Environmental Surveillance of Flood Control Infrastructure Impacted by Unsheltered Individuals Leads to the Detection of SARS-CoV-2 and Novel Mutations in the Spike Gene

Abstract

In the United States, the growing number of people experiencing homelessness has become a socioeconomic crisis with public health ramifications, recently exacerbated by the COVID-19 pandemic. We hypothesized that the environmental surveillance of flood control infrastructure may be an effective approach to understand the prevalence of infectious disease. From December 2021 through July 2022, we tested for SARS-CoV-2 RNA from two flood control channels known to be impacted by unsheltered individuals residing in upstream tunnels. Using qPCR, we detected SARS-CoV-2 RNA in these environmental water samples when significant COVID-19 outbreaks were occurring in the surrounding community. We also performed whole genome sequencing to identify SARS-CoV-2 lineages. Variant compositions were consistent with those of geographically and temporally matched municipal wastewater samples and clinical specimens. However, we also detected 10 of 22 mutations specific to the Alpha variant in the environmental water samples collected during January 2022-one year after the Alpha infection peak. We also identified mutations in the spike gene that have never been identified in published reports. Our findings demonstrate that environmental surveillance of flood control infrastructure may be an effective tool to understand public health conditions among unsheltered individuals-a vulnerable population that is underrepresented in clinical surveillance data.

Keywords: COVID-19; Cryptic mutations; SARS-CoV-2; Spike; Stormwater; Wastewater.

Figure 1

Characterization of SARS-CoV-2 and PMMoV RNA concentrations in environmental water samples (no recovery adjustment) and municipal wastewater samples (with recovery adjustment) from the Las Vegas Metropolitan Area. (A, B) SARS-CoV-2 concentrations and (C, D) PMMoV concentrations (both in log₁₀ gene copies/L) in environmental water samples collected from Flamingo Wash (FW) and Tropicana Wash (TW) from December 2021 to July 2022. The absence of bars for SARS-CoV-2 or PMMoV indicates no detection of the target. (E) Wastewater SARS-CoV-2 concentrations in log₁₀ gc/L (blue line) and sewershed-specific confirmed case counts per 100,000 people (gray bars) for the wastewater treatment plant (WWTP) in this study.

Figure 2

Variant prevalence in environmental water samples (i.e., Flamingo Wash and Tropicana Wash) and wastewater treatment plant (WWTP) samples, as determined by WGS with the following sequencing thresholds: >80% genome coverage at >100-fold sequencing depth.