I am not sure if this is what you want, but yesterday I experimented and followed a relatively simple to follow tutorial to add TOTP code 2-factor to my linux VPS server's openSSH login, when I login through Putty on windows. It asks me for a verification code, I plug in my Yubikey, authenticate with my password to the Yubico Authenticator program on my desktop, then I double click my VPS entry and copy the code, paste it into putty and press enter, then enter my account's password and press enter and then I am logged in. Through the process of setting it up I had to maximize my putty window to see the whole QR code, although they do provide the secret in text form that you can manually enter into the authenticator app to add the credential. Here is the guide:
https://www.digitalocean.com/community/ ... untu-16-04I hope that helps you out.