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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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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Authors. Published by Elsevier Ltd. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9250349/
https://www.ncbi.nlm.nih.gov/pubmed/35841797
http://dx.doi.org/10.1016/j.watres.2022.118809
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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
author_facet 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 PubMed
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.
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spelling pubmed-92503492022-07-05 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 Water Res Article 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. The Authors. Published by Elsevier Ltd. 2022-08-01 2022-07-02 /pmc/articles/PMC9250349/ /pubmed/35841797 http://dx.doi.org/10.1016/j.watres.2022.118809 Text en © 2022 The Authors. Published by Elsevier Ltd. 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
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
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9250349/
https://www.ncbi.nlm.nih.gov/pubmed/35841797
http://dx.doi.org/10.1016/j.watres.2022.118809
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