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.

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.

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.

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.

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.

Data will be available upon request to the corresponding author.

Editor-in-Chief: Geraldo Pereira Jotz.

Received: 07 May 2023

Accepted: 10 March 2025

Article published online:
03 March 2026

© 2026. The Author(s). This is an open access article published by Thieme under the terms of the Creative Commons Attribution 4.0 International License, permitting copying and reproduction so long as the original work is given appropriate credit (https://creativecommons.org/licenses/by/4.0/)

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Bibliographical Record
Stijn Bogaert, Hannah Lukasik, Panagiotis Georgiou, Philipp Gude, Sonja Farajzadeh, Stefan Dazert, Olaf Michel, Konstantin van Ackeren, Stefan Volkenstein. Hidden SARS-CoV-2 Omicron Infections in Young Children: What Routine Tests Do Not Tell. Int Arch Otorhinolaryngol 2026; 30: s00451809649.
DOI: 10.1055/s-0045-1809649