ArticleNature microbiology2022
Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC.
Article in Nature microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 papers, 1 of them a synthesis that pooled it.
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Who cites it
95 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A Systematic Review of Methodological Approaches to SARS-CoV-2 Wastewater Surveillance.Viruses · 2026Pooled it
- Review
- Real-time estimation of pathogen transmission dynamics from wastewater.Nature communications · 2026Article
- Understanding patterns of variant emergence and spread in an ongoing epidemic.medRxiv : the preprint server for health sciences · 2026Article
- WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiology.PLoS computational biology · 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
- Article
- Unsupervised detection and fitness estimation of emerging SARS-CoV-2 variants: Application to wastewater samples (ANRS0160).PLoS computational biology · 2025Article
- Unveiling the global urban virome through wastewater metagenomics.Nature communications · 2025Article
- Varaps: a python package for estimating SARS-CoV-2 lineages proportions from pooled sequencing data (ANRS0160).BMC bioinformatics · 2025Article
- Comprehensive wastewater genomic surveillance in the Netherlands: insights into country-wide SARS-CoV-2 lineage dynamics and implications for future surveillance.BMC public health · 2025Article
- Recovering wastewater RNA for virome sequencing by systematically optimized tangential-flow ultrafiltration and Nanotrap microbiome particles.Applied and environmental microbiology · 2025Article
- Shotgun metagenomics on indoor air for surveillance of respiratory, enteric, and skin viruses in a Belgian daycare setting, January to December 2022.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2025Article
- Estimated transmission dynamics of SARS-CoV-2 variants from wastewater are unbiased and robust to differential shedding.Nature communications · 2025Article
- Optimization of the Primary Sludge Processing Method for Wastewater Genomic Surveillance of SARS-CoV‑2.ACS ES&T water · 2025Article
- Real-time, multi-pathogen wastewater genomic surveillance with Freyja 2.medRxiv : the preprint server for health sciences · 2025Article
- Evolving infectious disease dynamics shape school-based intervention effectiveness.Nature communications · 2025Article
- Early detection of emerging SARS-CoV-2 Variants from wastewater through genome sequencing and machine learning.Nature communications · 2025Article
- Wastewater surveillance of SARS-CoV-2 from aircraft to citywide monitoring.Nature communications · 2025Article
35 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
24 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The continuing emergence of SARS-CoV-2 variants of concern and variants of interest emphasizes the need for early detection and epidemiological surveillance of novel variants. We used genomic sequencing of 122 wastewater samples from three locations in Switzerland to monitor the local spread of B.1.1.7 (Alpha), B.1.351 (Beta) and P.1 (Gamma) variants of SARS-CoV-2 at a population level. We devised a bioinformatics method named COJAC (Co-Occurrence adJusted Analysis and Calling) that uses read pairs carrying multiple variant-specific signature mutations as a robust indicator of low-frequency variants. Application of COJAC revealed that a local outbreak of the Alpha variant in two Swiss cities was observable in wastewater up to 13 d before being first reported in clinical samples. We further confirmed the ability of COJAC to detect emerging variants early for the Delta variant by analysing an additional 1,339 wastewater samples. While sequencing data of single wastewater samples provide limited precision for the quantification of relative prevalence of a variant, we show that replicate and close-meshed longitudinal sequencing allow for robust estimation not only of the local prevalence but also of the transmission fitness advantage of any variant. We conclude that genomic sequencing and our computational analysis can provide population-level estimates of prevalence and fitness of emerging variants from wastewater samples earlier and on the basis of substantially fewer samples than from clinical samples. Our framework is being routinely used in large national projects in Switzerland and the UK.
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