Increased resolution of African swine fever virus genome patterns based on profile HMMs of protein domains

Masembe, C. , Phan, M. V.T., Robertson, D. L. and Cotten, M. (2020) Increased resolution of African swine fever virus genome patterns based on profile HMMs of protein domains. Virus Evolution, 6(2), veaa044. (doi: 10.1093/ve/veaa044) (PMID:32913663) (PMCID:PMC7474929)

Abstract

African swine fever virus (ASFV), belonging to the Asfarviridae family, 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 protective vaccines 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 nature of the ASFV genome. We report here a novel alignment-free 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 determine the presence and characteristics 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.

• Item Type: Articles
• Additional Information: This work was supported by a Marie Sklodowska-Curie Individual Fellowship, funded by European Union’s Horizon 2020 Research and innovation programme (M.V.T.P., Grant No. 799417), by a Wellcome Trust Intermediate Fellowship (C.M., Grant No. 105684/Z/14/Z), by the ASF-RESIST African Union Commission (C.M., D.L.R., Grant No. AURG‐II‐1‐196‐2016), and MRC (M.C., D.L.R., MC UU 1201412).
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Robertson, Professor David and Masembe, Dr Charles and Cotten, Professor Matthew
• Authors: Masembe, C., Phan, M. V.T., Robertson, D. L., and Cotten, M.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity; College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Journal Name: Virus Evolution
• Publisher: Oxford University Press
• ISSN: 2057-1577
• ISSN (Online): 2057-1577
• Published Online: 19 June 2020
• Copyright Holders: Copyright © 2020 The Authors
• First Published: First published in Virus Evolution 6(2): veaa044
• Publisher Policy: Reproduced under a Creative Commons License

Project Code	Award No	Project Name	Principal Investigator	Funder's Name	Funder Ref	Lead Dept
		Viral Genomics and Bioinformatics	Andrew Davison	Medical Research Council (MRC)	MC_UU_12014/12	III-MRC-GU Centre for Virus Research