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Updated: Sep 2, 2025

Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples
Published on: June 30, 2023
Exhaled breath SARS-CoV-2 shedding patterns across variants of concern
Joren Raymenants1, Wout Duthoo2, Tim Stakenborg3
1Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000, Leuven, Belgium; Department of general internal medicine, University Hospitals Leuven, 3000, Leuven, Belgium.
Objectives:
We performed exhaled breath (EB) and nasopharyngeal (NP) quantitative polymerase chain reaction (qPCR) and NP rapid antigen testing (NP RAT) of SARS-CoV-2 infections with different variants.
Methods:
We included immuno-naïve alpha-infected (n = 11) and partly boosted omicron-infected patients (n = 8) as high-risk contacts. We compared peak NP and EB qPCR cycle time (ct) values between cohorts (Wilcoxon-Mann-Whitney test). Test positivity was compared for three infection phases using Cochran Q test.
Results:
Peak median NP ct was 11.5 (interquartile range [IQR] 10.1-12.1) for alpha and 12.2 (IQR 11.1-15.3) for omicron infections. Peak median EB ct was 25.2 (IQR 24.5-26.9) and 28.3 (IQR 26.4-30.8) for alpha and omicron infections, respectively. Distributions did not differ between cohorts for NP (P = 0.19) or EB (P = 0.09). SARS-CoV-2 shedding peaked on day 1 in EB (confidence interval [CI] 0.0 - 4.5) and day 3 in NP (CI 1.5 - 6.0). EB qPCR positivity equaled NP qPCR positivity on D0-D1 (P = 0.44) and D2-D6 (P = 1.0). It superseded NP RAT positivity on D0-D1 (P = 0.003) and D2-D6 (P = 0.008). It was inferior to both on D7-D10 (P < 0.001).
Conclusion:
Peak EB and nasopharynx shedding were comparable across variants. EB qPCR positivity matched NP qPCR and superseded NP RAT in the first week of infection.
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