{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,29]],"date-time":"2026-06-29T18:09:48Z","timestamp":1782756588925,"version":"3.54.5"},"update-to":[{"DOI":"10.1371\/journal.ppat.1012850","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,6,18]],"date-time":"2025-06-18T00:00:00Z","timestamp":1750204800000}}],"reference-count":37,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2025,6,9]],"date-time":"2025-06-09T00:00:00Z","timestamp":1749427200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006492","name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["75N93021C00045"],"award-info":[{"award-number":["75N93021C00045"]}],"id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Heart of Racing"},{"name":"Heart of Racing"},{"name":"Infish"},{"name":"Inkfish"}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>\n                    Beginning in early 2021, unique and highly divergent lineages of SARS-CoV-2 were sporadically found in wastewater sewersheds using a sequencing strategy focused on\n                    <jats:bold>amplifying<\/jats:bold>\n                    the most\n                    <jats:bold>rapidly evolving<\/jats:bold>\n                    region of SARS-CoV-2, the receptor binding domain (RBD). Because these RBD sequences did not match known circulating strains and their source was not known, we termed them \u201ccryptic lineages\u201d. To date, more than 20 cryptic lineages have been identified using the RBD-focused sequencing strategy. Here, we identified and characterized additional cryptic lineages from SARS-CoV-2 wastewater sequences submitted to NCBI\u2019s Sequence Read Archives (SRA). Wastewater sequence datasets were screened for individual sequence reads that contained combinations of mutations frequently found in cryptic lineages but not contemporary circulating lineages. Using this method, we identified 18 cryptic lineages that appeared in multiple (2\u201381) samples from the same sewershed, including 12 that were not previously reported. Partial consensus sequences were generated for each cryptic lineage by extracting and mapping sequences containing cryptic-specific mutations. Surprisingly, seven of the mutations that appeared convergently in cryptic lineages were reversions to sequences that were highly conserved in SARS-CoV-2-related enteric bat Sarbecoviruses. The apparent reversion to bat Sarbecovirus sequences is consistent with the notion that SARS-CoV-2 adaptation to replicate efficiently in respiratory tissues preceded the COVID-19 pandemic.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1012850","type":"journal-article","created":{"date-parts":[[2025,6,9]],"date-time":"2025-06-09T13:57:07Z","timestamp":1749477427000},"page":"e1012850","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":4,"title":["Detecting SARS-CoV-2 cryptic lineages using publicly available whole genome wastewater sequencing data"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6068-6046","authenticated-orcid":true,"given":"Reinier","family":"Suarez","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Devon A.","family":"Gregory","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David A.","family":"Baker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clayton A.","family":"Rushford","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Torin L.","family":"Hunter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas R.","family":"Minor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Clayton M.","family":"Russ","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emma E.","family":"Copen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David 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Nevada","volume":"57","author":"C Barber","year":"2023","journal-title":"Environ Sci Tech"},{"key":"ppat.1012850.ref003","article-title":"A scoping review of human pathogens detected in untreated human wastewater and sludge","author":"T Corrin","year":"2024","journal-title":"J Water Health"},{"key":"ppat.1012850.ref004","doi-asserted-by":"crossref","first-page":"152213","DOI":"10.1016\/j.scitotenv.2021.152213","article-title":"SARS-CoV-2 genome quantification in wastewaters at regional and city scale allows precise monitoring of the whole outbreaks dynamics and variants spreading in the population","volume":"810","author":"S Wurtzer","year":"2022","journal-title":"Sci Total Environ"},{"issue":"1","key":"ppat.1012850.ref005","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":"DS Smyth","year":"2022","journal-title":"Nat 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