{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T20:53:57Z","timestamp":1790456037127,"version":"4.1.0"},"reference-count":86,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T00:00:00Z","timestamp":1767225600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T00:00:00Z","timestamp":1767571200000},"content-version":"vor","delay-in-days":4,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Gates Foundation","doi-asserted-by":"publisher","award":["INV-052182"],"award-info":[{"award-number":["INV-052182"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MR\/X020258\/1"],"award-info":[{"award-number":["MR\/X020258\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Science of The Total Environment"],"published-print":{"date-parts":[[2026,1]]},"DOI":"10.1016\/j.scitotenv.2025.181333","type":"journal-article","created":{"date-parts":[[2026,1,6]],"date-time":"2026-01-06T13:42:58Z","timestamp":1767706978000},"page":"181333","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":1,"special_numbering":"C","title":["Comparison of the sensitivity of targeted and untargeted (metagenomic) methods for the detection of viral pathogens in wastewater"],"prefix":"10.1016","volume":"1013","author":[{"given":"Ben","family":"Bellekom","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine","family":"Troman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shannon","family":"Fitz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joyce Odeke","family":"Akello","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas C.","family":"Grassly","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander G.","family":"Shaw","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.scitotenv.2025.181333_bb0005","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2024.1305742","article-title":"Defining a metagenomic threshold for detecting low abundances of Providencia alcalifaciens in canine faecal samples","volume":"14","author":"Aardal","year":"2024","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0010","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.coesh.2020.09.003","article-title":"Surveillance of SARS-CoV-2 RNA in wastewater: methods optimization and quality control are crucial for generating reliable public health information","volume":"17","author":"Ahmed","year":"2020","journal-title":"Curr. Opin. Environ. Sci. Heal."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0015","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2021.149877","article-title":"Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance","volume":"805","author":"Ahmed","year":"2022","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0020","doi-asserted-by":"crossref","first-page":"1086","DOI":"10.1093\/infdis\/jit290","article-title":"Excretion of West Nile virus in urine during acute infection","volume":"208","author":"Barzon","year":"2013","journal-title":"J Infect Dis"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0025","first-page":"1","article-title":"Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance","volume":"15","author":"Becsei","year":"2024","journal-title":"Nat. Commun."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0030","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41545-019-0032-3","article-title":"Metagenomics and the development of viral water quality tools","volume":"2","author":"Bibby","year":"2019","journal-title":"npj Clean Water"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0035","doi-asserted-by":"crossref","first-page":"2530","DOI":"10.1128\/JCM.01052-16","article-title":"Norovirus whole-genome sequencing by SureSelect target enrichment: a robust and sensitive method","volume":"54","author":"Brown","year":"2016","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0040","doi-asserted-by":"crossref","DOI":"10.1128\/mbio.00591-22","article-title":"Microbiome analysis for wastewater surveillance during COVID-19","volume":"13","author":"Brumfield","year":"2022","journal-title":"MBio"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0045","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13073-024-01380-x","article-title":"Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses","volume":"16","author":"Buddle","year":"2024","journal-title":"Genome Med."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0050","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-020-20075-6","article-title":"Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis","volume":"11","author":"Bull","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0055","article-title":"Detecting SARS-CoV-2 in sludge samples: a systematic review","volume":"859","author":"C\u00e2mara","year":"2022","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0060","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00180-11","article-title":"Raw sewage harbors diverse viral populations","volume":"2","author":"Cantalupo","year":"2011","journal-title":"MBio"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0065","doi-asserted-by":"crossref","DOI":"10.1128\/mbio.01468-23","article-title":"Comparison of metagenomic and targeted methods for sequencing human pathogenic viruses from wastewater","volume":"14","author":"Child","year":"2023","journal-title":"MBio"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0070","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.virol.2017.06.019","article-title":"Use of Sequence-Independent, Single-Primer-Amplification (SISPA) for rapid detection, identification, and characterization of avian RNA viruses","volume":"509","author":"Chrzastek","year":"2017","journal-title":"Virology"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0075","doi-asserted-by":"crossref","DOI":"10.1128\/AEM.02168-17","article-title":"Metagenomics reveals the impact of wastewater treatment plants on the dispersal of microorganisms and genes in aquatic sediments","volume":"84","author":"Chu","year":"2018","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0080","doi-asserted-by":"crossref","DOI":"10.12688\/wellcomeopenres.17170.2","article-title":"Rapid viral metagenomics using SMART-9N amplification and nanopore sequencing","volume":"6","author":"Claro","year":"2023","journal-title":"Wellcome Open Res."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0085","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/mBio.02703-20","article-title":"Genome sequencing of sewage detects regionally prevalent SARS-CoV-2 variants","volume":"12","author":"Crits-Christoph","year":"2021","journal-title":"MBio"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0090","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0060204","article-title":"Identification of optimum sequencing depth especially for de novo genome assembly of small genomes using next generation sequencing data","volume":"8","author":"Desai","year":"2013","journal-title":"PloS One"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0095","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1214\/ss\/1032280214","article-title":"Bootstrap confidence intervals","volume":"11","author":"DiCiccio","year":"1996","journal-title":"Stat. Sci."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0100","first-page":"1","article-title":"Explaining the impact of mutations on quantification of SARS-CoV-2 in wastewater","volume":"14","author":"Endo","year":"2024","journal-title":"Sci. Reports"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0105","doi-asserted-by":"crossref","first-page":"870","DOI":"10.1016\/j.scitotenv.2017.08.249","article-title":"Metagenomics for the study of viruses in urban sewage as a tool for public health surveillance","volume":"618","author":"Fernandez-Cassi","year":"2018","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0110","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/femsmc\/xtad008","article-title":"Quantitative PCR versus metagenomics for monitoring antibiotic resistance genes: balancing high sensitivity and broad coverage","volume":"4","author":"Ferreira","year":"2023","journal-title":"FEMS Microbes"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0115","doi-asserted-by":"crossref","DOI":"10.1128\/msystems.00651-22","article-title":"A metagenomic investigation of spatial and temporal changes in sewage microbiomes across a university campus","volume":"7","author":"Fierer","year":"2022","journal-title":"mSystems"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0120","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2021.621719","article-title":"High throughput sequencing for the detection and characterization of RNA viruses","volume":"12","author":"Fitzpatrick","year":"2021","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0125","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2018.02924","article-title":"Hybrid capture-based next generation sequencing and its application to human infectious diseases","volume":"9","author":"Gaudin","year":"2018","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0130","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1128\/aem.48.3.531-538.1984","article-title":"Round robin investigation of methods for recovering human enteric viruses from sludge","volume":"48","author":"Goyal","year":"1984","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0135","doi-asserted-by":"crossref","DOI":"10.1016\/j.lanmic.2024.07.002","article-title":"Global wastewater surveillance for pathogens with pandemic potential: opportunities and challenges","volume":"6","author":"Grassly","year":"2025","journal-title":"The Lancet Microbe"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0140","doi-asserted-by":"crossref","DOI":"10.3390\/v12091050","article-title":"Metagenomic insights into the sewage RNA virosphere of a large city","volume":"12","author":"Guajardo-Leiva","year":"2020","journal-title":"Viruses"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0145","first-page":"1","article-title":"Integrated DNA and RNA extraction using magnetic beads from viral pathogens causing acute respiratory infections","volume":"7","author":"He","year":"2017","journal-title":"Sci. Reports"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0150","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.00859-22","article-title":"Simple and economical extraction of viral RNA and storage at ambient temperature","volume":"10","author":"Hernandez","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0155","doi-asserted-by":"crossref","first-page":"2047","DOI":"10.1128\/JCM.06557-11","article-title":"Detection of dengue virus genome in urine by real-time reverse transcriptase PCR: a laboratory diagnostic method useful after disappearance of the genome in serum","volume":"50","author":"Hirayama","year":"2012","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0160","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0170199","article-title":"Evaluation of methods for the concentration and extraction of viruses from sewage in the context of metagenomic sequencing","volume":"12","author":"Hjelms\u00f8","year":"2017","journal-title":"PloS One"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0165","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0210368","article-title":"Metagenomic analysis of viruses in toilet waste from long distance flights\u2014a new procedure for global infectious disease surveillance","volume":"14","author":"Hjelms\u00f8","year":"2019","journal-title":"PloS One"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0170","doi-asserted-by":"crossref","DOI":"10.3390\/v15020587","article-title":"Bioinformatic tools for NGS-based metagenomics to improve the clinical diagnosis of emerging, re-emerging and new viruses","volume":"15","author":"Iba\u00f1ez-Lligo\u00f1a","year":"2023","journal-title":"Viruses"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0175","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2023.163706","article-title":"Identification of SARS-CoV-2 variants in wastewater using targeted amplicon sequencing during a low COVID-19 prevalence period in Japan","volume":"887","author":"Iwamoto","year":"2023","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0180","first-page":"1","article-title":"Metagenomic community composition and resistome analysis in a full-scale cold climate wastewater treatment plant","volume":"17","author":"Jankowski","year":"2022","journal-title":"Environ. Microbiomes"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0185","doi-asserted-by":"crossref","first-page":"2215","DOI":"10.3389\/fpsyg.2019.02215","article-title":"Comparison of bootstrap confidence interval methods for GSCA using a Monte Carlo simulation","volume":"10","author":"Jung","year":"2019","journal-title":"Front. Psychol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0190","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2024.1272972","article-title":"Genomic surveillance of SARS-CoV-2 using long-range PCR primers","volume":"15","author":"Kandel","year":"2024","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0195","doi-asserted-by":"crossref","DOI":"10.1021\/acsestwater.3c00690","article-title":"Highly multiplexed reverse-transcription loop-mediated isothermal amplification and nanopore sequencing (LAMPore) for wastewater-based surveillance","author":"Kang","year":"2024","journal-title":"ACS EST Water"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0200","doi-asserted-by":"crossref","first-page":"8161","DOI":"10.1021\/acs.est.4c02638","article-title":"Considerations and opportunities for probe capture enrichment sequencing of emerging viruses from wastewater","volume":"58","author":"Kantor","year":"2024","journal-title":"Environ. Sci. Technol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0205","doi-asserted-by":"crossref","DOI":"10.1089\/bsp.2013.0008","article-title":"The effect of preprocessing by sequence-independent, single-primer amplification (SISPA) on metagenomic detection of viruses","volume":"11","author":"Karlsson","year":"2013","journal-title":"Biosecur. Bioterror."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0210","doi-asserted-by":"crossref","DOI":"10.1128\/aem.01853-22","article-title":"Monitoring enteroviruses and SARS-CoV-2 in wastewater using the polio environmental surveillance system in Japan","volume":"89","author":"Kitakawa","year":"2023","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0215","doi-asserted-by":"crossref","first-page":"1531","DOI":"10.1016\/S0140-6736(22)01804-9","article-title":"Sustained detection of type 2 poliovirus in London sewage between February and July, 2022, by enhanced environmental surveillance","volume":"400","author":"Klapsa","year":"2022","journal-title":"Lancet"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0220","doi-asserted-by":"crossref","first-page":"59","DOI":"10.21775\/cimb.024.059","article-title":"Comparing viral metagenomic extraction methods","volume":"24","author":"Klenner","year":"2017","journal-title":"Curr. Issues Mol. Biol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0225","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0300733","article-title":"Metagenomic analysis of sewage for surveillance of bacterial pathogens: a release experiment to determine sensitivity","volume":"19","author":"Kohle","year":"2024","journal-title":"PloS One"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0230","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/BF02289565","article-title":"Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis","volume":"29","author":"Kruskal","year":"1964","journal-title":"Psychometrika"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0235","doi-asserted-by":"crossref","DOI":"10.3389\/fmed.2022.836728","article-title":"Optimization of the SARS-CoV-2 ARTIC network V4 primers and whole genome sequencing protocol","volume":"9","author":"Lambisia","year":"2022","journal-title":"Front. Med."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0240","article-title":"Decay of enveloped SARS-CoV-2 and non-enveloped PMMoV RNA in raw sewage from university dormitories","volume":"14","author":"Li","year":"2023","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0245","doi-asserted-by":"crossref","first-page":"1654","DOI":"10.3201\/eid2608.201246","article-title":"US CDC real-time reverse transcription PCR panel for detection of severe acute respiratory syndrome coronavirus 2","volume":"26","author":"Lu","year":"2020","journal-title":"Emerg. Infect. Dis."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0250","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2020.136604","article-title":"Characterisation of the sewage virome: comparison of NGS tools and occurrence of significant pathogens","volume":"713","author":"Mart\u00ednez-Puchol","year":"2020","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0255","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2021.149562","article-title":"Exploring the diversity of coronavirus in sewage during COVID-19 pandemic: don\u2019t miss the forest for the trees","volume":"800","author":"Mart\u00ednez-Puchol","year":"2021","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0260","doi-asserted-by":"crossref","DOI":"10.1016\/j.watres.2020.116160","article-title":"Identification of multiple potential viral diseases in a large urban center using wastewater surveillance","volume":"184","author":"McCall","year":"2020","journal-title":"Water Res."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0265","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2021.145727","article-title":"Development of a large volume concentration method for recovery of coronavirus from wastewater","volume":"774","author":"McMinn","year":"2021","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0270","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/ncomms11257","article-title":"Fast and sensitive taxonomic classification for metagenomics with kaiju","volume":"7","author":"Menzel","year":"2016","journal-title":"Nat. Commun."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0275","doi-asserted-by":"crossref","DOI":"10.1099\/mgen.0.001184","article-title":"Tracking arboviruses, their transmission vectors and potential hosts by nanopore sequencing of mosquitoes","volume":"10","author":"Mirza","year":"2024","journal-title":"Microb. Genomics"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0280","article-title":"Effect of carrier yeast RNAs in the detection of SARS-CoV-2 by RT-LAMP","volume":"2023","author":"Morais-Armas","year":"2023","journal-title":"microPublication Biol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0285","doi-asserted-by":"crossref","DOI":"10.1128\/JCM.00557-20","article-title":"Comparative performance of SARS-CoV-2 detection assays using seven different primer-probe sets and one assay kit","volume":"58","author":"Nalla","year":"2020","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0290","doi-asserted-by":"crossref","first-page":"418","DOI":"10.2166\/wrd.2024.032","article-title":"Metagenomic analysis reveals differential effects of sewage treatment on the microbiome and antibiotic resistome in Bengaluru, India","volume":"14","author":"Nataraj","year":"2024","journal-title":"Water Reuse"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0295","doi-asserted-by":"crossref","first-page":"1922","DOI":"10.1001\/jama.2022.4908","article-title":"Association between SARS-CoV-2 viral load in wastewater and reported cases, hospitalizations, and vaccinations in Milan, March 2020 to November 2021","volume":"327","author":"Nattino","year":"2022","journal-title":"JAMA"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0300","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2017.00230","article-title":"Metagenomic sequencing for surveillance of food- and waterborne viral diseases","volume":"8","author":"Nieuwenhuijse","year":"2017","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0305","article-title":"A water-focused one-health approach for early detection and prevention of viral outbreaks","volume":"7","author":"O\u2019Brien","year":"2019","journal-title":"One Heal."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0310","doi-asserted-by":"crossref","DOI":"10.1002\/jmv.28753","article-title":"Metagenomics characterization of respiratory viral RNA pathogens in children under five years with severe acute respiratory infection in the Free State, South Africa","volume":"95","author":"Ogunbayo","year":"2023","journal-title":"J. Med. Virol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0315","doi-asserted-by":"crossref","DOI":"10.1016\/j.jviromet.2023.114677","article-title":"Evaluation of extraction and enrichment methods for recovery of respiratory RNA viruses in a metagenomics approach","volume":"314","author":"Ogunbayo","year":"2023","journal-title":"J. Virol. Methods"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0320","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1038\/s12276-020-0452-7","article-title":"Optimization of primer sets and detection protocols for SARS-CoV-2 of coronavirus disease 2019 (COVID-19) using PCR and real-time PCR","volume":"52","author":"Park","year":"2020","journal-title":"Exp. Mol. Med."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0325","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1038\/s41587-020-0684-z","article-title":"Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics","volume":"38","author":"Peccia","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0330","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2023.167844","article-title":"Development of highly sensitive one-step reverse transcription-quantitative PCR for SARS-CoV-2 detection in wastewater","volume":"907","author":"Raya","year":"2024","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0335","doi-asserted-by":"crossref","DOI":"10.1099\/ijsem.0.006300","article-title":"Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes","volume":"74","author":"Riesco","year":"2024","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0340","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2023.1161674","article-title":"Looking into sewage: how far can metagenomics help to detect human enteric viruses?","volume":"14","author":"Schaeffer","year":"2023","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0345","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2023.162069","article-title":"The dynamic relationship between COVID-19 cases and SARS-CoV-2 wastewater concentrations across time and space: considerations for model training data sets","volume":"871","author":"Schill","year":"2023","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0350","first-page":"9","article-title":"Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses","author":"Schloss","year":"2024","journal-title":"mSphere"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0355","doi-asserted-by":"crossref","DOI":"10.1128\/JCM.00920-20","article-title":"Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples by use of nanopore sequencing","volume":"58","author":"Shaw","year":"2020","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0360","doi-asserted-by":"crossref","DOI":"10.3390\/v12030318","article-title":"High prevalence of rotavirus a in raw sewage samples from Northeast Spain","volume":"12","author":"Silva-Sales","year":"2020","journal-title":"Viruses"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0365","doi-asserted-by":"crossref","DOI":"10.1016\/j.envint.2020.105689","article-title":"Future perspectives of wastewater-based epidemiology: monitoring infectious disease spread and resistance to the community level","volume":"139","author":"Sims","year":"2020","journal-title":"Environ. Int."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0370","doi-asserted-by":"crossref","DOI":"10.1128\/msystems.00614-21","article-title":"DNase treatment improves viral enrichment in agricultural soil viromes","volume":"6","author":"Sorensen","year":"2021","journal-title":"mSystems"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0375","first-page":"1","article-title":"Real-time evaluation of signal accuracy in wastewater surveillance of pathogens with high rates of mutation","volume":"14","author":"Thakali","year":"2024","journal-title":"Sci. Reports"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0380","doi-asserted-by":"crossref","first-page":"2470","DOI":"10.1128\/JCM.00330-16","article-title":"Comparison of next-generation sequencing technologies for comprehensive assessment of full-length hepatitis C viral genomes","volume":"54","author":"Thomson","year":"2016","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0385","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-023-42064-1","article-title":"Wastewater sequencing reveals community and variant dynamics of the collective human virome","volume":"14","author":"Tisza","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0390","first-page":"1","article-title":"Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore","volume":"3","author":"Tyson","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0395","doi-asserted-by":"crossref","first-page":"1299","DOI":"10.1038\/s41564-020-0761-6","article-title":"Analytical sensitivity and efficiency comparisons of SARS-CoV-2 RT\u2013qPCR primer\u2013probe sets","volume":"5","author":"Vogels","year":"2020","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0400","doi-asserted-by":"crossref","DOI":"10.1128\/AEM.02073-20","article-title":"Variations among viruses in influent water and effluent water at a wastewater plant over one year as assessed by quantitative PCR and metagenomics","volume":"86","author":"Wang","year":"2020","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0405","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1007\/s12560-023-09555-2","article-title":"Wastewater-based epidemiology of SARS-CoV-2: assessing prevalence and correlation with clinical cases","volume":"15","author":"Wani","year":"2023","journal-title":"Food Environ. Virol."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0410","doi-asserted-by":"crossref","DOI":"10.1016\/j.jviromet.2024.115063","article-title":"Wastewater sample storage for physicochemical and microbiological analysis","volume":"332","author":"Webster","year":"2025","journal-title":"J. Virol. Methods"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0415","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2164-5-36","article-title":"SMART amplification combined with cDNA size fractionation in order to obtain large full-length clones","volume":"5","author":"Wellenreuther","year":"2004","journal-title":"BMC Genomics"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0420","doi-asserted-by":"crossref","DOI":"10.1128\/mSystems.00614-20","article-title":"SARS-CoV-2 titers in wastewater are higher than expected from clinically confirmed cases","volume":"5","author":"Wu","year":"2020","journal-title":"mSystems"},{"key":"10.1016\/j.scitotenv.2025.181333_bb0425","doi-asserted-by":"crossref","first-page":"63323","DOI":"10.1007\/s11356-023-26571-8","article-title":"SARS-CoV-2 surveillance in medical and industrial wastewater\u2014a global perspective: a narrative review","volume":"30","author":"Yang","year":"2023","journal-title":"Environ. Sci. Pollut. Res. Int."},{"key":"10.1016\/j.scitotenv.2025.181333_bb0430","series-title":"Reverse Transcriptase Template Switching: A SMART\u2122 Approach for Full-Length cDNA Library Construction","first-page":"892","volume":"30","author":"Zhu","year":"2018"}],"container-title":["Science of The Total Environment"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0048969725029754?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0048969725029754?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T08:26:27Z","timestamp":1778833587000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0048969725029754"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1]]},"references-count":86,"alternative-id":["S0048969725029754"],"URL":"https:\/\/doi.org\/10.1016\/j.scitotenv.2025.181333","relation":{},"ISSN":["0048-9697"],"issn-type":[{"value":"0048-9697","type":"print"}],"subject":[],"published":{"date-parts":[[2026,1]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Comparison of the sensitivity of targeted and untargeted (metagenomic) methods for the detection of viral pathogens in wastewater","name":"articletitle","label":"Article Title"},{"value":"Science of The Total Environment","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.scitotenv.2025.181333","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Published by Elsevier B.V.","name":"copyright","label":"Copyright"}],"article-number":"181333"}}