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Wastewater surveillance uncovers regional diversity and dynamics of SARS-CoV-2 variants across nine states in the USA
Wastewater-based epidemiology (WBE) is a non-invasive and cost-effective approach for monitoring the spread of a pathogen within a community. WBE has been adopted as one of the methods to monitor the spread and population dynamics of the SARS-CoV-2 virus, but significant challenges remain in the bio...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10017378/ https://www.ncbi.nlm.nih.gov/pubmed/36933724 http://dx.doi.org/10.1016/j.scitotenv.2023.162862 |
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author | Fontenele, Rafaela S. Yang, Yiyan Driver, Erin M. Magge, Arjun Kraberger, Simona Custer, Joy M. Dufault-Thompson, Keith Cox, Erin Newell, Melanie Engstrom Varsani, Arvind Halden, Rolf U. Scotch, Matthew Jiang, Xiaofang |
author_facet | Fontenele, Rafaela S. Yang, Yiyan Driver, Erin M. Magge, Arjun Kraberger, Simona Custer, Joy M. Dufault-Thompson, Keith Cox, Erin Newell, Melanie Engstrom Varsani, Arvind Halden, Rolf U. Scotch, Matthew Jiang, Xiaofang |
author_sort | Fontenele, Rafaela S. |
collection | PubMed |
description | Wastewater-based epidemiology (WBE) is a non-invasive and cost-effective approach for monitoring the spread of a pathogen within a community. WBE has been adopted as one of the methods to monitor the spread and population dynamics of the SARS-CoV-2 virus, but significant challenges remain in the bioinformatic analysis of WBE-derived data. Here, we have developed a new distance metric, CoVdist, and an associated analysis tool that facilitates the application of ordination analysis to WBE data and the identification of viral population changes based on nucleotide variants. We applied these new approaches to a large-scale dataset from 18 cities in nine states of the USA using wastewater collected from July 2021 to June 2022. We found that the trends in the shift between the Delta and Omicron SARS-CoV-2 lineages were largely consistent with what was seen in clinical data, but that wastewater analysis offered the added benefit of revealing significant differences in viral population dynamics at the state, city, and even neighborhood scales. We also were able to observe the early spread of variants of concern and the presence of recombinant lineages during the transitions between variants, both of which are challenging to analyze based on clinically-derived viral genomes. The methods outlined here will be beneficial for future applications of WBE to monitor SARS-CoV-2, particularly as clinical monitoring becomes less prevalent. Additionally, these approaches are generalizable, allowing them to be applied for the monitoring and analysis of future viral outbreaks. |
format | Online Article Text |
id | pubmed-10017378 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-100173782023-03-16 Wastewater surveillance uncovers regional diversity and dynamics of SARS-CoV-2 variants across nine states in the USA Fontenele, Rafaela S. Yang, Yiyan Driver, Erin M. Magge, Arjun Kraberger, Simona Custer, Joy M. Dufault-Thompson, Keith Cox, Erin Newell, Melanie Engstrom Varsani, Arvind Halden, Rolf U. Scotch, Matthew Jiang, Xiaofang Sci Total Environ Article Wastewater-based epidemiology (WBE) is a non-invasive and cost-effective approach for monitoring the spread of a pathogen within a community. WBE has been adopted as one of the methods to monitor the spread and population dynamics of the SARS-CoV-2 virus, but significant challenges remain in the bioinformatic analysis of WBE-derived data. Here, we have developed a new distance metric, CoVdist, and an associated analysis tool that facilitates the application of ordination analysis to WBE data and the identification of viral population changes based on nucleotide variants. We applied these new approaches to a large-scale dataset from 18 cities in nine states of the USA using wastewater collected from July 2021 to June 2022. We found that the trends in the shift between the Delta and Omicron SARS-CoV-2 lineages were largely consistent with what was seen in clinical data, but that wastewater analysis offered the added benefit of revealing significant differences in viral population dynamics at the state, city, and even neighborhood scales. We also were able to observe the early spread of variants of concern and the presence of recombinant lineages during the transitions between variants, both of which are challenging to analyze based on clinically-derived viral genomes. The methods outlined here will be beneficial for future applications of WBE to monitor SARS-CoV-2, particularly as clinical monitoring becomes less prevalent. Additionally, these approaches are generalizable, allowing them to be applied for the monitoring and analysis of future viral outbreaks. Elsevier 2023-06-15 2023-03-16 /pmc/articles/PMC10017378/ /pubmed/36933724 http://dx.doi.org/10.1016/j.scitotenv.2023.162862 Text en Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. |
spellingShingle | Article Fontenele, Rafaela S. Yang, Yiyan Driver, Erin M. Magge, Arjun Kraberger, Simona Custer, Joy M. Dufault-Thompson, Keith Cox, Erin Newell, Melanie Engstrom Varsani, Arvind Halden, Rolf U. Scotch, Matthew Jiang, Xiaofang Wastewater surveillance uncovers regional diversity and dynamics of SARS-CoV-2 variants across nine states in the USA |
title | Wastewater surveillance uncovers regional diversity and dynamics of SARS-CoV-2 variants across nine states in the USA |
title_full | Wastewater surveillance uncovers regional diversity and dynamics of SARS-CoV-2 variants across nine states in the USA |
title_fullStr | Wastewater surveillance uncovers regional diversity and dynamics of SARS-CoV-2 variants across nine states in the USA |
title_full_unstemmed | Wastewater surveillance uncovers regional diversity and dynamics of SARS-CoV-2 variants across nine states in the USA |
title_short | Wastewater surveillance uncovers regional diversity and dynamics of SARS-CoV-2 variants across nine states in the USA |
title_sort | wastewater surveillance uncovers regional diversity and dynamics of sars-cov-2 variants across nine states in the usa |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10017378/ https://www.ncbi.nlm.nih.gov/pubmed/36933724 http://dx.doi.org/10.1016/j.scitotenv.2023.162862 |
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