Molecular detection of SARS-CoV-2 and other respiratory viruses in saliva and classroom air: a two winters tale

Objectives To compare the prevalence of SARS-CoV-2 and other respiratory viruses in saliva and bioaerosols between two winters and model the probability of virus detection in classroom air for different viruses. Methods We analyze saliva, air, and air cleaner filter samples from studies conducted in two Swiss secondary schools (age 14-17 years) over seven weeks during the winters of 2021/22 and 2022/23. Two bioaerosol sampling devices and HEPA filters from air cleaners were used to collect airborne virus particles in five classrooms. Daily bioaerosol samples were pooled for each sampling device before PCR analysis of a panel of 19 respiratory viruses and viral subtypes. The probability of detection of airborne viruses was modelled using an adjusted Bayesian logistic regression model. Results Three classes (58 students) participated in 2021/22, and two classes (38 students) in 2022/23. During winter 2021/22, SARS-CoV-2 dominated in saliva (19 of 21 positive samples) and bioaerosols (9 of 10). One year later, there were 50 positive saliva samples, mostly influenza B, rhinovirus, and adenovirus, and two positive bioaerosol samples, one rhinovirus and one adenovirus. The weekly probability of airborne detection was 34% (95%-credible interval [CrI] 22%−47%) for SARS-CoV-2 and 10% (95%-CrI 5%-16%) for other respiratory viruses. Conclusions There was a distinct shift in the distribution of respiratory viruses from SARS-CoV-2 during the Omicron wave to other respiratory viruses one year later. SARS-CoV-2 is more likely to be detected in the air than other endemic respiratory viruses, possibly reflecting differences in viral characteristics and the composition of virus-carrying particles that facilitate airborne long-range transmission.