There are many options how to scan your server for viruses or malware. One of them is clamv software.
1. Here is how to install it e.g. on Centos:
yum install clamav clamd
2. Than refresh the virus database with command:
you can schedule this command as cron task to update virus database periodically
3. To scan whole server for viruses execute command:
ionice -c3 nice -n 19 /usr/bin/clamscan -r --bell -i /
ionice and nice we used to minimize impact of scanning on other applications running on server