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Signal and Threema want nothing to do with WhatsApp
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What I'm talking about has nothing to do with the line protocol. Each client has encryption key pairs. The public key of the first party shares it with the other parties, and vice versa. If it's encrypted with the public key then the private key can decrypt it.
If Meta gets the private keys, they can decrypt any message they want independent of whatever protocol is being used.
But aren't these key pairs generated per session and/or per contact? So once you switch to a more secure / auditable client this only matters when communicating with people on whatsapp. But they presumably have a backdoor in their app for the NSA anyway.