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.

Early Detection of Novel SARS-CoV-2 Variants from Urban and Rural Wastewater through Genome Sequencing and Machine Learning

“…The SARS-CoV-2 virus is a single-stranded RNA virus that can be shed in wastewater through human waste such as feces, saliva, and urine 13,14 . In comparison to clinical testing, wastewater analyses provide a less-biased approach to viral monitoring, particularly in areas with limited healthcare resources and unclear testing hesitancy rates 15–19 . Throughout the COVID-19 pandemic, WBE served as a pivotal and cost-effective tool to monitor and characterize the emergence and spread of SARS-CoV-2 variants of concerns (VoCs), offering early detection for potential outbreaks 8,18,20–23 .…”

“…The SARS-CoV-2 virus is a single-stranded RNA virus that can be shed in wastewater through human waste such as feces, saliva, and urine 13,14 . In comparison to clinical testing, wastewater analyses provide a less-biased approach to viral monitoring, particularly in areas with limited healthcare resources and unclear testing hesitancy rates [15][16][17][18][19] .…”