{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T04:49:40Z","timestamp":1792126180262,"version":"4.4.0"},"reference-count":29,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T00:00:00Z","timestamp":1754006400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,4,20]],"date-time":"2025-04-20T00:00:00Z","timestamp":1745107200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000016","name":"U.S. Department of Health and Human Services","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000016","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100021250","name":"Center for Food Safety and Applied Nutrition","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100021250","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008510","name":"University of Maryland","doi-asserted-by":"publisher","award":["U01FD001418"],"award-info":[{"award-number":["U01FD001418"]}],"id":[{"id":"10.13039\/100008510","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006229","name":"Oak Ridge Institute for Science and Education","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006229","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100019781","name":"Joint Institute for Food Safety and Applied Nutrition, University of Maryland","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100019781","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000038","name":"US Food and Drug Administration","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000038","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Environmental Research"],"published-print":{"date-parts":[[2025,8]]},"DOI":"10.1016\/j.envres.2025.121633","type":"journal-article","created":{"date-parts":[[2025,4,18]],"date-time":"2025-04-18T18:49:27Z","timestamp":1745002167000},"page":"121633","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":2,"special_numbering":"C","title":["Harnessing methods, data analysis, and near-real-time wastewater monitoring for enhanced public health response using high throughput sequencing"],"prefix":"10.1016","volume":"278","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3958-3843","authenticated-orcid":false,"given":"Padmini","family":"Ramachandran","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2205-8062","authenticated-orcid":false,"given":"Tunc","family":"Kayikcioglu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3889-4404","authenticated-orcid":false,"given":"Tamara","family":"Walsky","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4930-0269","authenticated-orcid":false,"given":"Kathryn","family":"Judy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4337-7700","authenticated-orcid":false,"given":"Jasmine","family":"Amirzadegan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Candace Hope","family":"Bias","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bereket","family":"Tesfaldet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Balkey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dietrich","family":"EppSchmidt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hugh","family":"Rand","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Pettengill","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandra","family":"Tallent","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Brown","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tina","family":"Pfefer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9705-5897","authenticated-orcid":false,"given":"Ruth","family":"Timme","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5192-7047","authenticated-orcid":false,"given":"Amanda","family":"Windsor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7839-8309","authenticated-orcid":false,"given":"Christopher","family":"Grim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5996-7975","authenticated-orcid":false,"given":"Maria","family":"Hoffmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.envres.2025.121633_bib1","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2020.143192","article-title":"SARS-CoV-2 in hospital wastewater during outbreak of COVID-19: a review on detection, survival and disinfection technologies","volume":"761","author":"Achak","year":"2021","journal-title":"Sci. Total Environ."},{"issue":"24","key":"10.1016\/j.envres.2025.121633_bib2","doi-asserted-by":"crossref","DOI":"10.3390\/ijerph17249251","article-title":"Wastewater-based epidemiology (WBE) and viral detection in polluted surface water: a valuable tool for COVID-19 Surveillance-A brief review","volume":"17","author":"Aguiar-Oliveira","year":"2020","journal-title":"Int. J. Environ. Res. Publ. Health"},{"key":"10.1016\/j.envres.2025.121633_bib3","doi-asserted-by":"crossref","DOI":"10.1016\/j.envres.2020.110092","article-title":"Decay of SARS-CoV-2 and surrogate murine hepatitis virus RNA in untreated wastewater to inform application in wastewater-based epidemiology","volume":"191","author":"Ahmed","year":"2020","journal-title":"Environ. Res."},{"key":"10.1016\/j.envres.2025.121633_bib4","unstructured":"ARTIC primer revamping [Available from: https:\/\/community.artic.network\/c\/laboratory\/6."},{"key":"10.1016\/j.envres.2025.121633_bib5","doi-asserted-by":"crossref","DOI":"10.1016\/j.watres.2021.117516","article-title":"Variability in RT-qPCR assay parameters indicates unreliable SARS-CoV-2 RNA quantification for wastewater surveillance","volume":"203","author":"Bivins","year":"2021","journal-title":"Water Res."},{"issue":"5","key":"10.1016\/j.envres.2025.121633_bib6","doi-asserted-by":"crossref","DOI":"10.1016\/j.jinf.2024.106284","article-title":"Revealing patterns of SARS-CoV-2 variant emergence and evolution using RBD amplicon sequencing of wastewater","volume":"89","author":"Chen","year":"2024","journal-title":"J. Infect."},{"issue":"4","key":"10.1016\/j.envres.2025.121633_bib7","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1111\/rssc.12497","article-title":"Assessing the reproducibility of microbiome measurements based on concordance correlation coefficients","volume":"70","author":"Cui","year":"2021","journal-title":"J R Stat Soc Ser C Appl Stat."},{"key":"10.1016\/j.envres.2025.121633_bib8","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.coesh.2020.06.001","article-title":"Wastewater and public health: the potential of wastewater surveillance for monitoring COVID-19","volume":"17","author":"Farkas","year":"2020","journal-title":"Curr. Opin. Environ. Sci. Health"},{"key":"10.1016\/j.envres.2025.121633_bib9","doi-asserted-by":"crossref","DOI":"10.1016\/j.watres.2021.117710","article-title":"High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants","volume":"205","author":"Fontenele","year":"2021","journal-title":"Water Res."},{"issue":"1","key":"10.1016\/j.envres.2025.121633_bib10","doi-asserted-by":"crossref","DOI":"10.1093\/biomethods\/bpaa014","article-title":"Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and Oxford nanopore rapid barcoding","volume":"5","author":"Freed","year":"2020","journal-title":"Biol. Methods. Protoc."},{"key":"10.1016\/j.envres.2025.121633_bib11","unstructured":"GenomeTrakr-protocols-wastewater [Available from: https:\/\/www.protocols.io\/file-manager\/682C9E830C0A11EC806D0A58A9FEAC02."},{"key":"10.1016\/j.envres.2025.121633_bib12","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2020.143493","article-title":"Wastewater surveillance for SARS-CoV-2: lessons learnt from recent studies to define future applications","volume":"759","author":"Hamouda","year":"2021","journal-title":"Sci. Total Environ."},{"key":"10.1016\/j.envres.2025.121633_bib13","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.envres.2025.121633_bib14","doi-asserted-by":"crossref","DOI":"10.1016\/j.scitotenv.2023.165817","article-title":"The role of wastewater-based epidemiology for SARS-CoV-2 in developing countries: cumulative evidence from South Africa supports sentinel site surveillance to guide public health decision-making","volume":"903","author":"Iwu-Jaja","year":"2023","journal-title":"Sci. Total Environ."},{"issue":"7925","key":"10.1016\/j.envres.2025.121633_bib15","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/s41586-022-05049-6","article-title":"Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission","volume":"609","author":"Karthikeyan","year":"2022","journal-title":"Nature"},{"key":"10.1016\/j.envres.2025.121633_bib16","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.14596","article-title":"Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples","volume":"11","author":"Kayikcioglu","year":"2023","journal-title":"PeerJ"},{"issue":"4","key":"10.1016\/j.envres.2025.121633_bib17","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1038\/s41564-022-01089-w","article-title":"Metagenomics-enabled microbial surveillance","volume":"7","author":"Ko","year":"2022","journal-title":"Nat. Microbial."},{"key":"10.1016\/j.envres.2025.121633_bib18","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/j.chemolab.2015.02.019","article-title":"zCompositions- R package for multivariate imputation of left-censored data under a compositional approach","volume":"143","author":"Palarea-Albaladejo","year":"2015","journal-title":"Chemometr. Intell. Lab. Syst."},{"key":"10.1016\/j.envres.2025.121633_bib19","article-title":"SARS-CoV-2 genomes recovered by long amplicon tiling multiplex approach using nanopore sequencing and applicable to other sequencing platform","author":"Roy","year":"2020","journal-title":"bioRxiv"},{"issue":"10","key":"10.1016\/j.envres.2025.121633_bib20","doi-asserted-by":"crossref","DOI":"10.3390\/vaccines9101195","article-title":"Emerging SARS-CoV-2 variants: a review of its mutations, its implications and vaccine efficacy","volume":"9","author":"Ramesh","year":"2021","journal-title":"Vaccines"},{"issue":"1","key":"10.1016\/j.envres.2025.121633_bib21","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1038\/s41467-022-28246-3","article-title":"Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater","volume":"13","author":"Smyth","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.envres.2025.121633_bib22","doi-asserted-by":"crossref","first-page":"5378","DOI":"10.1016\/j.csbj.2022.09.028","article-title":"High-throughput sequencing technologies in the detection of livestock pathogens, diagnosis, and zoonotic surveillance","volume":"20","author":"Suminda","year":"2022","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"10.1016\/j.envres.2025.121633_bib23","unstructured":"Swift BioSciences. \u201cNEW- swift normalase\u2122 amplicon SARS-CoV-2 panels.\u201d [Available from: https:\/\/swiftbiosci.com\/swift-normalase-amplicon-sars-cov-2-panels-3\/."},{"key":"10.1016\/j.envres.2025.121633_bib24","unstructured":"The Pango nomenclature is being used by researchers and public health agencies worldwide to track the transmission and spread of SARS-CoV-2, including variants of concern. [Available from:https:\/\/cov-lineages.org\/."},{"key":"10.1016\/j.envres.2025.121633_bib25","article-title":"SARS-CoV-2 wastewater variant surveillance: pandemic response leveraging FDA's GenomeTrakr network","author":"Timme","year":"2024","journal-title":"medRxiv"},{"key":"10.1016\/j.envres.2025.121633_bib26","article-title":"Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore","author":"Tyson","year":"2020","journal-title":"bioRxiv"},{"key":"10.1016\/j.envres.2025.121633_bib27","series-title":"Varskip Multiplex PCR Designs for SARS-CoV-2 Sequencing","year":"2021"},{"issue":"9","key":"10.1016\/j.envres.2025.121633_bib28","doi-asserted-by":"crossref","DOI":"10.3390\/diagnostics12092128","article-title":"Application of high-throughput sequencing technology in the pathogen identification of diverse infectious diseases in nephrology departments","volume":"12","author":"Wang","year":"2022","journal-title":"Diagnostics"},{"key":"10.1016\/j.envres.2025.121633_bib29","doi-asserted-by":"crossref","DOI":"10.1016\/j.watres.2022.118535","article-title":"Making waves: wastewater surveillance of SARS-CoV-2 in an endemic future","volume":"219","author":"Wu","year":"2022","journal-title":"Water Res."}],"container-title":["Environmental Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0013935125008849?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0013935125008849?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T04:43:15Z","timestamp":1792125795000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0013935125008849"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8]]},"references-count":29,"alternative-id":["S0013935125008849"],"URL":"https:\/\/doi.org\/10.1016\/j.envres.2025.121633","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.12.10.24318772","asserted-by":"object"}]},"ISSN":["0013-9351"],"issn-type":[{"value":"0013-9351","type":"print"}],"subject":[],"published":{"date-parts":[[2025,8]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Harnessing methods, data analysis, and near-real-time wastewater monitoring for enhanced public health response using high throughput sequencing","name":"articletitle","label":"Article Title"},{"value":"Environmental Research","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.envres.2025.121633","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"121633"}}