Indoor Dust as a Matrix for Surveillance of COVID-19

Abstract

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 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) monitoring in bulk floor dust and related samples as a proof of concept of a noninvasive environmental surveillance methodology for coronavirus disease 2019 (COVID-19) and potentially other viral diseases. Surface swab, passive sampler, and bulk floor dust samples were collected from the rooms of individuals positive for COVID-19, and SARS-CoV-2 was measured with quantitative reverse transcription-PCR (RT-qPCR) and two digital PCR (dPCR) methods. Bulk dust samples had a geometric mean concentration of 163 copies/mg of dust and ranged from nondetects to 23,049 copies/mg of dust detected using droplet digital PCR (ddPCR). An average of 89% of bulk dust samples were positive for the virus by the 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 infectivity 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 in high-risk populations and buildings.IMPORTANCE Environmental surveillance to assess pathogen presence within a community is proving to be a critical tool to protect public health, and it is especially relevant during the ongoing COVID-19 pandemic. Importantly, environmental surveillance tools also allow for the detection of asymptomatic disease carriers and for routine monitoring of a large number of people as has been shown for SARS-CoV-2 wastewater monitoring. However, additional monitoring techniques are needed to screen for outbreaks in high-risk settings such as congregate care facilities. Here, we demonstrate that SARS-CoV-2 can be detected in bulk floor dust collected from rooms housing infected individuals. This analysis suggests that dust may be a useful and efficient matrix for routine surveillance of viral disease.

Keywords: COVID-19; SARS-CoV-2; built environment; dust; indoor environment; monitoring; outbreak; surveillance; vacuum; virus.

FIG 1

Heatmap displaying the geometric mean number of copies per microliter of RNA template of samples above the detection limit (samples below detection limit were excluded) (A) and the proportion of samples positive (as a percentage) (B) for bulk dust, surface swabs, and passive sampler as observed with three PCR-based methods. The variable n is the number of samples used to calculate the geometric mean (positive detects) in panel A or proportion of samples positive in panel B. For “Floor Dust,” n refers to the total number of bulk dust samples tested for SARS-COV-2, including the dust samples tested weekly over a period of 4 weeks. Items in white on the room diagram were not sampled, and items in white with a slash in the lower heatmaps were not detected. Colors on the room diagrams represent the average value among all three measurement methods.

FIG 2

(A) RNA concentration of bulk dust samples (average of four bags) from initial collection to 4 weeks as measured by ddPCR, dPCR, and qPCR. Error bars shown represent the 95% confidence interval of each measurement. (B to D) Cumulative normal probability plots for each measurement method show variability of RNA concentration values for each bulk bag collected.