No virus found, deleted public_html and started from 0% but Google Keeps index

You need to request Google to re-index your website.

However, if the crawler finds no content at all, it may or may not delete the previously cached pages. In this case, you will need to ask for support from Google WebMaster Tools. For the meantime, you can read these articles and follow the step by step, it may help:

• https://support.google.com/webmasters/answer/6065812
• https://stackoverflow.com/a/15278642
• https://www.google.com/webmasters/tools/submit-url

I hope it helps, good luck!

Thanks @yorman, I’ve already deleted all hacked sites with 404 error, but they keep coming all the time, new 404 pages, and I am not sure why google keeps indexing them. How can I stop this

I don’t have much information about how the Google Crawler works.

I know, however, that anyone can request an URL to be indexed by it. In the past, we have dealt with websites being blacklisted because a 3rd-party forum with no relationship with the original address contained multiple invalid links to the former website.

Reading this answer from 2011 [1]…

I believe you can use the “Fetch as Googlebot” tool to get rid of the broken URLs. You should know that one type of malware infects the access control file, commonly known as “htaccess”, to redirect certain HTTP requests using a specific User-Agent to malicious pages and return a 404 when the expected data is missing. This has happened to many websites that I have cleaned in the past.

Review your main “.htaccess” file before submitting the new “sitemap.xml” to Google.

[1] https://productforums.google.com/forum/#!topic/webmasters/xSJlFyCj7AA