bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2023,
Volume and Issue:
unknown
Published: Oct. 23, 2023
Motivation:
Charged
amino
acid
residues
on
the
spike
protein
of
severe
acute
respiratory
syndrome
coronavirus
2
(SARS-CoV-2)
have
been
shown
to
influence
its
binding
different
cell
surface
receptors,
non-specific
electrostatic
interactions
with
environment,
and
structural
stability
conformation.
It
is
therefore
important
obtain
a
good
understanding
mutations
that
affect
total
charge
which
arisen
across
SARS-CoV-2
lineages
during
course
virus'
evolution.
Results:
We
analyse
change
in
number
ionizable
acids
corresponding
proteins
almost
2200
emerged
over
span
pandemic.
Our
results
show
previously
observed
trend
toward
an
increase
positive
variants
concern
has
essentially
stopped
emergence
early
omicron
variants.
Furthermore,
recently
greater
diversity
terms
their
composition
acids.
also
demonstrate
patterns
are
characteristic
related
within
broader
clade
division
phylogenetic
tree.
Due
ubiquity
biological
our
findings
relevant
for
broad
range
studies
dealing
environment.
Availability:
The
data
underlying
article
available
online
Supplementary
Material.
Cell Reports Physical Science,
Journal Year:
2023,
Volume and Issue:
4(4), P. 101346 - 101346
Published: April 1, 2023
Viral
variants
of
concern
continue
to
arise
for
SARS-CoV-2,
potentially
impacting
both
methods
detection
and
mechanisms
action.
Here,
we
investigate
the
effect
an
evolving
spike
positive
charge
in
SARS-CoV-2
subsequent
interactions
with
heparan
sulfate
angiotensin
converting
enzyme
2
(ACE2)
glycocalyx.
We
show
that
positively
charged
Omicron
variant
evolved
enhanced
binding
rates
negatively
Moreover,
discover
while
spike-ACE2
affinity
is
comparable
Delta
variant,
are
significantly
enhanced,
giving
rise
a
ternary
complex
spike-heparan
sulfate-ACE2
large
proportion
double-bound
triple-bound
ACE2.
Our
findings
suggest
evolve
be
more
dependent
on
viral
attachment
infection.
This
discovery
enables
us
engineer
second-generation
lateral-flow
test
strip
harnesses
heparin
ACE2
reliably
detect
all
concern,
including
Omicron.
Bioinformatics Advances,
Journal Year:
2024,
Volume and Issue:
4(1)
Published: Jan. 1, 2024
Abstract
Motivation
Charged
amino
acid
residues
on
the
spike
protein
of
severe
acute
respiratory
syndrome
coronavirus
2
(SARS-CoV-2)
have
been
shown
to
influence
its
binding
different
cell
surface
receptors,
non-specific
electrostatic
interactions
with
environment,
and
structural
stability
conformation.
It
is
therefore
important
obtain
a
good
understanding
mutations
that
affect
total
charge
which
arisen
across
SARS-CoV-2
lineages
during
course
virus’
evolution.
Results
We
analyse
change
in
number
ionizable
acids
corresponding
proteins
almost
2200
emerged
over
span
pandemic.
Our
results
show
previously
observed
trend
toward
an
increase
positive
variants
concern
has
essentially
stopped
emergence
early
omicron
variants.
Furthermore,
recently
greater
diversity
terms
their
composition
acids.
also
demonstrate
patterns
are
characteristic
related
within
broader
clade
division
phylogenetic
tree.
Due
ubiquity
biological
our
findings
relevant
for
broad
range
studies
dealing
environment.
Availability
implementation
The
data
underlying
article
available
Supplementary
material.
ACS Applied Nano Materials,
Journal Year:
2024,
Volume and Issue:
7(8), P. 9136 - 9146
Published: April 15, 2024
We
report
a
silver
nanoparticle
(AgNP)
sensor
array
to
detect
SARS-CoV-2
viral
particles
utilizing
five
peptide
receptors
produce
colorimetric
response.
show
that
the
interaction
of
virus
with
peptides
interferes
shift
in
plasmonic
absorbance
and
hinders
formation
snowflake-like
fractal
assemblies
between
AgNPs
bridging
peptides.
The
limit
detection
water
was
500,000
copies/mL.
demonstrate
capabilities
distinguish
(Beta,
Delta,
Omicron
variants)
from
influenza
at
99%
confidence
level
through
linear
discriminant
analysis.
also
able
discriminate
three
out
negative
exhaled
breath
condensate
samples
positive
EBC
samples.
Small Science,
Journal Year:
2023,
Volume and Issue:
4(2)
Published: Dec. 21, 2023
Field‐effect
transistor‐based
biosensors
(FET
biosensors)
have
gained
significant
attention
in
the
context
of
global
SARS‐CoV‐2
pandemic
owing
to
their
label
free
and
highly
sensitive
detection
capabilities.
In
this
comprehensive
review,
recent
advances
use
electrochemical‐transistor‐based
for
label‐free
are
analyzed.
A
general
introduction
biosensor
system
is
initiated,
highlighting
its
critical
technical
requirements.
Various
structural
designs
working
principles
transducers
described,
essential
aspects
interface
engineering
improved
sensing
performance
summarized.
The
applications
discussed
detail.
Finally,
perspectives
future
development
systems
provided.
This
review
aims
provide
valuable
insights
guidance
design
optimization
biochemical
sensor
with
potential
impact
health
monitoring,
disease
diagnosis,
biosafety
field
vitro
diagnostic
products.
ACS Applied Bio Materials,
Journal Year:
2025,
Volume and Issue:
unknown
Published: April 9, 2025
The
COVID-19
pandemic
has
created
a
need
to
develop
protective
textiles
that
reduce
the
infection
of
SARS-CoV-2,
mainly
via
face
masks.
key
issue
in
designing
is
functionalization
with
antiviral
agents.
This
report
presents
tin
oxide
nanoparticles
(SnO2NPs)
as
novel,
efficient
agent
against
human
coronavirus
HCoV
229E
due
blocking
virus
entry,
attachment,
and
penetration
into
MRC-5
cells
nontoxicity.
SnO2NPs
were
obtained
by
sodium
stannate
hydrolysis
have
3
nm
diameter,
cubic
structure,
zeta
potential
-28.8.
applied
functionalize
mask
made
silk
fibroin.
Polydopamine
was
immobilize
particles.
negative
enhance
fabric
hydrophobicity,
which
crucial
for
properties.
functionalized
reveals
very
good
properties
antibacterial
activity
Gram-positive
-negative
bacteria.
Silk
retains
fibroin
β-sheet
nontoxic,
noncorrosive
skin,
high
thermophysiological
wear
comfort.The
highest
filtration
efficiency
3-layered
(60%),
while
breathing
resistance,
sufficient
FFP3
mask,
achieved
1-layered
(maximum
allowable
100
300
Pa,
respectively,
30
L/min
95
inhale
Pa
an
exhale
flow
rate
160
L/min).
can
be
useful
developing
advanced
textile
materials
control
spread
future
pandemics.
Virus Evolution,
Journal Year:
2023,
Volume and Issue:
9(2)
Published: June 29, 2023
Abstract
The
spike
protein
of
the
severe
acute
respiratory
syndrome
coronavirus
2
(SARS-CoV-2)
is
responsible
for
target
recognition,
cellular
entry,
and
endosomal
escape
virus.
At
same
time,
it
part
virus
that
exhibits
greatest
sequence
variation
across
many
variants
which
have
emerged
during
its
evolution.
Recent
studies
indicated
with
progressive
lineage
emergence,
positive
charge
on
has
been
increasing,
certain
positively
charged
amino
acids
(AAs)
improving
binding
to
cell
receptors.
We
performed
a
detailed
analysis
dissociable
AAs
more
than
1400
different
SARS-CoV-2
lineages,
confirms
these
observations
while
suggesting
this
progression
reached
plateau
Omicron
subvariants
not
increasing
further.
Analysis
nucleocapsid
shows
no
similar
increase
in
novel
variants,
further
indicates
being
evolutionarily
selected
for.
Furthermore,
comparison
proteins
known
coronaviruses
already
wild-type
carries
an
unusually
large
amount
when
compared
most
other
betacoronaviruses.
Our
study
sheds
light
evolutionary
changes
number
SARS-CoV-2,
complementing
existing
providing
stepping
stone
towards
better
understanding
relationship
between
viral
infectivity
transmissibility.
Journal of Computational Chemistry,
Journal Year:
2025,
Volume and Issue:
46(4)
Published: Feb. 2, 2025
ABSTRACT
The
spike
protein
of
SARS‐CoV‐2
is
a
challenging
target
for
theoretical
approaches.
Here
we
report
benchmark
calculation
the
droplet
model
by
fragment
molecular
orbital
(FMO)
at
second‐order
Møller‐Plesset
perturbation
(MP2)
level
on
supercomputer
Fugaku.
One
hundred
structure
samples
from
dynamics
(MD)
simulations
were
used
both
closed
and
open
forms
this
(PDB
IDs
6XLU
6XM0
respectively).
number
total
fragments
about
20,000,
job
time
per
was
2
h
8
racks
The Journal of Immunology,
Journal Year:
2025,
Volume and Issue:
unknown
Published: April 3, 2025
Abstract
This
review
provides
a
broad
overview
of
lessons
learned
in
the
five
years
since
COVID-19
was
identified.
It
is
bimodal
disease,
starting
with
an
initially
virus-driven
phase,
followed
by
resolution
or
ensuing
inappropriate
immune
activation
causing
severe
inflammation
that
no
longer
strictly
virus
dependent.
Humoral
immunity
beneficial
for
preventing
attenuating
early
stage,
without
benefit
once
later
stage
begins.
Neutralizing
antibodies
elicited
natural
infection
vaccination
are
short-lived
and
highly
vulnerable
to
viral
sequence
variation.
By
contrast,
cellular
immunity,
particularly
CD8+
T
cell
arm,
has
role
far
less
susceptible
variation,
longer-lived
than
antibodies.
Finally,
ill-defined
phenomenon
prolonged
symptoms
after
acute
infection,
termed
“long
COVID,”
poorly
understood
but
may
involve
various
immunologic
defects
hyperactivating
immunosuppressive.
Remaining
issues
include
needing
better
understand
dysregulation
disease
allow
more
tailored
therapeutic
interventions,
developing
antibody
strategies
cope
spike
variability,
prolonging
vaccine
efficacy,
unraveling
mechanisms
long
COVID
design
approaches.
PLoS ONE,
Journal Year:
2025,
Volume and Issue:
20(4), P. e0320891 - e0320891
Published: April 7, 2025
The
COVID-19
pandemic
offered
an
unprecedented
glimpse
into
the
evolution
of
its
causative
virus,
SARS-CoV-2.
It
has
been
estimated
that
since
outbreak
in
late
2019,
virus
explored
all
possible
alternatives
terms
missense
mutations
for
sites
polypeptide
chain.
Spike
protein
exhibits
largest
sequence
variation
particular,
with
many
individual
impacting
target
recognition,
cellular
entry,
and
endosomal
escape
virus.
Moreover,
recent
studies
unveiled
a
significant
increase
total
charge
on
spike
during
initial
period
pandemic.
While
this
trend
recently
come
to
halt,
we
perform
sequence-based
analysis
2665
SARS-CoV-2
variants
which
shows
ionizable
amino
acids
continue
occur
newly
emerging
variants,
notable
differences
between
lineages
from
different
clades.
What
is
more,
show
within
can
acquire
positive
charge,
prominent
preference
lysine
residues
over
arginine
residues.
This
lysine-to-arginine
ratio
increased
at
several
points
evolution,
most
BA.2.86
sublineages,
including
dominant
JN.1,
KP.3,
XEC
variants.
consequence
structural
regions
now
among
highest
viral
species
Coronaviridae
family.
impact
high
proteins
daughter
fitness
remains
unclear;
discuss
potential
mechanisms
could
play
role
serve
as
starting
point
further
studies.
