Abstract
Abstract
In our previous work, we developed an automated tool, AutoVEM, for real-time
monitoring the candidate key mutations and epidemic trends of SARS-CoV-2. In
this research, we further developed AutoVEM into AutoVEM2. AutoVEM2 is composed
of three modules, including call module, analysis module, and plot module, which
can be used modularly or as a whole for any virus, as long as the corresponding
reference genome is provided. Therefore, it’s much more flexible than AutoVEM.
Here, we analyzed three existing viruses by AutoVEM2, including SARS-CoV-2, HBV
and HPV-16, to show the functions, effectiveness and flexibility of AutoVEM2. We
found that the N501Y locus was almost completely linked to the other 16 loci in
SARS-CoV-2 genomes from the UK and Europe. Among the 17 loci, 5 loci were on the
S protein and all of the five mutations cause amino acid changes, which may
influence the epidemic traits of SARS-CoV-2. And some candidate key mutations of
HBV and HPV-16, including T350G of HPV-16 and C659T of HBV, were detected. In
brief, we developed a flexible automated tool to analyze candidate key mutations
and epidemic trends for any virus, which would become a standard process for
virus analysis based on genome sequences in the future.
Highlights
An automatic tool to quickly analyze candidate key mutations and
epidemic trends for any virus was developed.
Our integrated analysis method and tool could become a standard
process for virus mutation and epidemic trend analysis based on
genome sequences in the future.
N501Y with the other 16 highly linked mutation sites of
SARS-CoV-2 in the UK and Europe were further confirmed, and some
valuable mutation sites of HBV and HPV-16 were detected.
Publisher
Cold Spring Harbor Laboratory
Cited by
1 articles.
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