  The emerging global infectious COVID-19 coronavirus disease by novel Severe
Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presents critical threats
to global public health and the economy since it was identified in late
December 2019 in China. The virus has gone through various pathways of
evolution. For understanding the evolution and transmission of SARS-CoV-2,
genotyping of virus isolates is of great importance. We present an accurate
method for effectively genotyping SARS-CoV-2 viruses using complete genomes.
The method employs the multiple sequence alignments of the genome isolates with
the SARS-CoV-2 reference genome. The SNP genotypes are then measured by Jaccard
distances to track the relationship of virus isolates. The genotyping analysis
of SARS-CoV-2 isolates from the globe reveals that specific multiple mutations
are the predominated mutation type during the current epidemic. Our method
serves a promising tool for monitoring and tracking the epidemic of pathogenic
viruses in their gradual and local genetic variations. The genotyping analysis
shows that the genes encoding the S proteins and RNA polymerase, RNA primase,
and nucleoprotein, undergo frequent mutations. These mutations are critical for
vaccine development in disease control.
