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Development of an efficient wastewater testing protocol for high-throughput country-wide SARS-CoV-2 monitoring
Wastewater-based surveillance has been widely used as a non-intrusive tool to monitor population-level transmission of COVID-19. Although various approaches are available to concentrate viruses from wastewater samples, scalable methods remain limited. Here, we sought to identify and evaluate SARS-Co...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Authors. Published by Elsevier B.V.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8860745/ https://www.ncbi.nlm.nih.gov/pubmed/35217043 http://dx.doi.org/10.1016/j.scitotenv.2022.154024 |
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author | Mailepessov, Diyar Arivalan, Sathish Kong, Marcella Griffiths, Jane Low, Swee Ling Chen, Hongjie Hapuarachchi, Hapuarachchige Chanditha Gu, Xiaoqiong Lee, Wei Lin Alm, Eric J. Thompson, Janelle Wuertz, Stefan Gin, Karina Ng, Lee Ching Wong, Judith Chui Ching |
author_facet | Mailepessov, Diyar Arivalan, Sathish Kong, Marcella Griffiths, Jane Low, Swee Ling Chen, Hongjie Hapuarachchi, Hapuarachchige Chanditha Gu, Xiaoqiong Lee, Wei Lin Alm, Eric J. Thompson, Janelle Wuertz, Stefan Gin, Karina Ng, Lee Ching Wong, Judith Chui Ching |
author_sort | Mailepessov, Diyar |
collection | PubMed |
description | Wastewater-based surveillance has been widely used as a non-intrusive tool to monitor population-level transmission of COVID-19. Although various approaches are available to concentrate viruses from wastewater samples, scalable methods remain limited. Here, we sought to identify and evaluate SARS-CoV-2 virus concentration protocols for high-throughput wastewater testing. A total of twelve protocols for polyethylene glycol (PEG) precipitation and four protocols for ultrafiltration-based approaches were evaluated across two phases. The first phase entailed an initial evaluation using a small sample set, while the second phase further evaluated five protocols using wastewater samples of varying SARS-CoV-2 concentrations. Permutations in the pre-concentration, virus concentration and RNA extraction steps were evaluated. Among PEG-based methods, SARS-CoV-2 virus recovery was optimal with 1) the removal of debris prior to processing, 2) 2 h to 24 h incubation with 8% PEG at 4 °C, 3) 4000 xg or 14,000 xg centrifugation, and 4) a column-based RNA extraction method, yielding virus recovery of 42.4–52.5%. Similarly, the optimal protocol for ultrafiltration included 1) the removal of debris prior to processing, 2) ultrafiltration, and 3) a column-based RNA extraction method, yielding a recovery of 38.2%. This study also revealed that SARS-CoV-2 RNA recovery for samples with higher virus concentration were less sensitive to changes in the PEG method, but permutations in the PEG protocol could significantly impact virus yields when wastewater samples with lower SARS-CoV-2 RNA were used. Although both PEG precipitation and ultrafiltration methods resulted in similar SARS-CoV-2 RNA recoveries, the former method is more cost-effective while the latter method provided operational efficiency as it required a shorter turn-around-time (PEG precipitation, 9–23 h; Ultrafiltration, 5 h). The decision on which method to adopt will thus depend on the use-case for wastewater testing, and the need for cost-effectiveness, sensitivity, operational feasibility and scalability. |
format | Online Article Text |
id | pubmed-8860745 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | The Authors. Published by Elsevier B.V. |
record_format | MEDLINE/PubMed |
spelling | pubmed-88607452022-02-22 Development of an efficient wastewater testing protocol for high-throughput country-wide SARS-CoV-2 monitoring Mailepessov, Diyar Arivalan, Sathish Kong, Marcella Griffiths, Jane Low, Swee Ling Chen, Hongjie Hapuarachchi, Hapuarachchige Chanditha Gu, Xiaoqiong Lee, Wei Lin Alm, Eric J. Thompson, Janelle Wuertz, Stefan Gin, Karina Ng, Lee Ching Wong, Judith Chui Ching Sci Total Environ Short Communication Wastewater-based surveillance has been widely used as a non-intrusive tool to monitor population-level transmission of COVID-19. Although various approaches are available to concentrate viruses from wastewater samples, scalable methods remain limited. Here, we sought to identify and evaluate SARS-CoV-2 virus concentration protocols for high-throughput wastewater testing. A total of twelve protocols for polyethylene glycol (PEG) precipitation and four protocols for ultrafiltration-based approaches were evaluated across two phases. The first phase entailed an initial evaluation using a small sample set, while the second phase further evaluated five protocols using wastewater samples of varying SARS-CoV-2 concentrations. Permutations in the pre-concentration, virus concentration and RNA extraction steps were evaluated. Among PEG-based methods, SARS-CoV-2 virus recovery was optimal with 1) the removal of debris prior to processing, 2) 2 h to 24 h incubation with 8% PEG at 4 °C, 3) 4000 xg or 14,000 xg centrifugation, and 4) a column-based RNA extraction method, yielding virus recovery of 42.4–52.5%. Similarly, the optimal protocol for ultrafiltration included 1) the removal of debris prior to processing, 2) ultrafiltration, and 3) a column-based RNA extraction method, yielding a recovery of 38.2%. This study also revealed that SARS-CoV-2 RNA recovery for samples with higher virus concentration were less sensitive to changes in the PEG method, but permutations in the PEG protocol could significantly impact virus yields when wastewater samples with lower SARS-CoV-2 RNA were used. Although both PEG precipitation and ultrafiltration methods resulted in similar SARS-CoV-2 RNA recoveries, the former method is more cost-effective while the latter method provided operational efficiency as it required a shorter turn-around-time (PEG precipitation, 9–23 h; Ultrafiltration, 5 h). The decision on which method to adopt will thus depend on the use-case for wastewater testing, and the need for cost-effectiveness, sensitivity, operational feasibility and scalability. The Authors. Published by Elsevier B.V. 2022-06-20 2022-02-22 /pmc/articles/PMC8860745/ /pubmed/35217043 http://dx.doi.org/10.1016/j.scitotenv.2022.154024 Text en © 2022 The Authors 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 | Short Communication Mailepessov, Diyar Arivalan, Sathish Kong, Marcella Griffiths, Jane Low, Swee Ling Chen, Hongjie Hapuarachchi, Hapuarachchige Chanditha Gu, Xiaoqiong Lee, Wei Lin Alm, Eric J. Thompson, Janelle Wuertz, Stefan Gin, Karina Ng, Lee Ching Wong, Judith Chui Ching Development of an efficient wastewater testing protocol for high-throughput country-wide SARS-CoV-2 monitoring |
title | Development of an efficient wastewater testing protocol for high-throughput country-wide SARS-CoV-2 monitoring |
title_full | Development of an efficient wastewater testing protocol for high-throughput country-wide SARS-CoV-2 monitoring |
title_fullStr | Development of an efficient wastewater testing protocol for high-throughput country-wide SARS-CoV-2 monitoring |
title_full_unstemmed | Development of an efficient wastewater testing protocol for high-throughput country-wide SARS-CoV-2 monitoring |
title_short | Development of an efficient wastewater testing protocol for high-throughput country-wide SARS-CoV-2 monitoring |
title_sort | development of an efficient wastewater testing protocol for high-throughput country-wide sars-cov-2 monitoring |
topic | Short Communication |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8860745/ https://www.ncbi.nlm.nih.gov/pubmed/35217043 http://dx.doi.org/10.1016/j.scitotenv.2022.154024 |
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