Ongoing disease surveillance is a critical tool to mitigate viral outbreaks, especially during a pandemic. Environmental monitoring has significant promise even following widespread vaccination among high-risk populations. The goal of this work is to demonstrate molecular SARS-CoV-2 monitoring in bulk floor dust and related samples as a proof-of-concept of a non-invasive environmental surveillance methodology for COVID-19 and potentially other viral diseases.  Surface swab, passive sampler, and bulk floor dust samples were collected from rooms of individuals infected with COVID-19, and SARS-CoV-2 was measured with quantitative reverse transcription polymerase chain reaction (RT-qPCR) and two digital PCR (dPCR) methods. Bulk dust samples had geometric mean concentration of 159 copies/mg-dust and ranged from non-detects to 23,049 copies/mg-dust detected using ddPCR. An average of 88% of bulk dust samples were positive for the virus among detection methods compared to 55% of surface swabs and fewer on the passive sampler (19% carpet, 29% polystyrene). In bulk dust, SARS-CoV-2 was detected in 76%, 93%, and 97% of samples measured by qPCR, chip-based dPCR, and droplet dPCR respectively. Detectable viral RNA in the bulk vacuum bags did not measurably decay over 4 weeks, despite the application of a disinfectant before room cleaning.  Future monitoring efforts should further evaluate RNA persistence and heterogeneity in dust. This study did not measure virus viability in dust or potential transmission associated with dust. Overall, this work demonstrates that bulk floor dust is a potentially useful matrix for long-term monitoring of viral disease outbreaks in high-risk populations and buildings.

Samples were collected from two different homes, as well as isolation rooms used to quarantine individuals who tested positive for SARS-COV-2. Bulk dust was collected from both homes and from student isolation rooms. Surface swabs and a passive sampler collection were completed in one home. Viral RNA was measured using RT-qPCR, chip-based digital PCR, and droplet digital PCR.