Using the SQLite backup API, which pretty much corresponds to the .backup CLI command. It doesn't block any reads or writes, so the performance impact is minimal, even if you do it directly to slow-ish storage.
That's not great advice for a large database (and I wouldn't recommend it for small databases either). That incidentally works when the db is small enough that the copy is nearly atomic, but with a big copy, you can end up with a corrupt database. SQLite is designed such that a crashed system at any time does not corrupt a database. It's not designed such that a database can be copied linearly from beginning to end while it's being written to without corruption. Simply copying the database is only good enough if you can ensure that there are no write transactions opened during the entire copy.
A reliable backup will need to use the .backup command, the .dump command, the backup API[0], or filesystem or volume snapshots to get an atomic snapshot.