“CDC encourages laboratories to consider adoption of a multiplexed method that can facilitate detection and differentiation of SARS-CoV-2 and influenza viruses.”
Yes, but the multiplex method is still PCR. Specifically, they seem to be recommending the newly approved BioFire Respiratory Panel 2.1, that identifies 19 respiratory targets, including SARS-CoV-2, in one multiplex PCR test.
On March 17, 2021, FDA granted the first marketing authorization using the De Novo review pathway for the BioFire Respiratory Panel 2.1 (RP2.1) (PDF - 630 KB). The BioFire RP2.1 is for the simultaneous qualitative detection and identification of multiple respiratory viral and bacterial nucleic acids in nasopharyngeal swabs (NPS) obtained from individuals suspected of respiratory tract infections, including COVID-19.