Dr Benjamín Durán-Vinet1,2,3,4, Dr Karla Araya-Castro2, Dr Gert-Jan Jeunen5, Dr Sebastian Alvarez-Costes1, Gracie Kroos1, Amorangi Rayner3, Donna Huber6, Sara Ferreira1, Jackson Treece1, Dr Yusmiati Liau7, Dr Antoinette Piaggio8, Dr Jo-Ann Stanton9, Dr Anastasija Zaiko10, Associate Professor Htin Lin Aung3, Associate Professor Michael Knapp1, Dr Annabel Whibley7,11, Dr Alana Alexander1, Dr Nathan Kenny2, Distinguished Professor Neil Gemmell1
1Department of Anatomy, University Of Otago, Dunedin, New Zealand, 2Department of Biochemistry, University of Otago, Dunedin, New Zealand, 3Department of Immunology and Microbiology, Dunedin, New Zealand, 4CRISPR Hub, Genetics Otago Centre, University of Otago, Dunedin, New Zealand, 5School of Biological and Marine Sciences, University of Plymouth, Plymouth, United Kingdom, 6Van Hall Larenstein University of Applied Sciences, Leeuwarden, Netherlands, 7Grapevine Improvement, Bragato Research Institute, Lincoln, New Zealand, 8United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, United States, 9Exymes NZ Ltd, Dunedin, New Zealand, 10Sequench NZ Ltd, Nelson, New Zealand, 11School of Biological Sciences, University of Auckland, Auckland, New Zealand
Abstract:
Environmental DNA (eDNA) researchers have long sought an “all-terrain” biosurveillance tool: a highly portable, versatile, low-cost and robust detection platform offering exceptional sensitivity and species-level specificity. One potential solution has emerged from an ancient evolutionary arms race: the CRISPR-Cas systems. Used by bacteria and archaea to defend against invading viruses, CRISPR-Cas entered the spotlight in 2017 as powerful tools for nucleic-acid detection and have since transformed a wide range of research and diagnostic fields, including eDNA.
Over the past five years, our group has integrated isothermal amplification, CRISPR-based detection, an AI-guided assay-design backbone, and eDNA analysis into a unified, next-generation environmental biosurveillance platform. Our vision is to provide a frontline tool that strengthens biosecurity intelligence and supports rapid, evidence-based decision-making at the point of need, delivered with quick turnaround times to enhance responses to known and emerging biosecurity threats.
This integration led to the development of SENTINEL: Smart Environmental Nucleic-acid Tracking using Inference from Neural networks for Early-warning Localisation. SENTINEL has now been validated across a diverse portfolio of biosecurity and environmental applications, from aquatic and terrestrial invasive species and livestock biosurveillance to agricultural biosecurity and endangered taonga species. The platform enables highly sensitive fluorescence-based detection and can be adapted to portable formats suitable for point-of-need deployment as lateral flow devices. Across our validation studies, SENTINEL has achieved attomolar-range detection (10-18M), corresponding to approximately 5 copies µL-1, and has detected genomic DNA at concentrations as low as 0.00001 ng µL-1 (10 fg µL-1). Its high specificity also enables differential identification of closely related species and subspecies complexes that differ by only a small number of single-nucleotide polymorphisms. SENTINEL often achieves detection within 30 min in an eDNA context and shows enhanced resistance to inhibitors.
This presentation will introduce the biology and diversity of CRISPR-Cas systems and examine their emerging importance for biosecurity. It will then explore CRISPR-based environmental biosurveillance, or CRISPR-eBx, including its current capabilities in lab and point-of-need applications, alongside its advantages and limitations. Finally, the presentation will discuss ongoing technological developments and the scientific, operational and commercial challenges that must be addressed to enable scalable, end-user-ready CRISPR-eBx systems.