Credits

About This Project

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.

Collaborators

• Nucleic Acid Observatory, SecureBio: SecureBio. SecureBio funds most sequencing flow cells through their sponsor, Open Philanthropy.
• Rachel Poretsky, University of Illinois, Chicago: Poretskly lab
• Jason Rothman, University of California, Riverside: Jason Rothman

Community partners

• Columbia, MO: Columbia/Boone County Public Health and Human Services; Columbia Sewer Utility. They have also created a great FAQ and set of links providing more information about many of the viruses on these dashboards.
• Riverside, CA: Riverside Water Quality Control Plant; Riverside University Health System - Public Health
• Boston, MA: Massachusetts Water Resources Authority

Data & Analysis

• 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 12s library preparation to make them compatible with next-generation sequencing technology. Finally, the prepared libraries are sequenced on an Illumina MiSeq instrument at the University of Missouri, generating millions of short reads that represent the genetic material present in the sample.
• Analysis Pipeline: The raw sequencing data is processed through a custom analysis pipeline, details to come.

• 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.