Location: Foreign Animal Disease Research
Project Number: 3022-32000-064-019-R
Project Type: Reimbursable Cooperative Agreement
Start Date: Oct 1, 2020
End Date: Feb 28, 2023
Objective:
1) To develop and optimize targeted (AmpliSeq) next generation sequencing (NGS) diagnostics for NAHLN scope and/or emerging diseases;
(2) To develop and optimize random (RandSeq) metagenomics to enhance the NAHLN capability to detect novel and/or emerging diseases; and
(3) To develop and optimize streamlined bioinformatics pipelines for targeted and random NGS diagnostic applications.
These objectives are directly aligned with Farm Bill Section 12101 and the NAHLN Enhancement funding opportunity priorities. The work will specifically address priorities nos. 1, 3 and 4 of the 2019 NAHLN funding opportunity announcement: “1. Test procedures, reference materials and equipment; 3. Interconnected electronic reporting and transmission of data; and 4. Enhancement of laboratory emergency preparedness. Availability of standardized NGS protocols for routine diagnostics and surveillance and of streamlined bioinformatics pipelines for NGS data analysis will significantly improve the capacity and preparedness of the NAHLN to detect foreign animal and emerging diseases.
Approach:
1) ARS will develop and optimize targeted amplicon-based (AmpliSeq) assays for detection and molecular characterization of pathogens (Food-and-mouth disease virus [FMDV], Vesicular stomatitis virus [VSV], Senecavirus A [SVA], African swine fever virus [ASFV], Classical swine fever virus [CSFV], Newcastle disease virus [NDV], and Avian influenza virus [AIV]), causing important NAHLN-scope diseases affecting cattle, swine, and poultry. These assays will be developed using the inexpensive, portable, and field-deployable Oxford Nanopore MinION sequencing platform.
2) ARS will develop and optimize random metagenomics sequencing protocols and procedures for pathogen detection and characterization. These protocols and procedures will be optimized using the benchtop Illumina iSeq 100 sequencing platform. This approach involves the use of random sequencing (RandSeq) of nucleic acids for unbiased detection of pathogens and complex multi-pathogen infections directly from clinical samples.
3) ARS will develop NGS analysis pipelines for rapid data analysis and result reporting for the assays developed in Objectives 1 and 2 described above.
