facility.