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Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater

Author

Listed:
  • Nicolae Sapoval

    (Rice University)

  • Yunxi Liu

    (Rice University)

  • Esther G. Lou

    (Rice University)

  • Loren Hopkins

    (8000 N. Stadium Dr.
    Rice University)

  • Katherine B. Ensor

    (Rice University)

  • Rebecca Schneider

    (8000 N. Stadium Dr.)

  • Lauren B. Stadler

    (Rice University)

  • Todd J. Treangen

    (Rice University)

Abstract

As clinical testing declines, wastewater monitoring can provide crucial surveillance on the emergence of SARS-CoV-2 variant of concerns (VoCs) in communities. In this paper we present QuaID, a novel bioinformatics tool for VoC detection based on quasi-unique mutations. The benefits of QuaID are three-fold: (i) provides up to 3-week earlier VoC detection, (ii) accurate VoC detection (>95% precision on simulated benchmarks), and (iii) leverages all mutational signatures (including insertions & deletions).

Suggested Citation

  • Nicolae Sapoval & Yunxi Liu & Esther G. Lou & Loren Hopkins & Katherine B. Ensor & Rebecca Schneider & Lauren B. Stadler & Todd J. Treangen, 2023. "Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater," Nature Communications, Nature, vol. 14(1), pages 1-7, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-38184-3
    DOI: 10.1038/s41467-023-38184-3
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    References listed on IDEAS

    as
    1. Davida S. Smyth & Monica Trujillo & Devon A. Gregory & Kristen Cheung & Anna Gao & Maddie Graham & Yue Guan & Caitlyn Guldenpfennig & Irene Hoxie & Sherin Kannoly & Nanami Kubota & Terri D. Lyddon & M, 2022. "Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
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    Cited by:

    1. Yunxi Liu & Nicolae Sapoval & Pilar Gallego-García & Laura Tomás & David Posada & Todd J. Treangen & Lauren B. Stadler, 2024. "Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Kayla G. Barnes & Joshua I. Levy & Jillian Gauld & Jonathan Rigby & Oscar Kanjerwa & Christopher B. Uzzell & Chisomo Chilupsya & Catherine Anscombe & Christopher Tomkins-Tinch & Omar Mbeti & Edward Ca, 2023. "Utilizing river and wastewater as a SARS-CoV-2 surveillance tool in settings with limited formal sewage systems," Nature Communications, Nature, vol. 14(1), pages 1-11, December.

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