How to clean viruses from web pages

[Neo]

To clean the virus, follow given steps.

1. Most likely these exploits are caused by compromised FTP credentials. So start with your own computer. Scan it for spyware. Some people reported good results with Malwarebytes.
2. Then (from a clean computer) change FTP passwords.
   Try not to store them inside programs that you use to upload files to a server.
3. Whenever possible use secure connections. I.e. use SFTP instead of plain FTP. Many shared hosting plans include SFTP.
4. Finally, remove the malicious code from all server files (.html, .php, .js, etc.). The easiest way to do it, is replace them with clean files from a backup.