The study developed FitNMF, a model for detecting SARS-CoV-2 variants in wastewater next-generation sequencing data. Wastewater holds pooled, fragmented viral genomes from many people, so complete genomes cannot be assembled. FitNMF uses the time structure of the samples and competition between variants. It jointly infers mutational signatures, relative abundances and fitness advantages of circulating variants. The authors tested it on simulated data and on 2021 to 2024 time series from six Swiss wastewater treatment plants. It identified and quantified emerging variants de novo, though the real-data test covers only these six Swiss plants.
Why it is interesting: Existing wastewater pipelines are limited in detecting new variants absent from clinical sequencing data. This model infers variants and their fitness advantages from the pooled wastewater signal alone.
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