Hidden SARS-CoV-2 Omicron Infections in Young Children: What Routine Tests Do Not Tell.

Introduction: The coronavirus disease 2019 (COVID-19) pandemic caused a global emergency. Screening protocols vary regarding the epidemiological situation and the dominant virus variant. Implementing these protocols can be particularly challenging in young children.

Objective: To evaluate the diagnostic accuracy of routine polymerase chain reaction (PCR) testing in small children. Furthermore, hidden severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Omicron infections, missed by routine PCR testing, were intraoperatively analyzed, and multiple testing methods were compared.

Methods: The present prospective cohort study was performed between March and May 2022. All children aged ≤ 6 years who were admitted for adenoidectomy and/or tonsillotomy to the Department of Otorhinolaryngology - Head and Neck Surgery of the Saint Elisabeth Hospital, in Bochum, Germany, were included. Routine PCR swabs were performed ≤ 24 hours before surgery. Intraoperatively, rapid antigen tests, separate naso- and oropharyngeal PCR swabs, adenoid and/or tonsillar tissue for PCR analysis, and serological tests were collected.

Results: We included 55 children with negative preoperative PCR tests. Intraoperatively, SARS-CoV-2 particles were detected in 51% of the sample. Among children without a history of SARS-CoV-2 infection within 90 days before surgery, the prevalence was 43%. Compared with the PCR results regarding tissue, the preoperative PCR screening had a sensitivity of 20%, and, in the intraoperative PCR screening, the optimally performed swabs had a sensitivity of 79%. In total, 29% of the positive cases had a cycle threshold (Ct) value < 30. Nasopharyngeal PCR tests detected significantly more SARS-CoV-2 infections than oropharyngeal swabs.

Conclusion: Routine PCR tests in infants may present a high rate of false-negative results and a low sensitivity. These findings question preoperative screening protocols that include testing asymptomatic children who have recovered from a recent SARS-CoV-2 infection.