{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,17]],"date-time":"2026-10-17T20:53:36Z","timestamp":1792270416971,"version":"4.4.0"},"update-to":[{"DOI":"10.1371\/journal.ppat.1011688","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,1,10]],"date-time":"2024-01-10T00:00:00Z","timestamp":1704844800000}}],"reference-count":12,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2023,12,28]],"date-time":"2023-12-28T00:00:00Z","timestamp":1703721600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000026","name":"National Institute on Drug Abuse","doi-asserted-by":"publisher","award":["U01DA053893"],"award-info":[{"award-number":["U01DA053893"]}],"id":[{"id":"10.13039\/100000026","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>Deep sequencing of wastewater to detect SARS-CoV-2 has been used during the COVID-19 pandemic to monitor viral variants as they appear and circulate in communities. SARS-CoV-2 lineages of an unknown source that have not been detected in clinical samples, referred to as cryptic lineages, are sometimes repeatedly detected from specific locations. We have continued to detect one such lineage previously seen in a Missouri site. This cryptic lineage has continued to evolve, indicating continued selective pressure similar to that observed in Omicron lineages.<\/jats:p>","DOI":"10.1371\/journal.ppat.1011688","type":"journal-article","created":{"date-parts":[[2023,12,28]],"date-time":"2023-12-28T13:29:13Z","timestamp":1703770153000},"page":"e1011688","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":5,"title":["Continued selection on cryptic SARS-CoV-2 observed in Missouri wastewater"],"prefix":"10.1371","volume":"19","author":[{"given":"Devon A.","family":"Gregory","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clayton","family":"Rushford","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Torin","family":"Hunter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chung-Ho","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christie","family":"Darby","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicole","family":"Niehues","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth","family":"Semkiw","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melissa","family":"Reynolds","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeff","family":"Wenzel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6431-7133","authenticated-orcid":true,"given":"Marc C.","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,12,28]]},"reference":[{"issue":"9","key":"ppat.1011688.ref001","doi-asserted-by":"crossref","first-page":"e0257454","DOI":"10.1371\/journal.pone.0257454","article-title":"Protocol for safe, affordable, and reproducible isolation and quantitation of SARS-CoV-2 RNA from wastewater","volume":"16","author":"M Trujillo","year":"2021","journal-title":"PLoS ONE"},{"key":"ppat.1011688.ref002","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.3390\/v13081647","article-title":"Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner","volume":"13","author":"D.A. Gregory","year":"2021","journal-title":"Viruses"},{"key":"ppat.1011688.ref003","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":"D.S. Smyth","year":"2022","journal-title":"Nat Commun"},{"issue":"10","key":"ppat.1011688.ref004","doi-asserted-by":"crossref","first-page":"e1010636","DOI":"10.1371\/journal.ppat.1010636","article-title":"Genetic diversity and evolutionary convergence of cryptic SARS- CoV-2 lineages detected via wastewater sequencing","volume":"18","author":"DA Gregory","year":"2022","journal-title":"PLoS Pathog"},{"key":"ppat.1011688.ref005","article-title":"Tracing the origin of SARS-CoV-2 Omicron-like spike sequences detected in wastewater","author":"MM Shafer","year":"2023","journal-title":"medRxiv"},{"issue":"2","key":"ppat.1011688.ref006","article-title":"The COVID-19 Genomics UK (COG-UK) consortium, Recurrent SARS-CoV-2 mutations in immunodeficient patients","volume":"8","author":"SAJ Wilkinson","year":"2022","journal-title":"Virus Evolution"},{"key":"ppat.1011688.ref007","doi-asserted-by":"crossref","first-page":"850","DOI":"10.1126\/science.abf9302","article-title":"Prospective mapping of viral mutations that escape antibodies used to treat COVID-19","volume":"371","author":"Tyler N. Starr","year":"2021","journal-title":"Science"},{"issue":"11","key":"ppat.1011688.ref008","doi-asserted-by":"crossref","first-page":"e1010951","DOI":"10.1371\/journal.ppat.1010951","article-title":"Deep mutational scans for ACE2 binding, RBD expression, and antibody escape in the SARS-CoV-2 Omicron BA.1 and BA.2 receptor-binding domains.","volume":"18","author":"TN Starr","year":"2022","journal-title":"PLoS Pathog"},{"key":"ppat.1011688.ref009","doi-asserted-by":"crossref","first-page":"4572","DOI":"10.1093\/bioinformatics\/btab705","article-title":"New strategies to improve minimap2 alignment accuracy","volume":"37","author":"H. Li","year":"2021","journal-title":"Bioinformatics"},{"issue":"21","key":"ppat.1011688.ref010","doi-asserted-by":"crossref","first-page":"e01062","DOI":"10.1128\/JVI.01062-20","article-title":"Optimized Pseudotyping Conditions for the SARS-COV-2 Spike Glycoprotein","volume":"94","author":"MC Johnson","year":"2020","journal-title":"J Virol"},{"key":"ppat.1011688.ref011","doi-asserted-by":"crossref","DOI":"10.3389\/fbinf.2022.818619","article-title":"A Freely Available DNA Manipulation and Visualization Program","volume":"2","author":"MW Davis","year":"2022","journal-title":"Front Bioinforma"},{"issue":"22","key":"ppat.1011688.ref012","doi-asserted-by":"crossref","first-page":"11945","DOI":"10.1128\/JVI.05171-11","article-title":"Sequences in Gibbon Ape Leukemia Virus Envelope That Confer Sensitivity to HIV-1 Accessory Protein","volume":"85","author":"SK Janaka","year":"2011","journal-title":"Vpu. J Virol"}],"updated-by":[{"DOI":"10.1371\/journal.ppat.1011688","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2024,1,10]],"date-time":"2024-01-10T00:00:00Z","timestamp":1704844800000}}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1011688","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,10]],"date-time":"2024-01-10T13:35:56Z","timestamp":1704893756000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1011688"}},"subtitle":[],"editor":[{"given":"Thomas E.","family":"Morrison","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,12,28]]},"references-count":12,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2023,12,28]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1011688","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.09.18.23295717","asserted-by":"object"}]},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,12,28]]}}}