This wastewater surveillance dashboard provides real-time viral monitoring data across multiple cities through deep sequencing analysis of municipal wastewater samples generously provided by community partners. We hope to reach 75 sewersheds in the next year, so if you know other communities who might like to participate and make wastewater sequencing results public, please let Dave O'Connor (dhoconno@wisc.edu) or Marc Johnson (marcjohnson@health.missouri.edu; @solidevidence on Twitter and BlueSky) know. Key contributors from Marc's lab include Clayton Rushford, Alejandro Tovar-Mendez, and Devon Gregory. Nick Minor and Will Gardner in Dave's lab are responsible for data analysis and visualization. NVD is performed using UW-Madison Center for High Throughput Computing resources.
Data Collection: Wastewater samples are collected from designated sewersheds and sent to Marc Johnson's laboratory at the University of Missouri for processing. The laboratory employs a multi-step process to prepare the samples for analysis. First, samples are filtered through a 0.22 um filter to remove bacteria and other solids. Samples are then mixed with polyethylene glycol (PEG) and precipitated ti concentrate and viruses from the wastewater samples. This step is crucial as viral particles are typically present in low concentrations in raw wastewater, so sequencing from wastewater without enrichment can miss viral sequences. Following precipitation, total nucleic acids are extracted from the virus-enriched samples. The extracted nucleic acids then undergo library preparation to make them compatible with next-generation sequencing technology. Finally, the prepared libraries are sequenced on an Illumina NovaSeq instrument at the University of Missouri, generating billions of short reads that represent the genetic material present in the sample.
Analysis Pipeline: The raw sequencing data is processed through a metagenomic analysis pipeline, NVD, developed by Dave O’Connor to identify viral sequences. This pipeline was developed specifically for identifying and exploring metagenomes for families of viruses that infect humans (and often animals). NVD results are stored on a Labkey Server SDMS. Results from a curated list of viruses and sites that have agreed to have their data made public are retrieved from Labkey, analyzed, and visualized. ChatGPT 4.1 inspects the visualizations and creates the narrative discussions.
Update Frequency: Wastewater samples are delivered to Marc Johnson's lab weekly. It typically takes two to three weeks for nucleic acids to be isolated, sequenced, andalyzed, and available for inclusion in the dashboards. The dashboards themselves update automatically each night.
Data Usage & Licensing
This data provided here is intended for public use and is made available under a CC BY-NC-SA 4.0 license that allows unrestricted sharing and adapting for non-commercial use.
Disclaimer
The raw data published on this dashboard has been obtained from deidentified and aggregated materials collected in accordance with the law and ethical guidelines governing the research studies. This data is made available for informational purposes only. This data set has not been independently verified, validated, or peer reviewed. It may contain errors, omissions, or artifacts inherent to the methods used in data collection and processing and is provided as is without any warranty of accuracy or completeness.
This data is neither intended for clinical or diagnostic purposes nor should it be used for making public policy. Users must not rely on this dataset to inform health care decisions, public health strategies, or regulatory actions. Any conclusions drawn from this data are the sole responsibility of the user.
By accessing or using this data, you assume all risks and acknowledge these limitations. You further agree to use this data responsibly, in compliance with all applicable legal and ethical standards.
About Lungfish
Lungfish is a project funded by Inkfish Medical. Dave O'Connor, Shelby O'Connor, and Marc Johnson jointly lead the Lungfish project from their labs at the University of Wisconsin-Madison and University of Missouri.