Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater

• Published in: Water research (Oxford) Vol. 221; p. 118809
• Main 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, Feng Jun Desmond, Kwok, Germaine WC, Tay, Joey YR, Pasquali, Paolo, Thompson, Janelle, Alborali, Giovanni Loris, Alm, Eric J
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.08.2022; The Authors. Published by Elsevier Ltd
• Subjects: Alleles; COVID-19; COVID-19 infection; COVID-19 Testing; flight; Humans; immune evasion; Italy; monitoring; Omicron; public health; Real-Time Polymerase Chain Reaction; RNA; RNA, Viral; RT-qPCR; SARS-CoV-2; SARS-CoV-2 - genetics; Severe acute respiratory syndrome coronavirus 2; Surveillance; vaccination; Vaccine breakthrough; Variant; Wastewater; Wastewater - analysis; wastewater treatment; water; Italy; COVID-19; Variant; SARS-CoV-2; Surveillance; Vaccine breakthrough; Omicron; Wastewater; RT-qPCR
• ISSN: 0043-1354; 1879-2448; 1879-2448
• DOI: 10.1016/j.watres.2022.118809

•Allele-specific RT-qPCR assay for quantitative detection of the Omicron variant.•Assay validated against 10-month longitudinal wastewater treatment plant samples.•SARS-CoV-2 RNA concentrations and variant frequencies in wastewater agree with clinical data.•Assays reveal the rapid displacement of the Delta variant by the Omicron variant.•Assays derived enable accurate tracking of the dynamics of variant displacement. 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. [Display omitted]