Please beware that on February 23, 2018 GitHub.com deprecated some of the security algorithms in their ssh implementation and the tools which did not have support for the newer algorithms stopped working.
TeamCity versions before version 2017.2.1 are partially affected.
It is recommended to upgrade to the latest TeamCity version which already has all the necessary support.
Patches for TeamCity versions 10+ are also available. Check all the details and links to the patches. Upgrade to the latest is highly recommended for all the earlier versions.
As a workaround you can try switching to "https://" URL in the affected VCS roots and provide your github.com credentials for authentication. This will work however only if you run TeamCity with Java 1.8. For agent-side checkout make sure to upgrade native git client on agent machines as old git can still fail with error like "unable to access 'https://github.com/...': error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version"
Using https might not work for some specific cases, so upgrade is by far the most preferred way to get a fix for this issue and also get a fully supported version with many fixes, improvements, latest security updates and lots of new features.
The error can manifest in the messages like:
List remote refs failed: com.jcraft.jsch.JSchException: Session.connect: java.net.SocketTimeoutException: Read timed out
Unable to collect changes: Failed to collect changes, error: List remote refs failed: com.jcraft.jsch.JSchException: Algorithm negotiation fail
List remote refs failed: com.jcraft.jsch.JSchException: Session.connect: java.io.IOException: End of IO Stream Read
There was a problem while connecting to github.com:22
Could not read from remote repository.
Please make sure you have the correct access rights and the repository exists.
Error downloading patch into temporary file "...": Failed to obtain stream from server. Server status: 404 (Not Found)