More details on Chicago region wastewater surveillance project

Chicagoland Prototype Coronavirus Assessment Network Node (PCANN)

Here is more detail about Chicago region project, as promised by my October 14 Substack newsletter .

This multi-institution, multi-disciplinary prototype project (and application to Walder Foundation) includes following (as well as contractors and more collaborators): Discovery Partners Institutue (University of Illinois); University of Illinois-Chicago (UIC); Argonne National Laboratory (ANL); Northweatern University (NU); University of Chicago; and Chicago Department of Public Health.

— Collaborators include Metropolitan Water Reclamation District of Greater Chicago (MWRD), Chicago Department of Public Health (CDPH), multiple research institutions, and Current (which has worked closely with the project research and utility partners on a two-year waterway monitoring project and brings expertise in sampling protocol design and logistics, as well as civic and community partnerships central to the project’s broader impact).

Application to Walder Foundation (which has not been published) provided:

— Executive Summary

— Goals and rationale

— Research Design, Scope, and Approach: Precision Wastewater-Based Epidemiology (pWBE).

— Approach: Five Interlocking Teams

— Organization and Investigator Capabilities and Collaboration

— Budget Narrative

My understanding of Budget Narrative for each of PCANN’s five, multi-disciplinary, multi-institutional, interlocking teams follows:

• Sampling Design and Strategy: Identifying Vulnerable Communities

— Precision WBE (pWBE) prototype will initially involve weekly sampling at the three wastewater treatment facilities serving Chicago and 15 to 20 locations within Chicago’s sewer network to be selected in collaboration with MRWD and public health authorities.

— Project will also make use of archived samples.

— Project expects to refine sampling locations and frequency based on comparison of pWBE hotspot identification and CDPH case data.

— Budget narrative: Wastewater sampling ($205k). Current will coordinate a UIC/ANL-led design ($45k) with MWRD using an approved contractor to perform the sampling ($160k). Roughly 20 locations will be sampled weekly throughout the project’s first six months and 4-6 locations will be sampled semi-weekly during the second six months.

• Pathogen Identification and Quantification

— Budget narrative: Pathogen identification and quantification ($490k) brings together complementary scientific expertise and laboratory facilities at UIC (qPCR and ddPCR) and ANL (deep genetic sequencing). NU and Stemloop will test new biosensors to detect SARS-CoV-2 on-site. Budget for ANL and UIC includes both scientific analysis and laboratory supplies and instrument use costs—a total of $135k at ANL and $245k at UIC. NU/Stemloop on-site testing is budgeted at $110k.

— For more background on startup Stemloop, see “Khalid selected for elite entrepreneurship program at Argonne!”

• Geographic source identification

• Data infrastructure and services

• Support for the infrastructure and developing tools for sharing and reporting

— Budget narratives:

— Geographic source identification ($220k) will combine modeling and analysis from NU ($180k) with Artificial Intelligence (AI) capabilities integrated by ANL ($40k) and COVID-19 case data provided by CDPH. Flow modeling of Chicago wastewater systems (UIUC) is supported by the National Science Foundation (NSF) SAVEUR project (PI Packman; NSF Program Officer has approved this use). Policy Integration ($155k) will be designed, implemented, and evaluated by a team including CDPH, UIC’s School of Public Health ($75), DPI ($70k), and NU ($10k).

— Data infrastructure and services ($170k) will include data sharing and sample preservation infrastructure deployed by ANL ($100k).

— Support for the infrastructure and developing tools for sharing and reporting will be done by DPI ($70k).