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YubiKeys are hardware security keys that provide One Time Pads (OTP), namely U2F (Universal 2nd Factor) cryptographic tokens through a USB and/or NFC interface. This means you have to explicitly authorize a new SSH session by tapping the YubiKey. The private SSH key, which is normally on your SSD or cloud instance, should be useless to a malicious user who does not have access to the physical YubiKey on which the second private key is stored.
Configuring 2FA (Two Factor Authentication) with YubiKeys on SSH sessions is ideal for bastion hosts, also known as stepping stone servers that connect to your VPC (Virtual Private Cloud).