Try a few good local malware removal tools like:
– Malware bytes anti malware
– Reason Core Security
In general, the issue is local not on network/host side. You could do a full backup swing of data, clean that and then reupload to your webserver. Given that databases are just text and can’t be infected.
Anyways, any professional company host has much stronger than that anyways so any virus wouldn’t stand 2 seconds in a decent hoster/vps/dedicated server environment.
If you host it yourself, use linux and nod – with good iptables – would be a good start ??
Regards,