Detecting SARS-CoV-2 cryptic lineages using publicly available whole genome wastewater sequencing data.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40489546", "kind": "science-record", "revision": 1, "content_hash": "sha256:2871ccb2aa2b0b5cb69182a2c4b32cbe88ba16e0d76b681822523b0ef1564319", "created_at": "2026-11-01T20:30:36Z", "updated_at": "2026-11-01T20:30:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Detecting SARS-CoV-2 cryptic lineages using publicly available whole genome wastewater sequencing data.", "doi": "10.1371/journal.ppat.1012850", "pmid": "40489546", "authors": ["Reinier Suarez", "Devon A Gregory", "David A Baker", "Clayton A Rushford", "Torin L Hunter", "Nicholas R Minor", "Clayton M Russ", "Emma E Copen", "David H O'Connor", "Marc C Johnson"], "journal": "PLoS pathogens", "year": 2025, "abstract": "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 amplifying the most rapidly evolving 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 \"cryptic lineages\". 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's 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 (2-81) 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.", "claims": [{"id": "claim-data-access", "statement": "To comply with submission guidelines, many low-abundance polymorphisms were excluded from the analysis. A comprehensive report is available upon request from the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40489546", "locator": "sections[10] \"Supporting information\" paragraph 7", "quote": "To comply with submission guidelines, many low-abundance polymorphisms were excluded from the analysis. A comprehensive report is available upon request from the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using this method, we identified 18 cryptic lineages that appeared in multiple (2–81) samples from the same sewershed, including 12 that were not previously reported.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40489546", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Using this method, we identified 18 cryptic lineages that appeared in multiple (2–81) samples from the same sewershed, including 12 that were not previously reported."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Using this method, we identified 18 cryptic lineages that appeared in multiple (2–81) samples from the same sewershed, including 12 that were not previously reported.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:40489546"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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