Abstract
In 2018, there was an outbreak of African swine fever (ASF) in China,
which spread to other provinces in the following three years, severely
damaging 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, requiring only a small number of tissues.
The pig spleen were crushed and homogenized, and the tissue and cell
fragments were removed by low-speed centrifugation. The virus-like
particles (VLPs) in the solution were purified and concentrated by
filtration and over-speed centrifugation. After obtaining the relatively
pure VLP sample, nucleic acids were extracted simultaneously by
co-extraction of viral DNA (dsDNA, ssDNA) and RNA (ssRNA, dsRNA). Then,
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.