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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can replicate in the upper and lower respiratory tract. We aimed to evaluate whether symptom characteristics and symptom duration prior to sampling are associated with test positivity in upper or lower respiratory tract samples. We conducted a retrospective cohort study in the Central Denmark Region from 14 April 2020 to 2 November 2020 including hospitalised patients with SARS-CoV-2 reverse transcriptase-polymerase chain reaction samples from both the upper and lower respiratory tract within 48 h and at least one positive test result. Of 122 patients, 101 were positive in both samples (83%), 7 (5%) were positive only in the upper respiratory tract sample, and 14 (11%) were only positive in the lower respiratory tract sample. The median number of symptoms was 4 (IQR 3, 5.75) and 5 (IQR 3, 7), respectively, in patients with only a positive upper respiratory tract sample and in concordant positive patients; while 1 (IQR 1, 3) in patients with only a positive upper respiratory tract sample. 98% (120/122) of patients would have been diagnosed with coronavirus disease 2019 if supplemental sampling from the lower respiratory tract was guided by lower respiratory tract symptoms. No substantial difference in the duration of symptoms was observed across the three patient groups. The presence of lower respiratory tract symptoms could have been used to determine whether supplemental sampling from the lower respiratory tract was necessary. Symptom duration was not associated with test positivity in the upper or lower respiratory tract.

Sampling from upper and/or lower respiratory tract when diagnosing coronavirus disease 2019 (COVID-19) – results from a Danish cohort study