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Title: Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater
Authors: 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, Desmond Feng Jun
Kwok, Germaine W. C.
Tay, Joey Y. R.
Pasquali, Paolo
Thompson, Janelle
Alborali, Giovanni Loris
Alm, Eric J.
Keywords: Engineering::Environmental engineering
Issue Date: 2022
Source: Lee, W. L., Armas, F., Guarneri, F., Gu, X., Formenti, N., Wu, F., Chandra, F., Parisio, G., Chen, H., Xiao, A., Romeo, C., Scali, F., Tonni, M., Leifels, M., Chua, D. F. J., Kwok, G. W. C., Tay, J. Y. R., Pasquali, P., Thompson, J., ...Alm, E. J. (2022). Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater. Water Research, 221, 118809-.
Project: NRF2019-THE001-0003a 
Journal: Water Research 
Abstract: 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.
ISSN: 0043-1354
DOI: 10.1016/j.watres.2022.118809
Schools: Asian School of the Environment 
Organisations: Campus for Research Excellence and Technological Enterprise (CREATE)
Research Centres: Singapore Centre for Environmental Life Sciences and Engineering 
Rights: © 2022 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (
Fulltext Permission: open
Fulltext Availability: With Fulltext
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