{
  "abstract": "Background: Wastewater surveillance is a valuable tool for monitoring SARS-CoV-2 at the community level. As the virus diversified into many variants and subvariants that share overlapping mutations, resolving them accurately from wastewater becomes a key bioinformatic challenge. Objectives and aims: This study evaluated two distinct bioinformatic approaches, multilocus sequence typing (MLST) and Freyja, for identifying SARS-CoV-2 variants and subvariants in Oregon wastewater samples collected from February 2021 to February 2022. Methods: The MLST approach identified SARS-CoV-2 variants using unique mutations curated from clinical samples. In contrast, the Freyja approach resolved variant and subvariant abundances using genome wide mutation profiles weighted by sequencing depth. In this study, the variant and subvariants relative abundances produced by both approaches were compared against those observed in clinical surveillance data. Results: Both approaches identified SARS-CoV-2 variants at relative abundances that agreed closely with those observed in clinical surveillance data. However, only the Freyja approach identified over 200 Delta subvariants, divided into three clades (21A, 21I and 21J) and two levels (Level 1 and 2) based on Pango subvariants. Delta subvariants showed strong agreement at Level 1 subvariants (rs = 0.892–0.944), while agreement at Level 2 subvariants was inconsistent (rs = 0.324–0.903). Conclusions: The Freyja approach provided enhanced resolution of SARS-CoV-2 variants and subvariants in wastewater, at abundances that agreed with clinical surveillance. This added resolution is a critical advantage for public health surveillance as SARS-CoV-2 continues to evolve and share mutations across variants and subvariants.",
  "abstract_shown": true,
  "affiliations": [
    "School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, Oregon, United States of America",
    "Center for Quantitative Life Sciences, Oregon State University, Corvallis, Oregon, United States of America",
    "Public Health Division, Oregon Health Authority, Portland, Oregon, United States of America"
  ],
  "article_type": "Research Article",
  "arxiv": null,
  "author_total": 7,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Anirudh Bhatia"
    },
    {
      "affs": [
        1
      ],
      "name": "Justin Elser"
    },
    {
      "affs": [
        2
      ],
      "name": "Steven J. Carrell"
    },
    {
      "name": "Brent Kronmiller"
    },
    {
      "name": "Melissa Sutton"
    },
    {
      "name": "Christine Kelly"
    },
    {
      "name": "Tyler S. Radniecki"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/aa13j8m4b0yny.bib",
  "cited_by": 0,
  "doi": "10.1371/journal.pone.0357591",
  "fulltext_url": null,
  "id": "aa13j8m4b0yny",
  "issns": [
    "1932-6203"
  ],
  "landing_url": "https://doi.org/10.1371/journal.pone.0357591",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "2725|SARS-CoV-2 detection and testing"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Gene identification and analysis/Mutation detection"
    ],
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      "plos",
      "/Biology and life sciences/Genetics/Genomics"
    ],
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      "plos",
      "/Biology and life sciences/Genetics/Mutation/Mutation databases"
    ],
    [
      "plos",
      "/Biology and life sciences/Microbiology/Medical microbiology/Microbial pathogens/Viral pathogens/Coronaviruses/SARS coronavirus/SARS CoV 2"
    ],
    [
      "plos",
      "/Biology and life sciences/Molecular biology/Molecular biology techniques/Sequencing techniques/Genome sequencing"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Viruses/RNA viruses/Coronaviruses/SARS coronavirus/SARS CoV 2"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Viruses/Viral pathogens/Coronaviruses/SARS coronavirus/SARS CoV 2"
    ],
    [
      "plos",
      "/Medicine and health sciences/Epidemiology/Disease surveillance/Infectious disease surveillance"
    ],
    [
      "plos",
      "/Medicine and health sciences/Medical conditions/Infectious diseases/Infectious disease control/Infectious disease surveillance"
    ],
    [
      "plos",
      "/Medicine and health sciences/Pathology and laboratory medicine/Pathogens/Microbial pathogens/Viral pathogens/Coronaviruses/SARS coronavirus/SARS CoV 2"
    ],
    [
      "plos",
      "/People and places/Geographical locations/North America/United States/Oregon"
    ],
    [
      "plos",
      "/Research and analysis methods/Database and informatics methods/Bioinformatics"
    ],
    [
      "plos",
      "/Research and analysis methods/Database and informatics methods/Biological databases/Mutation databases"
    ],
    [
      "plos",
      "/Research and analysis methods/Molecular biology techniques/Sequencing techniques/Genome sequencing"
    ]
  ],
  "openalex": "W7212034250",
  "pdf_url": "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0357591&type=printable",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-09",
  "publisher": "Public Library of Science",
  "ris": "https://research.draconitic.com/paper/aa13j8m4b0yny.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:56Z",
      "native_id": "10.1371/journal.pone.0357591",
      "source": "plos",
      "url": "https://doi.org/10.1371/journal.pone.0357591"
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  "subjects": [
    {
      "field": "biology",
      "origin": "plos:genetics",
      "subfield": "genetics-genomics"
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  "title": "Correlation assessment of SARS-CoV-2 variants and their subvariants present in clinical and wastewater samples in Oregon, USA (February 7, 2021 - February 26, 2022) using the Freyja bioinformatics approach",
  "title_text": "Correlation assessment of SARS-CoV-2 variants and their subvariants present in clinical and wastewater samples in Oregon, USA (February 7, 2021 - February 26, 2022) using the Freyja bioinformatics approach",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:17:56Z",
  "url": "https://research.draconitic.com/paper/aa13j8m4b0yny",
  "venue": "PLOS One",
  "versions": []
}