bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2023,
Volume and Issue:
unknown
Published: June 8, 2023
Abstract
Recombination
is
an
ongoing
and
increasingly
important
feature
of
circulating
lineages
SARS-CoV-2,
challenging
how
we
represent
the
evolutionary
history
this
virus
giving
rise
to
new
variants
potential
public
health
concern
by
combining
transmission
immune
evasion
properties
different
lineages.
Detection
recombinant
strains
challenging,
with
most
methods
looking
for
breaks
between
sets
mutations
that
characterise
distinct
In
addition,
many
basic
approaches
fundamental
study
viral
evolution
assume
recombination
negligible,
in
a
single
phylogenetic
tree
can
genetic
ancestry
strains.
Here
present
initial
version
sc2ts,
method
automatically
detect
recombinants
real
time
cohesively
integrate
them
into
genealogy
form
ancestral
graph
(ARG),
which
jointly
records
mutation,
inheritance.
We
infer
two
ARGs
under
sampling
strategies,
their
properties.
One
contains
1.27
million
sequences
sampled
up
June
30,
2021,
second
more
sparsely
sampled,
consisting
657K
2022.
find
both
are
highly
consistent
known
features
SARS-CoV-2
evolution,
recovering
backbone
phylogeny,
mutational
spectra,
recapitulating
details
on
majority
Using
well-established
feature-rich
tskit
library,
also
be
stored
concisely
processed
efficiently
using
standard
Python
tools.
For
example,
ARG
sequences—encoding
inferred
reticulate
ancestry,
variation,
extensive
metadata—requires
58MB
storage,
loads
less
than
second.
The
ability
fully
effects
downstream
analyses,
quickly
recombinants,
utilise
efficient
convenient
platform
computation
based
well-engineered
technologies
makes
sc2ts
promising
approach.
Carbon,
Journal Year:
2023,
Volume and Issue:
210, P. 118058 - 118058
Published: April 29, 2023
The
Coronavirus
Disease
2019
(COVID-19)
pandemic
has
led
to
collaboration
between
nanotechnology
scientists,
industry
stakeholders,
and
clinicians
develop
solutions
for
diagnostics,
prevention,
treatment
of
Severe
Acute
Respiratory
Syndrome
2
(SARS-CoV-2)
infections.
Nanomaterials,
including
carbon-based
materials
(CBM)
such
as
graphene
carbon
nanotubes,
have
been
studied
their
potential
in
viral
research.
CBM
unique
effects
on
microorganisms,
immune
interaction,
sensitivity
diagnostics
made
them
a
promising
subject
SARS-CoV-2
This
review
discusses
the
interaction
with
applicability,
physical
chemical
properties,
known
interactions
components,
proposed
treatment,
uses.
Microorganisms,
Journal Year:
2024,
Volume and Issue:
12(2), P. 416 - 416
Published: Feb. 19, 2024
Porcine
deltacoronavirus
(PDCoV)
has
shown
large-scale
global
spread
since
its
discovery
in
Hong
Kong
2012.
In
this
study,
a
total
of
4897
diarrheal
fecal
samples
were
collected
from
the
Guangxi
province
China
2020
to
2023
and
tested
using
RT-qPCR.
total,
362
(362/4897,
7.39%)
positive
for
PDCoV.
The
S,
M,
N
gene
sequences
obtained
34
after
amplification
sequencing.
These
PDCoV
sequences,
together
with
other
S
reference
countries,
analyzed.
Phylogenetic
analysis
revealed
that
Chinese
strains
have
diverged
recent
years.
Bayesian
new
1.3
lineage
began
diverge
Comparing
amino
acids
those
lineages,
showed
variations
mutations,
deletions,
insertions,
some
demonstrated
same
as
or
similar
1.2
lineage.
addition,
recombination
interlineage
CHGX-MT505459-2019
CHGX-MT505449-2017
province.
summary,
results
provide
information
on
prevalence
evolution
southern
China,
which
will
facilitate
better
comprehension
prevention
Vaccines,
Journal Year:
2022,
Volume and Issue:
10(3), P. 444 - 444
Published: March 14, 2022
The
severe
acute
respiratory
syndrome
coronavirus
2
(SARS-CoV-2)
pandemic
has
induced
the
explosion
of
vaccine
research.
Currently,
according
to
data
World
Health
Organization,
there
are
several
vaccines
in
clinical
(145)
and
preclinical
(195)
stages,
while
at
least
10
already
phase
4
(post-marketing).
Vaccines
have
proven
be
safe,
effective,
able
reduce
spread
SARS-CoV-2
infection
its
variants,
as
well
consequences
development
disease-19
(COVID-19).
In
two-dose
primary
vaccination,
different
time
intervals
between
two
doses
been
used.
Recently,
special
attention
paid
assessing
immunogenicity
following
booster
administration.
third
dose
against
COVID-19
may
administered
8
weeks
after
second
dose.
Israel,
a
fourth
approved
immunocompromised
groups.
main
objective
this
review
is
describe
principal
results
studies
on
effectiveness
first-to-fourth
vaccination
reinfection
by
variants
incidence
disease/death
caused
COVID-19.
shown
high
level
protection
from
symptomatic
Accelerating
mass
third-dose
could
potentially
induce
variants.
Scientific Reports,
Journal Year:
2022,
Volume and Issue:
12(1)
Published: Nov. 12, 2022
Abstract
Coronaviruses
of
the
genera
Gammacoronavirus
and
Deltacoronavirus
are
globally
widespread
circulate
primarily
in
wild
domestic
birds.
Prior
studies
have
established
frequently
occurring
crossover
events
from
avian
to
mammalian
reservoirs.
However,
there
is
limited
understanding
diversity
geographical
distribution
coronaviruses
among
In
this
study,
surveillance
birds
Russia
during
2020
revealed
presence
12%
samples
Targeted
NGS
approach
was
used
for
evaluation
genetic
based
on
RdRp
gene.
While
gammacoronviruses
were
found
both
poultry,
deltacoronaviruses
only
represent
first
detections
Russia.
A
number
cases
with
simultaneous
detection
gamma-
one
bird
reported.
The
results
study
highlight
importance
further
research
concerning
spread
within
migrating
throughout
territory
across
globe.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2023,
Volume and Issue:
unknown
Published: June 8, 2023
Abstract
Recombination
is
an
ongoing
and
increasingly
important
feature
of
circulating
lineages
SARS-CoV-2,
challenging
how
we
represent
the
evolutionary
history
this
virus
giving
rise
to
new
variants
potential
public
health
concern
by
combining
transmission
immune
evasion
properties
different
lineages.
Detection
recombinant
strains
challenging,
with
most
methods
looking
for
breaks
between
sets
mutations
that
characterise
distinct
In
addition,
many
basic
approaches
fundamental
study
viral
evolution
assume
recombination
negligible,
in
a
single
phylogenetic
tree
can
genetic
ancestry
strains.
Here
present
initial
version
sc2ts,
method
automatically
detect
recombinants
real
time
cohesively
integrate
them
into
genealogy
form
ancestral
graph
(ARG),
which
jointly
records
mutation,
inheritance.
We
infer
two
ARGs
under
sampling
strategies,
their
properties.
One
contains
1.27
million
sequences
sampled
up
June
30,
2021,
second
more
sparsely
sampled,
consisting
657K
2022.
find
both
are
highly
consistent
known
features
SARS-CoV-2
evolution,
recovering
backbone
phylogeny,
mutational
spectra,
recapitulating
details
on
majority
Using
well-established
feature-rich
tskit
library,
also
be
stored
concisely
processed
efficiently
using
standard
Python
tools.
For
example,
ARG
sequences—encoding
inferred
reticulate
ancestry,
variation,
extensive
metadata—requires
58MB
storage,
loads
less
than
second.
The
ability
fully
effects
downstream
analyses,
quickly
recombinants,
utilise
efficient
convenient
platform
computation
based
well-engineered
technologies
makes
sc2ts
promising
approach.