ArticleEnvironmental science & technology2024
Evaluation of the Impact of Concentration and Extraction Methods on the Targeted Sequencing of Human Viruses from Wastewater.
Article in Environmental science & technology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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Who cites it
17 citing papers in PubMed, 30 citations in OpenAlex.
- Genomic wastewater surveillance of human and animal influenza A viruses in California during the 2024-2025 flu season.medRxiv : the preprint server for health sciences · 2026Article
- A New In-Line GAC-Based Device for Concentrating Viruses in Treated Wastewater: Implications for Full-Scale UV C LED Treatment.ACS ES&T water · 2026Article
- Review
- SARS-CoV-2 wastewater genomic surveillance: approaches, challenges, and opportunities.Genome biology · 2026Review
- Review
- Recovering wastewater RNA for virome sequencing by systematically optimized tangential-flow ultrafiltration and Nanotrap microbiome particles.Applied and environmental microbiology · 2025Article
- Developing and Benchmarking One Health Genomic Surveillance Tools for Influenza A Virus in Wastewater.Research square · 2025Article
- Developing and Benchmarking One Health Genomic Surveillance Tools for Influenza A Virus in Wastewater.bioRxiv : the preprint server for biology · 2025Article
- Benchmarking Concentration and Extraction Methods for Wastewater-Based Surveillance of Eight Human Respiratory Viruses: Implications for Rapid Application to Novel Pathogens.Environmental science & technology · 2025Article
- Novel Workflows for Separate Isolation of Pathogen RNA or DNA from Wastewater: Detection by Innovative and Conventional qPCR.Bio-protocol · 2025Article
- The Impact of Viral Concentration Method on Quantification and Long Amplicon Nanopore Sequencing of SARS-CoV-2 and Noroviruses in Wastewater.Microorganisms · 2025Article
- RBD Amplicon Sequencing and Evolutionary Analysis of SARS-CoV-2 Variants from Wastewater Samples.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Effective Inhibitor Removal from Wastewater Samples Increases Sensitivity of RT-dPCR and Sequencing Analyses and Enhances the Stability of Wastewater-Based Surveillance.Microorganisms · 2024Article
- Genomic surveillance of Canadian airport wastewater samples allows early detection of emerging SARS-CoV-2 lineages.Scientific reports · 2024Article
- Revealing patterns of SARS-CoV-2 variant emergence and evolution using RBD amplicon sequencing of wastewater.The Journal of infection · 2024Article
- RBD amplicon sequencing of wastewater reveals patterns of variant emergence and evolution.medRxiv : the preprint server for health sciences · 2024Article
- Considerations and Opportunities for Probe Capture Enrichment Sequencing of Emerging Viruses from Wastewater.Environmental science & technology · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sequencing human viruses in wastewater is challenging due to their low abundance compared to the total microbial background. This study compared the impact of four virus concentration/extraction methods (Innovaprep, Nanotrap, Promega, and Solids extraction) on probe-capture enrichment for human viruses followed by sequencing. Different concentration/extraction methods yielded distinct virus profiles. Innovaprep ultrafiltration (following solids removal) had the highest sequencing sensitivity and richness, resulting in the successful assembly of several near-complete human virus genomes. However, it was less sensitive in detecting SARS-CoV-2 by digital polymerase chain reaction (dPCR) compared to Promega and Nanotrap. Across all preparation methods, astroviruses and polyomaviruses were the most highly abundant human viruses, and SARS-CoV-2 was rare. These findings suggest that sequencing success can be increased using methods that reduce nontarget nucleic acids in the extract, though the absolute concentration of total extracted nucleic acid, as indicated by Qubit, and targeted viruses, as indicated by dPCR, may not be directly related to targeted sequencing performance. Further, using broadly targeted sequencing panels may capture viral diversity but risks losing signals for specific low-abundance viruses. Overall, this study highlights the importance of aligning wet lab and bioinformatic methods with specific goals when employing probe-capture enrichment for human virus sequencing from wastewater.
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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.