ArticleWater research2022
Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater.
Article in Water research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 39 citations in OpenAlex.
- An integrated framework for early detection and transmissibility assessment of emerging variants in wastewater.International journal of hygiene and environmental health · 2026Article
- Overview of SARS-CoV-2 genomic surveillance in Central America and the Dominican Republic from February 2020 to January 2023: the impact of PAHO and COMISCA's collaborative efforts.Frontiers in public health · 2026Article
- Development of multiplex allele-specific RT-qPCR assays for differentiation of SARS-CoV-2 Omicron subvariants.Applied microbiology and biotechnology · 2024Article
- Real-Time Monitoring of SARS-CoV-2 Variants in Oklahoma Wastewater through Allele-Specific RT-qPCR.Microorganisms · 2024Article
- Wastewater surveillance monitoring of SARS-CoV-2 variants of concern and dynamics of transmission and community burden of COVID-19.Emerging microbes & infections · 2023Article
- Utilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems.Nature communications · 2023Article
- Article
- "Nano COVID-19": Nanopore sequencing of spike gene to identify SARS-CoV-2 variants of concern.Experimental biology and medicine (Maywood, N.J.) · 2023Article
- Making waves: Integrating wastewater surveillance with dynamic modeling to track and predict viral outbreaks.Water research · 2023Article
- The Rise and Fall of Omicron BA.1 Variant as Seen in Wastewater Supports Epidemiological Model Predictions.Viruses · 2023Article
- Wastewater-based modeling, reconstruction, and prediction for COVID-19 outbreaks in Hungary caused by highly immune evasive variants.Water research · 2023Article
- An improved method for determining frequency of multiple variants of SARS-CoV-2 in wastewater using qPCR assays.The Science of the total environment · 2023Article
- Article
- Development and application of an RT‒PCR assay for the identification of the delta and omicron variants of SARS-COV-2.Heliyon · 2023Article
- The emergence of a virus variant: dynamics of a competition model with cross-immunity time-delay validated by wastewater surveillance data for COVID-19.Journal of mathematical biology · 2023Article
- Wastewater monitoring in tourist cities as potential sentinel sites for near real-time dynamics of imported SARS-CoV-2 variants.The Science of the total environment · 2023Article
- The Detection of Periodic Reemergence Events of SARS-CoV-2 Delta Strain in Communities Dominated by Omicron.Pathogens (Basel, Switzerland) · 2022Article
- Review
- Article
- The one health perspective to improve environmental surveillance of zoonotic viruses: lessons from COVID-19 and outlook beyond.ISME communications · 2022Review
Corrections and comments
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Authors and funding
21 authors at 7 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.