Simultaneous detection of multiple viral pathogens in vacuumed dust from different building types

Environmental monitoring of viral pathogens will be a critical tool to prevent morbidity and mortality in future pandemics and yearly disease cycles. One approach in early stages of utilization is monitoring viruses from building dust. To date, these efforts have primarily used PCR-based methods to target individual viruses. Additional methods that can identify multiple viruses simultaneously, and in a semi-quantitative manner, would increase the efficiency and utility of these efforts. The goal of this project was to evaluate a whole-genome, hybrid-capture based high-throughput sequencing approach for measuring pathogens in building dust. We utilized the Illumina Viral Surveillance Panel v2 to enrich for targeted amplification of viral nucleic acid followed by sequencing in 27 samples from school, university, and professional settings. We identified 54 viruses that included pathogens such as SARS-CoV-2, influenza, adenovirus, norovirus, cytomegalovirus, Epstein-Barr virus, and more. Three of the viruses that are known to be associated with childhood infection were significantly more prevalent in child-associated settings than in buildings primarily occupied by adults (fdr p<0.05). A total of 85% of all collected samples contained at least one rhinovirus. Abundances of SARS-CoV-2 and influenza A viruses were estimated with traditional qPCR methods, and were correlated with relative abundances estimated from the sequencing data (R=0.76 and 0.42, p=0.000005 and 0.03, respectively). The methods utilized here measure nucleic acid and does not indicate viability. Overall, our results demonstrate a novel environmental surveillance technique for simultaneous and semi-quantitative measurement of multiple viral pathogens using building dust that can help us better understand viral spread, inform public health policy, and promote health.