Diagnostic yield of reflex multiplex PCR after a negative rapid antigen test in children hospitalized with presumed viral acute respiratory tract infection: a prospective cohort study.

backgroundAcute respiratory infections, mostly viral, are a leading cause of childhood hospitalization. Rapid antigen tests are fast but cover few viruses; multiplex PCR detects many more. The value of reflex PCR after a negative antigen test is uncertain.

aimsTo compare the diagnostic yield of antigen testing alone and with reflex multiplex PCR, and to describe the viral spectrum, age associations, and antibiotic exposure.

methodsIn this single-center prospective cohort, 245 children hospitalized with presumed viral acute respiratory infection (October 2022-October 2023) underwent a five-target rapid antigen test; antigen-negative children had reflex multiplex PCR at the physician's discretion. This was a diagnostic-yield study under partial verification; sensitivity and specificity were intentionally not estimated.

resultsA virus was detected in 140 of 245 children (57.1%); antigen testing alone identified 59 (24.1%). Of 186 antigen-negative children, 99 underwent reflex PCR and 81 (81.8%) were positive (48 with a missed panel-covered virus, 33 with off-panel viruses only). Rhinovirus/enterovirus, not covered by antigen testing, was most frequent (27.9% of identified children). Antibiotics were given to 198 children (80.8%), with no significant difference by viral detection (p = 0.103). Blood cultures and atypical bacterial targets were negative in tested children; typical respiratory bacteria were not systematically investigated.

conclusionsA negative antigen test did not exclude a respiratory virus; reflex PCR improved detection, varying by virus and age. With selective testing, the yield is a lower bound. Antibiotic exposure was high regardless of viral detection; its appropriateness could not be judged without systematic bacterial testing.