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

Wei Lin Lee, Federica Armas, Flavia Guarneri, Xiaoqiong Gu, Nicoletta Formenti, Fuqing Wu, Franciscus Chandra, Giovanni Parisio, Hongjie Chen, Amy Xiao, Claudia Romeo, Federico Scali, Matteo Tonni, Mats Leifels, Feng Jun Desmond Chua, Germaine Wc Kwok, Joey Yr Tay, Paolo Pasquali, Janelle Thompson, Giovanni Loris AlboraliEric J Alm

Research output: Journal article (peer-reviewed)Journal article

24 Citations (Scopus)


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.

Original languageEnglish
Article number118809
Pages (from-to)118809
JournalWater Research
Publication statusPublished - 01 Aug 2022
Externally publishedYes


  • Alleles
  • COVID-19
  • COVID-19 Testing
  • Humans
  • RNA, Viral
  • Real-Time Polymerase Chain Reaction
  • SARS-CoV-2/genetics
  • Wastewater/analysis


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