Applicability of Neighborhood and Building Scale Wastewater-Based Genomic Epidemiology to Track the SARS-CoV-2 Pandemic and other Pathogens.

The benefits of wastewater-based epidemiology (WBE) for tracking the viral load of SARS-CoV-2, the causative agent of COVID-19, have become apparent since the start of the pandemic. However, most sampling occurs at the wastewater treatment plant influent and therefore can only monitor SARS-CoV-2 concentration and spread within the entire catchment, which can encompass multiple municipalities. Furthermore, most WBE only quantifies the virus, and therefore miss crucial information that can be gained by sequencing SARS-CoV-2. Here we demonstrate feasibility of sampling at the neighborhood or building complex level using a mix of quantitative polymerase chain reaction (qPCR) and targeted sequencing to provide a more refined understanding of the local dynamics of SARS-CoV-2 strains. When coupled with the higher-level treatment plant samples, this creates an opportunity for health officials to monitor the spread of the virus at different spatial and temporal scales to inform policy decisions. Here we demonstrate the feasibility of tracking SARS-CoV-2 at the neighborhood, hospital, and nursing home level with the ability to detect one COVID-19 positive out of 60 nursing home residents. The viral load obtained was correlative with the number of COVID-19 patients being treated in the hospital. Sequencing of the samples over time demonstrated that nonsynonymous mutations fluctuate in the viral population, and wastewater-based sequencing could be an efficient approach to monitor for vaccine or convalescent plasma escape mutants, as well as mutations that could reduce the efficacy of diagnostics. Furthermore, while SARS-CoV-2 was detected by untargeted RNA sequencing, qPCR and targeted whole genome amplicon sequencing were more reliable methods for tracking the pandemic. From our sequencing data, clades and shifts in mutation profiles within the community were traceable and could be used to determine if vaccine or diagnostics need to be adapted to ensure continued efficacy. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=75 SRC="FIGDIR/small/21251939v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@fc0505org.highwire.dtl.DTLVardef@1adc11borg.highwire.dtl.DTLVardef@611205org.highwire.dtl.DTLVardef@e64715_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LINeighborhood or building level wastewater analysis accurately detects SARS-CoV-2 C_LIO_LISARS-CoV-2 was detected in wastewater from one infected person out of 60 residents C_LIO_LITotal RNAseq did not accurately detect SARS-CoV-2 in wastewater samples. C_LIO_LITargeted whole genome sequencing of wastewater samples identified Spike mutations. C_LI