How Can We Check Is our site has virus or not. Firstly our site will be slow down automatically if it is attacked by virus or some other activities also may showing that your site has been attacked by a virus.
so spamy links showing in your site so its also another case of virus attack

check this site it has a virus attack and I repaired this site and now its all right ...
Movie site

Virustotal scans websites for viruses as well

Yup May be this is fine xp78 but not for all cases so its depends upon the problem.

Trend Micro Housecall suggested by jim can anyone tell me if any one use this for scanning...

hire a security consultant company for security assessment and present them with your logs, perhaps they can dig something out of them if the system is infected by malware such as communication to command and control server
However, if you want to do it yourself and you have no experience I would highly advise you to check those courses Here

If your antivirus software is telling you that a file contains a virus, you shouldn't blindly assume that you're dealing with a false positive; use that opportunity to ask yourself if you really need to install that application. If you do, make sure to check with VirusTotal first, make sure the download is from a reputable place, and then make that judgment call on your own.

by cheking firewall option in antiviras API.

it can be get DDOS attack, if yur site going slow down. it's not virus