ArticleThe Science of the total environment2023
Identification of a rare SARS-CoV-2 XL hybrid variant in wastewater and the subsequent discovery of two infected individuals in Nevada.
Article in The Science of the total environment, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 15 citations in OpenAlex.
- SARS-CoV-2 wastewater genomic surveillance: approaches, challenges, and opportunities.Genome biology · 2026Review
- Identification of circulating human papillomavirus types through high-throughput sequencing of Canadian municipal and institutional wastewater samples.Applied and environmental microbiology · 2025Article
- Early detection of emerging SARS-CoV-2 Variants from wastewater through genome sequencing and machine learning.Nature communications · 2025Article
- Public health actions in response to pathogen detection in wastewater and the environment: a scoping review.Frontiers in public health · 2025Article
- 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.Environmental science & technology letters · 2024Article
- Tracing the origin of SARS-CoV-2 omicron-like spike sequences detected in an urban sewershed: a targeted, longitudinal surveillance study of a cryptic wastewater lineage.The Lancet. Microbe · 2024Article
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Authors and funding
13 authors at 3 institutions in 1 country.
Funding
Abstract
The identification of novel SARS-CoV-2 variants can predict new patterns of COVID-19 community transmission and lead to the deployment of public health resources. However, increased access to at-home antigen tests and reduced free PCR tests have recently led to data gaps for the surveillance of evolving SARS-CoV-2 variants. To overcome such limitations, we asked whether wastewater surveillance could be leveraged to detect rare variants circulating in a community before local detection in human cases. Here, we performed whole genome sequencing (WGS) of SARS-CoV-2 from a wastewater treatment plant serving Las Vegas, Nevada in April 2022. Using metrics that exceeded 100× depth at a coverage of >90 % of the viral genome, we identified a variant profile similar to the XL recombinant lineage containing 26 mutations found in BA.1 and BA.2 and three private mutations. Prompted by the discovery of this rare lineage in wastewater, we analyzed clinical COVID-19 sequencing data from Southern Nevada and identified two cases infected with the XL lineage. Taken together, our data highlight how wastewater genome sequencing data can be used to discover rare SARS-CoV-2 lineages in a community and complement local public health surveillance.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.