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PCRを推奨しないのではなく、１回の検査で新型コロナウイルスとインフルエンザウイルス（AとB）を検出する手法をリリースしたので、そちらに切り替える話だと思うが？

CDC released a second assay in July 2020, the CDC Influenza SARS-CoV-2 (Flu SC2) Multiplex Assay, which permits public health laboratories to run three tests in a single reaction well. The Flu SC2 Multiplex is more efficient in its use of test reagents, allows higher throughput, and simultaneously gives accurate results about the presence of SARS-CoV-2, influenza A, and influenza B nucleic acid in a patient specimen.
https://www.cdc.gov/coronavirus/2019-ncov/lab/testing.html