Rapid antigen tests, immunofluorescent tests, and virus culture have been reported to often lack in assay specificity and/or sensitivity, testing time, and ability to subtype for influenza, compared with molecular methods.  In a study of the nucleic acid amplification tests ID Now (Abbott), Cobas Influenza A/B Assay (Roche Molecular Diagnostics), and Xpert Xpress Flu (Cepheid), Kanwar et al found the three products to have comparable sensitivities for influenza A (93.2%, 100%, 100%, respectively) and B (97.2%, 94.4%, 91.7%, respectively) detection. In addition, each product had greater than 97% specificity for influenza A and B detection. 
Rapid antigen tests generally have a sensitivity of 50-70% and a specificity of 90-95%. Limited studies have demonstrated very low sensitivity for detection of 2009 H1N1 with some commercial brands. [10, 11, 12, 13, 14, 15] A study by Fowlkes et al found that of 3681 patients who tested positive for influenza on real-time reverse transcription polymerase chain reaction (RT-RT-PCR) assay, 40% displayed negative results on rapid influenza diagnostic testing. PCR assays were run for influenza A (H1N1, H1N1pdm09, H3N2) and influenza B. 
In 2017, the US Food and Drug Administration (FDA) reclassified rapid antigen-based tests from class I to class II to improve the quality of these tests for influenza.  The FDA has required manufacturers to meet minimum sensitivity and specificity requirements compared with culture and/or molecular methods,  with these requirements being higher than previously used for FDA clearance of new products. To continue to market these antigen tests, companies had to modify them to meet these new specifications.
Immunofluorescent tests, with nasopharyngeal specimens, have been reported to have high sensitivity and specificity for identification of influenza A and B. 
Very early and very late in respiratory season, and when disease prevalence in the community is low, positive rapid antigen diagnostic test results should be confirmed by an alternate method, such as viral culture or a molecular test. 
Hospitalized patients with a serious respiratory condition should preferably be tested by a molecular method for influenza, and in many cases, institutions are shifting towards respiratory virus syndromic testing, which targets multiple pathogens in a single assay, including parainfluenza, adenovirus, respiratory syncytial virus, coronaviruses, and rhinoviruses/enteroviruses. 
Previously, only high-complexity tests that required a long turnaround time were performed using molecular methods, some of which are listed in Table 4. More recently, simple, rapid molecular tests have been developed and marketed for use as point-of-care devices (waived tests listed in Table 4). These tests are comparable to rapid antigen tests in fulfilling the needs of outpatient clinics in that they are rapid and easy to use as a point-of-care device. In addition, their sensitivity and specificity are similar to those of high-complexity molecular tests. The downside is that they are more expensive than rapid antigen tests.