I don’t really know what has replaced it but the it is possibly the one mentioned in this piece about Trump testing positive (PCR) and then negative using a different test.
CDC Is Withdrawing Its PCR Test for COVID | Health.com
https://www.health.com/condition/infectious-diseases/coronavirus/cdc-pcr-test
"Bottom line: The CDC's original PCR test for COVID isn't going away because of inaccurate results—it's just that there are more comprehensive tests available that can help doctors figure out whether you have COVID, the flu, or some other bug, and give you the right treatment. Taking this test "off the market" helps push labs to adopt those other tests that can check for multiple viruses."