Skip to main content
ARS Home » Research » Publications at this Location » Publication #415325
Research Project: Intervention Strategies to Control and Eradicate Foreign Animal Diseases of Swine

Location: Location not imported yet.

Title: A standardized pipeline for assembly and annotation of the African swine fever virus genome

Author
item Spinard Iii, Edward
item Dinhobl, Mark
item ERDELYAN, CASS - Friedrich-Loeffler-institut
item O'DWYER, JAMES - Csiro Australian Animal Health Laboratory
item FENSTER, JACOB - Oak Ridge Institute For Science And Education (ORISE)
item BIRTLEY, HILLARY - Oak Ridge Institute For Science And Education (ORISE)
item TESLER, NICOLAS - Oak Ridge Institute For Science And Education (ORISE)
item CALVELAGE, STEN - Friedrich-Loeffler-institut
item LEIJON, MIKAEL - National Veterinary Institute - Sweden
item STEINAA, LUCILLA - International Livestock Research Institute (ILRI) - Kenya
item O’DONNELL, VIVIAN - Animal And Plant Health Inspection Service (APHIS)
item BLOME, SANDREA - Friedrich-Loeffler-institut
item BASTOS, ARMANDA - University Of Pretoria
item LACASTA, ANNA - International Livestock Research Institute (ILRI) - Kenya
item STAHL, KARL - University Of Pretoria
item HUA-JI, QIU - Accra Veterinary Laboratory
item NILUBOL, DACHRIT - University Of Pretoria
item O’DOOM, THEOPHILUS - Accra Veterinary Laboratory
item OHOUKO, OKRI - Universite` D` Abomey-Calavi
item DOUGNON, VICTORIEN - Universite` D` Abomey-Calavi
item FABURAY, BONTO - Animal And Plant Health Inspection Service (APHIS)
item MESAMBE, CHARLES - Makerere University
item NETHERTON, CHRISTOPHER - The Pirbright Institute
item AMBAGALA, ARUNA - Canadian Food Inspection Agency-National Centre For Foreign Animal Disease
item WILLIAMS, DAVID - Csiro Australian Animal Health Laboratory
item RIBECCA, PAOLO - Uk Health Security Agency
item Borca, Manuel
item Gladue, Douglas

Submitted to: Viruses
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/6/2024
Publication Date: 8/13/2024
Citation: Spinard Iii, E.J., Dinhobl, M.W., Erdelyan, C., O'Dwyer, J., Fenster, J., Birtley, H., Tesler, N., Calvelage, S., Leijon, M., Steinaa, L., O’Donnell, V., Blome, S., Bastos, A., Lacasta, A., Stahl, K., Hua-Ji, Q., Nilubol, D., O’Doom, T., Ohouko, O.F., Dougnon, V.T., Faburay, B., Mesambe, C., Netherton, C., Ambagala, A., Williams, D., Ribecca, P., Borca, M.V., Gladue, D.P. 2024. A standardized pipeline for assembly and annotation of the African swine fever virus genome. Viruses. 16(8). Article 1293. https://doi.org/10.3390/v16081293.
DOI: https://doi.org/10.3390/v16081293

Interpretive Summary: This study was to standardize a methodology across all of the Global African swine fever Research Alliance labs, to annotate, and analyze next generation sequencing analysis, and lead to accurate genomes being uploaded into databases. This free to use software will help all labs, even those with limited bioinformatics backgrounds.

Technical Abstract: The long double-stranded DNA genome of African swine fever virus (ASFV), has been difficult to fully sequence even with next-generation sequence (NGS) data. A gap analysis was conducted at the Global Alliance for African Swine Fever, where it was determined that a standardized, automatic pipeline for NGS analysis was in urgent need. Many of the sequenced and publicly available ASFV isolates had missing or incorrect annotations, and most worldwide research labs, collecting isolates of ASFV from outbreaks, did not have the capability to analyze NGS. Furthermore most analysis was limited to aligning NGS sequencing reads to a reference, for which very few exist in ASFV. Here we present the development through the Global alliance of African swine fever partners, an automated, standardized pipeline for analysis of NGS reads that automatically annotates, and provides an upload file for NCBI, etc.