Wastewater surveillance uncovers regional diversity and dynamics of SARS-CoV-2 variants across nine states in the USA

• DOI: 10.1016/j.scitotenv.2023.162862
• Publication Date: 2023-03-16T07:04:30Z
• Authors: Rafaela S. Fontenele; Yiyan Yang; Erin M. Driver; Arjun Magge; Simona Kraberger; Joy M. Custer; Keith Dufault-Tho...; Erin Cox; Melanie Engstrom ...; Arvind Varsani; Rolf U. Halden; Matthew Scotch; Xiaofang Jiang
• Keywords: Divergence (linguistics); Identification

Wastewater-based epidemiology (WBE) is a non-invasive and cost-effective approach for monitoring the spread of pathogen within community. WBE has been adopted as one methods to monitor population dynamics SARS-CoV-2 virus, but significant challenges remain in bioinformatic analysis WBE-derived data. Here, we have developed new distance metric, CoVdist, an associated tool that facilitates application ordination data identification viral changes based on nucleotide variants. We applied these approaches large-scale dataset from 18 cities nine states USA using wastewater collected July 2021 June 2022. found trends shift between Delta Omicron lineages were largely consistent with what was seen clinical data, offered added benefit revealing differences at state, city, even neighborhood scales. also able observe early variants concern presence recombinant during transitions variants, both which are challenging analyze clinically-derived genomes. The outlined here will be beneficial future applications SARS-CoV-2, particularly becomes less prevalent. Additionally, generalizable, allowing them outbreaks.