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

Charles Masembe,Matthew Cotten,David L Robertson,My V T Phan

doi:10.1093/ve/veaa044

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.

Highlights

African swine fever virus (ASFV), belonging to the Asfarviridae family, was first described in Kenya nearly 100 years ago (Eustace Montgomery 1921)
We identified all regions from the forty-seven ASFV genomes coding for proteins positive for profile hidden Markov models (HMMs) of the Pfam collection
The domain content and their scores were used to examine patterns of the forty-seven ASFV genomes in GenBank in the following manner

Summary

Introduction

African swine fever virus (ASFV), belonging to the Asfarviridae family, was first described in Kenya nearly 100 years ago (Eustace Montgomery 1921). The virus is endemic in most subSaharan African countries where it naturally infects warthogs and bush pigs and is frequently transmitted via soft ticks. In sub-Saharan Africa, infections of warthogs and bush pigs have a typically mild disease outcome. In domestic swine or wild boars, ASFV infections can result in a more serious disease with much greater mortality: between 90 per cent and 100 per cent. Of great concern for animal welfare and the food industry, ASFV infections are responsible for increasing swine mortality in several parts of the world (Pikalo et al 2019). Outside of Africa, the virus has previously been reported in Portugal, and in Haiti in sporadic outbreaks, probably as a result of imports from West Africa (Bastos et al 2003; Phologane, Bastos, and Penrith 2005)

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Results

Conclusion