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Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater

Author

Listed:
  • Yunxi Liu

    (Rice University)

  • Nicolae Sapoval

    (Rice University)

  • Pilar Gallego-García

    (Universidade de Vigo
    SERGAS-UVIGO)

  • Laura Tomás

    (Universidade de Vigo
    SERGAS-UVIGO)

  • David Posada

    (Universidade de Vigo
    SERGAS-UVIGO
    Universidade de Vigo)

  • Todd J. Treangen

    (Rice University)

  • Lauren B. Stadler

    (Rice University)

Abstract

Wastewater surveillance for SARS-CoV-2 provides early warnings of emerging variants of concerns and can be used to screen for novel cryptic linked-read mutations, which are co-occurring single nucleotide mutations that are rare, or entirely missing, in existing SARS-CoV-2 databases. While previous approaches have focused on specific regions of the SARS-CoV-2 genome, there is a need for computational tools capable of efficiently tracking cryptic mutations across the entire genome and investigating their potential origin. We present Crykey, a tool for rapidly identifying rare linked-read mutations across the genome of SARS-CoV-2. We evaluated the utility of Crykey on over 3,000 wastewater and over 22,000 clinical samples; our findings are three-fold: i) we identify hundreds of cryptic mutations that cover the entire SARS-CoV-2 genome, ii) we track the presence of these cryptic mutations across multiple wastewater treatment plants and over three years of sampling in Houston, and iii) we find a handful of cryptic mutations in wastewater mirror cryptic mutations in clinical samples and investigate their potential to represent real cryptic lineages. In summary, Crykey enables large-scale detection of cryptic mutations in wastewater that represent potential circulating cryptic lineages, serving as a new computational tool for wastewater surveillance of SARS-CoV-2.

Suggested Citation

  • 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.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-48334-w
    DOI: 10.1038/s41467-024-48334-w
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