I hear people saying that there site has been hit with a virus? How can one protect the website? How does the virus infect the site and using what gateway? Does it use the email server?
Thanks for your help

various ways afaik, a few are as follows:

1) an FTP password leaks with the ability to change files on the site, or the password is cracked.

2) an exploit in the servers installation is exploited and the site is changed or a virus installed.

3) an administrator for the domain gets a virus/trojan on his/her computer it is monitored until the user logs onto the site and the password is grabbed.

4) an exploit in the code for the site is found and exploited.

there are thousands of other methods, but those are a few.

any of these methods allow the attacker to gain user/root permissions on the server and install a virus on it.

this must be nightmare for web hosting companies! :angry:
Can we install any anti virus programs? will it reduce the performance of server?

no because once they have root on the box they can simply disable the virus checker. if your machine security of breached the only thing you can do it reformat it !!