# New tools for tick-borne pathogen surveillance

> **NIH NIH R01** · UNIVERSITY OF MINNESOTA · 2024 · $698,772

## Abstract

Project Summary
Tick and rodent surveillance for pathogens requires substantial technical expertise and laboratory infrastructure.
Most surveillance activities focus on detection of one or two potential pathogens in the vector or reservoir
population and non-target pathogens remain undetected. To overcome the current limitations associated with
traditional tick surveillance methods, we are proposing a novel dual metagenomic and metatranscriptomic
sequencing solution using cutting-edge nanopore adaptive sampling (NAS) protocols. The NAS method leverages
Oxford Nanopore Technologies sequencing technology (a portable MinION sequencer) and a recently developed
bioinformatic pipeline that facilitates the immediate mapping of individual nucleotide molecules (DNA, cDNA,
or RNA) to a given reference as each molecule is sequenced. User-defined thresholds then specify the retention
or rejection of specific molecules, informed by the real-time reference mapping results as they are physically
passing through a given sequencing nanopore. Hundreds to thousands of individual sequencing pores are
controlled in real-time using a powerful Graphics Processing Unit (GPU) and the NAS software with retain/reject
decisions made in less than a second for each individual pore. This allows for sensitive detection of a very wide
range of targeted pathogen and host species barcoding sequences without becoming swamped in the sea of non-
target host and symbiotic bacterial nucleic acids. The system can be field deployed and requires minimal
infrastructure. An internet connection is not required.
 In the course of this proposed study, we will test NAS for diagnostic accuracy (sensitivity, specificity, and
threshold of detection), test for detection of a variety of in vitro grown DNA and RNA-based pathogens,
differentiate closely related pathogen species and strains, develop and ground truth protocols for field testing on
wild ticks and rodents from a well-characterized region (Minnesota), and comprehensively field test the methods
and protocols in a region predicted to have the one of the highest densities of emerging rodent-associated
zoonoses in the US (central Kansas). We expect NAS to become an important and affordable tool with a wide
variety of surveillance applications.

## Key facts

- **NIH application ID:** 10750992
- **Project number:** 5R01AI155472-02
- **Recipient organization:** UNIVERSITY OF MINNESOTA
- **Principal Investigator:** Peter A Larsen
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $698,772
- **Award type:** 5
- **Project period:** 2022-12-08 → 2027-11-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10750992

## Citation

> US National Institutes of Health, RePORTER application 10750992, New tools for tick-borne pathogen surveillance (5R01AI155472-02). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10750992. Licensed CC0.

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