Predicting COVID-19 cases using SARS-CoV-2 RNA in air, surface swab and wastewater samples

Abstract

Genomic footprints of pathogens shed by infected individuals can be traced in environmental samples, which can serve as a noninvasive method of infectious disease surveillance. The research evaluates the efficacy of environmental monitoring of SARS-CoV-2 RNA in air, surface swabs and wastewater to predict COVID-19 cases. Using a prospective experimental design, air, surface swabs, and wastewater samples were collected from a college dormitory housing roughly 500 students from March to May 2021 at the University of Miami, Coral Gables, FL. Students were randomly screened for COVID-19 during the study period. SARS-CoV-2 concentration in environmental samples was quantified using Volcano 2nd Generation-qPCR. Descriptive analyses were conducted to examine the associations between time-lagged SARS-CoV-2 in environmental samples and COVID-19 cases. SARS-CoV-2 was detected in air, surface swab and wastewater samples on 52 (63.4 %), 40 (50.0 %) and 57 (68.6 %) days, respectively. On 19 (24 %) of 78 days SARS-CoV-2 was detected in all three sample types. COVID-19 cases were reported on 11 days during the study period and SARS-CoV-2 was also detected two days before the case diagnosis on all 11 (100 %), 9 (81.8 %) and 8 (72.7 %) days in air, surface swab and wastewater samples, respectively. SARS-CoV-2 detection in environmental samples was an indicator of the presence of local COVID-19 cases and a 3-day lead indicator for a potential outbreak at the dormitory building scale. Proactive environmental surveillance of SARS-CoV-2 or other pathogens in multiple environmental media has potential to guide targeted measures to contain and/or mitigate infectious disease outbreaks within communities.

Keywords: Air, surface and wastewater; COVID-19; COVID-19 epidemiology; Environmental surveillance; SARS-CoV-2.

Graphical abstract

Fig. 1

Concentration of SARS-CoV-2 in wastewater, surface and air samples and COVID-19 cases in a UM dormitory, March–May 2021. Maroon vertical lines indicate dates when COVID-19 cases were reported; on two days, 4/19/2021 and 4/23/201 represented by a single line two COVID-19 cases were reported, lines on these days represent two cases each. Black dots indicate days when COVID-19 monitoring occurred in the dormitory and dark orange symbols indicate days when COVID-19 case(s) were detected.

Fig. 2

One-day lagged moving average of SARS-CoV-2 in air and surface samples (on y-axis) with respect to SARS-CoV-2 in wastewater samples (on x-axis), March–May 2021 (wastewater concentration on x-axis). Dark orange symbol shows SARS-CoV-2 values in air and wastewater samples, respectively; red circle around orange indicates COVID-19 case detection; green symbol shows SARS-CoV-2 values on surface and in wastewater samples; brown circle around green circle indicates COVID-19 case detection on days these samples were collected.