Liu, YunxiSapoval, NicolaeGallego-García, PilarTomás, LauraPosada, DavidTreangen, Todd J.Stadler, Lauren B.2024-08-022024-08-022024Liu, Y., Sapoval, N., Gallego-García, P., Tomás, L., Posada, D., Treangen, T. J., & Stadler, L. B. (2024). Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater. Nature Communications, 15(1), 4545. https://doi.org/10.1038/s41467-024-48334-whttps://hdl.handle.net/1911/117585Wastewater 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.engExcept where otherwise noted, this work is licensed under a Creative Commons Attribution (CC BY) license.  Permission to reuse, publish, or reproduce the work beyond the terms of the license or beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.Journal articles41467-024-48334-whttps://doi.org/10.1038/s41467-024-48334-w