ArticleGenome biology2022
Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- metaWEPP: leveraging biobank-scale intra-species phylogenies for near-haplotype resolution in metagenomic analysis.NAR genomics and bioinformatics · 2026Article
- Benchmarking the impact of reference genome selection on taxonomic profiling accuracy.BMC genomics · 2026Article
- WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiology.PLoS computational biology · 2026Article
- Review
- 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
- 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
- Nightlife and low immunity drove transmission of SARS-CoV-2 gamma in Luxembourg, 2021.Scientific reports · 2025Article
- Beyond clinical data: the role of sewage monitoring in tracking pandemic trends of SARS-CoV-2.Frontiers in microbiology · 2025Article
- Amplicon sequencing of pasteurized retail dairy enables genomic surveillance of H5N1 avian influenza virus in United States cattle.PloS one · 2025Article
- Revealing patterns of SARS-CoV-2 variant emergence and evolution using RBD amplicon sequencing of wastewater.The Journal of infection · 2024Article
- SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes.Bioinformatics (Oxford, England) · 2024Article
- A program for real-time surveillance of SARS-CoV-2 genetics.Scientific reports · 2024Article
- RBD amplicon sequencing of wastewater reveals patterns of variant emergence and evolution.medRxiv : the preprint server for health sciences · 2024Article
- Online dashboards for SARS-CoV-2 wastewater-based epidemiology.Future microbiology · 2024Review
- Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater.Nature communications · 2024Article
- Considerations and Opportunities for Probe Capture Enrichment Sequencing of Emerging Viruses from Wastewater.Environmental science & technology · 2024Review
- Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data.Microbial genomics · 2024Article
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Abstract
Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter the ongoing pandemic. Predicting lineage abundance from wastewater, however, is technically challenging. We show that by sequencing SARS-CoV-2 RNA in wastewater and applying algorithms initially used for transcriptome quantification, we can estimate lineage abundance in wastewater samples. We find high variability in signal among individual samples, but the overall trends match those observed from sequencing clinical samples. Thus, while clinical sequencing remains a more sensitive technique for population surveillance, wastewater sequencing can be used to monitor trends in mutant prevalence in situations where clinical sequencing is unavailable.
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