Abstract
In 2018, there was an outbreak of African swine fever (ASF) in China, which spread to other provinces in the following 3 years and severely damaged China's pig industry. ASF is caused by the African swine fever virus (ASFV). Given that the genome of the African swine fever virus is very complex and whole genome information is currently inadequate, it is important to efficiently obtain virus genome sequences for genomic and epidemiological studies. The prevalent ASFV strains have low genetic variability; therefore, whole genome sequencing analysis provides a basis for the study of ASFV. We provide a method for the efficient sequencing of whole genomes, which requires only a small number of tissues. The database construction method was selected according to the genomic types of ASFV, and the whole ASFV genome was obtained through data filtering, host sequence removal, virus classification, data assembly, virus sequence identification, statistical analysis, gene prediction, and functional analysis. Our proposed method will facilitate ASFV genome sequencing and novel virus discovery.
Highlights
African swine fever (ASF) is a highly contagious and fatal swine disease
The DNA of each liquid layer was extracted with the OMEGA nucleic acid extraction kit, and qPCR was performed on each liquid layer with specific African swine fever virus primers to determine the virus Cq value in each liquid layer (Figure 1B)
The African swine fever virus (ASFV) genome is relatively conserved and its natural variation is very slow, but interaction with the host and stimulation by environmental factors can accelerate the transmission of ASFV (28)
Summary
ASF is a highly contagious and fatal swine disease. The pathogen of ASF is the African swine fever virus (ASFV), which is the only member of the family Asfarviridae and the only known DNA arbovirus (1, 2). ASFV has a large (170–193 kbp) double-stranded DNA genome containing [151–167] genes, which are involved in viral replication and assembly as well as in modulating host cellular functions and immune evasion (3). ASF was first described in Kenya in 1921; it spread to other African, European, Caribbean, and South American countries (3, 5, 6). The disease was introduced into Georgia in 2007 and spread throughout Eastern Europe, including Russia, Belarus, Ukraine, Estonia, Lithuania, Latvia, Romania, Moldova, Czech Republic, and Poland (7–9).
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