Title | Increased resolution of African Swine Fever Virus genome patterns based on profile HMM protein domains |
Publication Type | Journal Article |
Year of Publication | 2020 |
Authors | Masembe, C, Phan, MVT, Robertson, DL, Cotten, M |
Date Published | January 14, 202 |
Abstract | African Swine Fever Virus (ASFV) was originally described in Africa almost 100 years ago and is now spreading uncontrolled across Europe and Asia and threatening to destroy the domestic pork industry. Neither effective antiviral drugs nor a protective vaccine are currently available. Efforts to understand the basis for viral pathogenicity and the development of attenuated potential vaccine strains are complicated by the large and complex ASFV genome. We report here a novel method of documenting viral diversity based on profile Hidden Markov Model domains on a genome scale. The method can be used to infer genomic relationships independent of genome alignments and also reveal ASFV genome sequence differences that alter the presence of functional protein domains in the virus. We show that the method can quickly identify differences and shared patterns between virulent and attenuated ASFV strains and will be a useful tool for developing much-needed vaccines and antiviral agents to help control this virus. The tool is rapid to run and easy to implement, readily available as a simple Docker image. |
URL | https://www.biorxiv.org/content/10.1101/2020.01.12.903104v1 |
DOI | 10.1101/2020.01.12.903104 |
MRC-University of Glasgow, Centre for Virus Research
Global African Swine Fever Research Alliance
US National Wildlife Research Center
Swedish University of Agricultural Sciences
The National Veterinary Institute Sweden
The International Livestock Research Institute (ILRI)
Ministry of Agriculture, Animal Industry and Fisheries (MAAIF)
Charles Masembe (BVM, MSc., PhD),
Associate Professor (Molecular Genetics & Evolution),
Wellcome Trust Fellow,