I manually write html pages and upload them. I was surprised to find that Google stated that my site may harm your computer. I checked it out and found that my html was infected with this virus. I scanned my pc and found nothing. Then I uploaded the virus free pages.

A few weeks later I now get the same message. Am I infected or is my web host? I dont have the patch for this vulnerability installed (its happening now).

I've emailed my web host and am waiting for a reply. The server runs linux apparently.

There was probably a security vulnerability at the web host site. I would await their response before doing anything and I would suggest that you don't run any of the coding until you get things squared away.