Background: Influenza is a seasonal epidemic that poses significant health risks. Early antiviral treatment is recommended, making rapid and accurate diagnostic testing essential. Although rapid antigen tests (RATs) are widely used, they have limited sensitivity. In contrast, rapid nucleic acid amplification tests (NAATs) may offer improved diagnostic accuracy. This study compares the performance of a rapid NAAT and RAT for influenza in the emergency department.

Methods: This prospective comparative study evaluated the rapid NAAT (ID NOW Influenza A&B, Abbott) and the RAT (BD Veritor System for Rapid Detection of Flu A + B, BD). Paired nasopharyngeal swabs were tested as point-of-care tests. Discordant results and agreement between the two tests were evaluated.

Results: A total of 453 patients were analyzed from December 2023 to February 2025. Mean age was 50.6 ± 20.6 years; 239 (52.8 %) were male. Influenza was detected in 166 (36.6 %) patients. Mean time from symptom onset to testing was 32.4 ± 62.1 h. Rapid NAAT-positive but RAT-negative cases were significantly more frequent (P < 0.001), supporting the higher sensitivity of the rapid NAAT. Cohen´s kappa coefficient between tests was 0.750 (95 % CI 0.685-0.815, P < 0.001). This suggests systematic differences in sensitivity rather than random disagreement. Among patients tested within 48 h of symptom onset, discordance remained significant (P < 0.001).

Conclusion: In patients with suspected influenza in the emergency department, although rapid NAAT and RAT demonstrated good agreement, the cases that tested positive by the rapid NAAT but negative by the RAT were significantly more frequent. This suggests that rapid NAAT may be a more suitable diagnostic tool in the emergency department, as rapid NAAT can help avoid false negatives, enable timely antiviral treatment, and improve clinical decision-making within the critical treatment window.