The overall objective of this project is to adopt oxford nanopore technology (ONT), a third-generation sequencing platform, as a molecular pocd for avian FAD (IAV-a and VND) in the field or in…

The Department of Agriculture Animal and Plant Health Inspection Service awarded Iowa State University a $404,919 cooperative agreement from the Plant and Animal Disease, Pest Control, and Animal Care federal grant program (CFDA 10.025). The overall objective is to adopt Oxford Nanopore sequencing technology as a point-of-care diagnostic for avian influenza in field or resource-limited settings. Iowa State University will evaluate sample extraction and sequencing workflows for field use, develop a portable bioinformatics pipeline for real-time analysis without internet, assemble a mobile sequencing kit, and conduct head-to-head comparison of clinical samples tested with the new protocols versus existing laboratory methods. Under a $12,500 subaward, the Agricultural Research Service will collaborate on direct sequencing of RNA and DNA mixtures from poultry samples, advise on host nucleic acid depletion and target enrichment method optimization, assist with bioinformatics pipeline creation, and validate sensitivity and accuracy compared to other sequencing platforms.

The overall objective of this project is to adopt oxford nanopore technology (ONT), a third-generation sequencing platform, as a molecular pocd for avian FAD (IAV-a and VND) in the field or in resource-limited setups. The outcome of this project will be a full protocol that describe the use of ONT as a pocd including a complete description of all needed equipment, sample extraction, sequencing method, cost per sample and turnaround time to release the results. Achieving this will provide accurate and rapid results to producers and decision makers to act effectively and timely. The successful adoption of ONT as a molecular pocd can be used not only for avian FAD but has the potential be used in a variety of applications, including at the borders to aid in controlling all FAD. This project explores new technology in an applied approach to strengthen the nation's capacity to respond to any future outbreak of FAD. Objective 1: evaluate the suitability and reliability of different ONT workflow for field application (RNA extraction library preparation and viral target enrichment) objective 2: the development of a portable standalone-bioinformatics pipeline (psbp) for real-time data analysis on local computing resources independent of internet connection. Objective 3: assembly of mobile-sequencing kit (MSK) and testing the newly validated protocols under field conditions (at farm level or resource-limited lab). Objective 4: head-to-head comparison of results generated from clinical samples submitted to one of nalhn labs and the newly validated pocd protocols. No subawards.