Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater
On November 26, 2021, the B.1.1.529 COVID-19 variant was classified as the Omicron variant of concern (VOC). Reports of higher transmissibility and potential immune evasion triggered flight bans and heightened health control measures across the world to stem its distribution. Wastewater-based survei...
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| Format: | Article |
| Language: | English |
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Elsevier BV
2023
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| Online Access: | https://hdl.handle.net/1721.1/147743 |
| _version_ | 1810974076097789952 |
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| author | Lee, Wei Lin Armas, Federica Guarneri, Flavia Gu, Xiaoqiong Formenti, Nicoletta Wu, Fuqing Chandra, Franciscus Parisio, Giovanni Chen, Hongjie Xiao, Amy Romeo, Claudia Scali, Federico Tonni, Matteo Leifels, Mats Chua, Feng Jun Desmond Kwok, Germaine WC Tay, Joey YR Pasquali, Paolo Thompson, Janelle Alborali, Giovanni Loris Alm, Eric J |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Lee, Wei Lin Armas, Federica Guarneri, Flavia Gu, Xiaoqiong Formenti, Nicoletta Wu, Fuqing Chandra, Franciscus Parisio, Giovanni Chen, Hongjie Xiao, Amy Romeo, Claudia Scali, Federico Tonni, Matteo Leifels, Mats Chua, Feng Jun Desmond Kwok, Germaine WC Tay, Joey YR Pasquali, Paolo Thompson, Janelle Alborali, Giovanni Loris Alm, Eric J |
| author_sort | Lee, Wei Lin |
| collection | MIT |
| description | On November 26, 2021, the B.1.1.529 COVID-19 variant was classified as the Omicron variant of concern (VOC). Reports of higher transmissibility and potential immune evasion triggered flight bans and heightened health control measures across the world to stem its distribution. Wastewater-based surveillance has demonstrated to be a useful complement for clinical community-based tracking of SARS-CoV-2 variants. Using design principles of our previous assays that detect SARS-CoV-2 variants (Alpha and Delta), we developed an allele-specific RT-qPCR assay which simultaneously targets the stretch of mutations from Q493R to Q498R for quantitative detection of the Omicron variant in wastewater. We report their validation against 10-month longitudinal samples from the influent of a wastewater treatment plant in Italy. SARS-CoV-2 RNA concentrations and variant frequencies in wastewater determined using these variant assays agree with clinical cases, revealing rapid displacement of the Delta variant by the Omicron variant within three weeks. These variant trends, when mapped against vaccination rates, support clinical studies that found the rapid emergence of SARS-CoV-2 Omicron variant being associated with an infection advantage over Delta in vaccinated persons. These data reinforce the versatility, utility and accuracy of these open-sourced methods using allele-specific RT-qPCR for tracking the dynamics of variant displacement in communities through wastewater for informed public health responses. |
| first_indexed | 2024-09-23T08:17:44Z |
| format | Article |
| id | mit-1721.1/147743 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T08:17:44Z |
| publishDate | 2023 |
| publisher | Elsevier BV |
| record_format | dspace |
| spelling | mit-1721.1/1477432023-01-27T03:50:39Z Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater Lee, Wei Lin Armas, Federica Guarneri, Flavia Gu, Xiaoqiong Formenti, Nicoletta Wu, Fuqing Chandra, Franciscus Parisio, Giovanni Chen, Hongjie Xiao, Amy Romeo, Claudia Scali, Federico Tonni, Matteo Leifels, Mats Chua, Feng Jun Desmond Kwok, Germaine WC Tay, Joey YR Pasquali, Paolo Thompson, Janelle Alborali, Giovanni Loris Alm, Eric J Massachusetts Institute of Technology. Department of Biological Engineering On November 26, 2021, the B.1.1.529 COVID-19 variant was classified as the Omicron variant of concern (VOC). Reports of higher transmissibility and potential immune evasion triggered flight bans and heightened health control measures across the world to stem its distribution. Wastewater-based surveillance has demonstrated to be a useful complement for clinical community-based tracking of SARS-CoV-2 variants. Using design principles of our previous assays that detect SARS-CoV-2 variants (Alpha and Delta), we developed an allele-specific RT-qPCR assay which simultaneously targets the stretch of mutations from Q493R to Q498R for quantitative detection of the Omicron variant in wastewater. We report their validation against 10-month longitudinal samples from the influent of a wastewater treatment plant in Italy. SARS-CoV-2 RNA concentrations and variant frequencies in wastewater determined using these variant assays agree with clinical cases, revealing rapid displacement of the Delta variant by the Omicron variant within three weeks. These variant trends, when mapped against vaccination rates, support clinical studies that found the rapid emergence of SARS-CoV-2 Omicron variant being associated with an infection advantage over Delta in vaccinated persons. These data reinforce the versatility, utility and accuracy of these open-sourced methods using allele-specific RT-qPCR for tracking the dynamics of variant displacement in communities through wastewater for informed public health responses. 2023-01-26T17:52:18Z 2023-01-26T17:52:18Z 2022 2023-01-26T17:44:48Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/147743 Lee, Wei Lin, Armas, Federica, Guarneri, Flavia, Gu, Xiaoqiong, Formenti, Nicoletta et al. 2022. "Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater." Water Research, 221. en 10.1016/J.WATRES.2022.118809 Water Research Creative Commons Attribution-NonCommercial-NoDerivs License http://creativecommons.org/licenses/by-nc-nd/4.0/ application/pdf Elsevier BV Elsevier |
| spellingShingle | Lee, Wei Lin Armas, Federica Guarneri, Flavia Gu, Xiaoqiong Formenti, Nicoletta Wu, Fuqing Chandra, Franciscus Parisio, Giovanni Chen, Hongjie Xiao, Amy Romeo, Claudia Scali, Federico Tonni, Matteo Leifels, Mats Chua, Feng Jun Desmond Kwok, Germaine WC Tay, Joey YR Pasquali, Paolo Thompson, Janelle Alborali, Giovanni Loris Alm, Eric J Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater |
| title | Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater |
| title_full | Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater |
| title_fullStr | Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater |
| title_full_unstemmed | Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater |
| title_short | Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater |
| title_sort | rapid displacement of sars cov 2 variant delta by omicron revealed by allele specific pcr in wastewater |
| url | https://hdl.handle.net/1721.1/147743 |
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