Identification of Highly Transmissible Sars-Cov-2 Variants in Sewage Predicts Clinical Disease Burden

The decline in diagnostic testing for SARS-CoV-2 is expected to delay the tracking of COVID-19 variants of concern and interest in the United States. We hypothesize that wastewater surveillance programs, which are agnostic to clinical testing, can provide an effective alternative for detecting emerging viral variants and assessing COVID-19 incidence. Here, we analyzed SARS-CoV-2 RNA concentrations in wastewater from eight locations across Southern Nevada between March 2020 and April 2021. Trends in SARS-CoV-2 RNA concentrations matched changes in COVID-19 incidence confirmed through diagnostic testing. To test for the prevalence of variants of concern, we performed amplicon-based whole genome sequencing of SARS-CoV-2 for 86 wastewater samples and identified the B.1.1.7 and B.1.429 lineages in December 2020. Whole genome sequencing for both lineages in 575 clinical samples failed to identify the variants until January 2021, suggesting that ‘pooled’ wastewater samples may expedite viral variant detection when sequencing of clinical samples is limited. By calibrating fecal shedding and wastewater surveillance data to reported seroprevalence, we developed a model estimating that ~36% of individuals in Southern Nevada had been infected by SARS-CoV-2 as of April 2021, which is significantly higher than the 10% of individuals confirmed through clinical testing. Our data underscore the growing application of wastewater-based epidemiology in not only the identification and characterization of infectious agents, but also the detection of viral variants that may be missed when diagnostic testing is limited or unavailable.