ArticleEuro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin2022
Inferring transmission fitness advantage of SARS-CoV-2 variants of concern from wastewater samples using digital PCR, Switzerland, December 2020 through March 2021.
Article in Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Real-time estimation of pathogen transmission dynamics from wastewater.Nature communications · 2026Article
- Bio-Rad and QIAGEN digital PCR platforms provide equivalent quantification for wastewater-based SARS-CoV-2 surveillance.Applied and environmental microbiology · 2026Article
- The P protein T25M substitution is involved in the quasispecies and virulence of Newcastle disease virus.Microbiology spectrum · 2026Article
- Tracking SARS-CoV-2 genomic variants in wastewater sequencing data with LolliPop.PLoS computational biology · 2026Article
- SARS-CoV-2 wastewater genomic surveillance: approaches, challenges, and opportunities.Genome biology · 2026Review
- Unsupervised detection and fitness estimation of emerging SARS-CoV-2 variants: Application to wastewater samples (ANRS0160).PLoS computational biology · 2025Article
- Estimated transmission dynamics of SARS-CoV-2 variants from wastewater are unbiased and robust to differential shedding.Nature communications · 2025Article
- Diagnostic performance of allele-specific RT-qPCR and genomic sequencing in wastewater-based surveillance of SARS-CoV-2.Eco-Environment & Health · 2025Article
- Digital PCR in Virology: Current Applications and Future Perspectives.Molecular diagnosis & therapy · 2025Review
- A scoping review of global SARS-CoV-2 wastewater-based epidemiology in light of COVID-19 pandemic.Heliyon · 2024Article
- Detection of SARS-COV-2 variants and their proportions in wastewater samples using next-generation sequencing in Finland.Scientific reports · 2024Article
- Digital PCR Discriminates between SARS-CoV-2 Omicron Variants and Immune Escape Mutations.Microbiology spectrum · 2023Article
- A review of current effective COVID-19 testing methods and quality control.Archives of microbiology · 2023Review
- From Alpha to Omicron BA.2: New digital RT-PCR approach and challenges for SARS-CoV-2 VOC monitoring and normalization of variant dynamics in wastewater.The Science of the total environment · 2022Article
- Case report: BA.1 subvariant showing a BA.2-like pattern using a variant-specific PCR assay due to a single point mutation downstream the spike 69/70 deletion.Virology journal · 2022Article
- Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC.Nature microbiology · 2022Article
- Making waves: Wastewater surveillance of SARS-CoV-2 in an endemic future.Water research · 2022Article
- Unlocking capacities of genomics for the COVID-19 response and future pandemics.Nature methods · 2022Article
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12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
BackgroundThroughout the COVID-19 pandemic, SARS-CoV-2 genetic variants of concern (VOCs) have repeatedly and independently arisen. VOCs are characterised by increased transmissibility, increased virulence or reduced neutralisation by antibodies obtained from prior infection or vaccination. Tracking the introduction and transmission of VOCs relies on sequencing, typically whole genome sequencing of clinical samples. Wastewater surveillance is increasingly used to track the introduction and spread of SARS-CoV-2 variants through sequencing approaches.AimHere, we adapt and apply a rapid, high-throughput method for detection and quantification of the relative frequency of two deletions characteristic of the Alpha, Beta, and Gamma VOCs in wastewater.MethodsWe developed drop-off RT-dPCR assays and an associated statistical approach implemented in the R package WWdPCR to analyse temporal dynamics of SARS-CoV-2 signature mutations (spike Δ69-70 and ORF1a Δ3675-3677) in wastewater and quantify transmission fitness advantage of the Alpha VOC.ResultsBased on analysis of Zurich wastewater samples, the estimated transmission fitness advantage of SARS-CoV-2 Alpha based on the spike Δ69-70 was 0.34 (95% confidence interval (CI): 0.30-0.39) and based on ORF1a Δ3675-3677 was 0.53 (95% CI: 0.49-0.57), aligning with the transmission fitness advantage of Alpha estimated by clinical sample sequencing in the surrounding canton of 0.49 (95% CI: 0.38-0.61).ConclusionDigital PCR assays targeting signature mutations in wastewater offer near real-time monitoring of SARS-CoV-2 VOCs and potentially earlier detection and inference on transmission fitness advantage than clinical sequencing.
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