Cooperative Ecosystem Studies Unit, Great Lakes Northern Forests CESU | G20AS00136

Opportunity Information: Apply for G20AS00136

The Cooperative Ecosystem Studies Unit (CESU) Great Lakes Northern Forests opportunity (Funding Opportunity Number G20AS00136) is a US Geological Survey (USGS) research funding announcement issued by the Department of the Interior through the USGS National Wildlife Health Center. It is a discretionary award made as a cooperative agreement, meaning the project is expected to involve substantial involvement and collaboration with the federal partner during the work. The opportunity falls under the Science and Technology and other Research and Development activity category and is listed under CFDA 15.808. The solicitation was created on August 17, 2020, with an original closing date of August 28, 2020.

The purpose of the project is to evaluate, in a practical and performance-focused way, how sensitive two newer, relatively low-cost next-generation sequencing (NGS) platforms are when used for viral pathogen detection and genome recovery. The work is framed around the need for faster and more accessible sequencing-based diagnostics, especially for emerging pathogens where time-to-answer can directly affect outbreak response and decision-making. Rather than focusing on developing a brand-new technology, the project aims to rigorously characterize what these already-available platforms can reliably detect and assemble under realistic sample conditions, and then convert those findings into standardized methods that other laboratories can quickly adopt.

One major component targets the Oxford Nanopore MinION platform. Nanopore sequencing is highlighted for its ability to stream data in real time, enabling analysis to begin immediately instead of waiting for a run to finish, which can take hours or days on more conventional sequencing systems. Under this award, the recipient is expected to characterize the sensitivity of the MinION for identifying a viral pathogen directly from a sample, with an emphasis on speed, including demonstrating identification in as little as 30 minutes. In practical terms, that sensitivity work typically involves determining the lowest viral quantity and/or lowest fraction of viral material in a background of host or environmental nucleic acids that still produces a confident identification within the desired time window, and documenting the conditions and workflow steps that control that performance.

The second major component focuses on the Illumina iSeq 100 system. The iSeq is positioned as a scaled-down Illumina platform that still provides the high data density associated with Illumina sequencing, but in a format better suited to single, high-value samples rather than high-throughput batch processing. The project will characterize the minimal amount of virus needed in a sample to successfully assemble a whole viral genome using the iSeq 100. This part of the work is about defining the practical threshold where a lab can move from simple detection to full-genome recovery, which is important for downstream uses like strain typing, tracking transmission, and identifying mutations relevant to virulence, host range, or diagnostic escape.

A final set of deliverables is strongly oriented toward implementation and technology transfer. The project will standardize the resulting procedures for both platforms into formal standard operating procedures (SOPs), improve the analytical software used for analyzing data generated by each system, and then disseminate the methods and tools so that other laboratories can adopt them quickly. The announcement specifically references NAHLN labs (the National Animal Health Laboratory Network), signaling that a key goal is operational readiness across a broader lab network, not just a single research demonstration. In other words, the award is meant to produce reproducible, transferable workflows and analysis approaches that reduce guesswork for labs trying to stand up rapid sequencing-based pathogen detection.

In terms of funding structure and scale, the opportunity anticipates a single award with an award ceiling of $386,575. Eligibility is limited to CESU partners under the Great Lakes Northern Forests CESU (the notice lists eligible applicants as "Others" with clarification in the full eligibility text), which generally means only organizations formally participating in that CESU consortium can apply. Overall, the grant supports applied research that benchmarks rapid pathogen identification and whole-genome assembly thresholds on two accessible sequencing platforms, and then turns the results into standardized, shareable protocols and improved analytics to strengthen rapid detection capacity for emerging pathogens.

• The Department of the Interior, U. S. Geological Survey in the science and technology and other research and development sector is offering a public funding opportunity titled "Cooperative Ecosystem Studies Unit, Great Lakes Northern Forests CESU" and is now available to receive applicants.
• Interested and eligible applicants and submit their applications by referencing the CFDA number(s): 15.808.
• This funding opportunity was created on Aug 17, 2020.
• Applicants must submit their applications by Aug 28, 2020. (Agency may still review applications by suitable applicants for the remaining/unused allocated funding in 2026.)
• Each selected applicant is eligible to receive up to $386,575.00 in funding.
• The number of recipients for this funding is limited to 1 candidate(s).
• Eligible applicants include: Others (see text field entitled Additional Information on Eligibility for clarification).

Apply for G20AS00136

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