Exhaled breath SARS-CoV-2 shedding patterns across variants of concern

Abstract

Background

We performed exhaled breath (EB) and nasopharyngeal (NP) qPCR and NP rapid antigen testing (RAT) throughout SARS-CoV-2 infections with different variants.

Methods

We recruited 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 (Cochran Q test).

Results

Peak median NP CT was 11.5 (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), 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 (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 It superseded NP RAT positivity on D0-D1 (p=0.003) and D2-D6 (p=0.008).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).

Conclusions

Peak exhaled breath and nasopharynx shedding were comparable across variants. EB qPCR positivity matched NP qPCR and superseded NP RAT in the first week of infection.