Location: Foreign Animal Disease Research
Project Number: 3022-32000-063-030-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Aug 1, 2022
End Date: Jul 31, 2025
Objective:
Currently many countries with African Swine Fever Virus (ASFV) have next generation sequencers, but lack the ability to analyze the sequences. This has left a lag in the available sequences of ASFV to be only a few, with unknown quality scores. The establishment of a database will not only allow for quality scores to be given, but also allow for collection of raw data from ASFV infected countries which is a major gap in ASFV research. This collaborative research project will establish a unique database for ASFV allowing users to upload raw sequencing data.
Specific objectives include:
1. UKHSA will establishing a web based curated database for all available African swine fever virus genomes.
2. ARS and UKHSA will establish a genomics pipeline for submitting raw sequencing data.
3. ARS will provide different types of raw sequencing data from published genomes to test genomics pipeline.
4. UKHSA and ARS will promote the database for inclusion of sample data from partner laboratories.
5. UKHSA will provide access to the database to ARS and partner laboratories.
Approach:
1. Cooperator will establish a web based curated database for all available African swine fever virus genomes. ASFV Genomes would be curated by designing an ASFV- specific pipeline and added to a database compatible with the viral bio-informatics research center (VBRC) tools, thus allowing viral sequences to be queried and processed interactively once they are in the database. By modernizing of the resource (both code and tools) with focus being placed on code modularity and maintainability, more streamlined workflows, and a plugin system for quicker prototyping and testing.
2. We both will establish a genomics pipeline for submitting raw sequencing data this will be done by trial and error.
3. We will provide different types of raw sequencing data from published genomes to test genomics pipeline by sequencing new isolates of ASFV.
4. We will promote the database for inclusion of sample data from partner laboratories by leveraging the existing ecosystem of VBRC tools, one would create an optimal system able to guarantee at the same time quality and ease of use. This will support ASFV genome annotation by providing a database for well-annotated genomes and a variety of software tools for their interactive comparison and analysis.
5. Cooperator will allow access to the database by providing a username and password.
