SARS-CoV-2 infection dynamics revealed by wastewater sequencing analysis and deconvolution

Area of Science:

• Environmental microbiology
• Virology
• Bioinformatics

Background:

• Wastewater-based epidemiology (WBE) is crucial for monitoring infectious diseases like SARS-CoV-2.
• Accurate and scalable tools are needed to analyze WBE sequencing data for tracking viral dynamics and lineages.
• Existing methods may lack the reproducibility and comprehensiveness required for continuous surveillance.

Purpose of the Study:

• To present PiGx SARS-CoV-2, a reproducible computational pipeline for analyzing wastewater sequencing data.
• To demonstrate the pipeline's accuracy in quantifying SARS-CoV-2 variant proportions using simulated and real-world data.
• To reconstruct SARS-CoV-2 lineage dynamics in Berlin and New York City using wastewater surveillance.

Main Methods:

• Development of an end-to-end computational pipeline (PiGx SARS-CoV-2) for raw sequencing data processing.
• In silico and spiked-in sample analyses to validate variant proportion calculations.
• Application of the pipeline to wastewater samples from Berlin and New York City, including analysis of short-read data.
• Geospatial time series analysis and deconvolution techniques.

Main Results:

• PiGx SARS-CoV-2 accurately calculates variant proportions, including Variants of Concern (VOCs), from environmental and spiked-in samples.
• Reconstruction of SARS-CoV-2 lineage dynamics in Berlin, showing the emergence of Alpha and replacement of Delta by Omicron variants.
• Successful reproduction of cryptic lineage proportions from New York City targeted sequencing data.
• Demonstrated high accuracy with industrial-scale, very-short-read data.

Conclusions:

• PiGx SARS-CoV-2 is a highly reproducible, scalable, and automated pipeline for analyzing wastewater sequencing data.
• The pipeline accurately reconstructs viral lineage dynamics and can identify new mutations and emerging lineages.
• This approach supports continuous monitoring and early-warning systems for SARS-CoV-2 and other pathogens through WBE.