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.

中文翻译：

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基于蛋白质结构域的 HMM 谱提高非洲猪瘟病毒基因组模式的分辨率

摘要 非洲猪瘟病毒 (ASFV) 属于 Asfarviridae 家族，大约 100 年前最初在非洲被描述，现在在欧洲和亚洲不受控制地传播，并威胁到国内猪肉产业。目前既没有有效的抗病毒药物也没有保护性疫苗。由于 ASFV 基因组庞大而复杂，了解病毒致病性基础和开发减毒潜在疫苗株的努力变得复杂。我们在此报告了一种基于基因组规模上的轮廓隐藏马尔可夫模型域来记录病毒多样性的新型无比对方法。该方法可用于推断独立于基因组比对的基因组关系，还可以揭示 ASFV 基因组序列差异，这些差异决定了病毒中功能性蛋白质结构域的存在和特征。我们表明，该方法可以快速识别强毒和减毒 ASFV 毒株之间的差异和共同模式，并将成为开发急需的疫苗和抗病毒药物以帮助控制这种病毒的有用工具。该工具运行迅速且易于实施，可作为简单的 Docker 映像轻松获得。