Document Type
Article
Publication Date
2-1-2023
Publication Title
Science of The Total Environment
Volume
858
First page number:
1
Last page number:
6
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.
Keywords
SARS-CoV-2; COVID-19; Virus; Wastewater; Mutation; Hybrid
Disciplines
Medicine and Health Sciences
File Format
File Size
1097 KB
Language
English
Rights
IN COPYRIGHT. For more information about this rights statement, please visit http://rightsstatements.org/vocab/InC/1.0/
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Repository Citation
Vo, V.,
Harrington, A.,
Afzal, S.,
Papp, K.,
Chang, C.,
Baker, H.,
Aguilar, P.,
Buttery, E.,
Picker, M. A.,
Lockett, C.,
Gerrity, D.,
Kan, H.,
Oh, E. C.
(2023).
Identification of a Rare SARS-CoV-2 XL Hybrid Variant in Wastewater and the Subsequent Discovery of Two Infected Individuals in Nevada.
Science of The Total Environment, 858
1-6.
Available at:
http://dx.doi.org/10.1016/j.scitotenv.2022.160024