Characterization of SARS-CoV-2 Variants in Military and Civilian Personnel of an Air Force Airport during Three Pandemic Waves in Italy
Microorganisms,
Год журнала:
2023,
Номер
11(11), С. 2711 - 2711
Опубликована: Ноя. 5, 2023
We
investigated
SARS-CoV-2
variants
circulating,
from
November
2020
to
March
2022,
among
military
and
civilian
personnel
at
an
Air
Force
airport
in
Italy
order
classify
viral
isolates
a
potential
hotspot
for
virus
spread.
Positive
samples
were
subjected
Next-Generation
Sequencing
(NGS)
of
the
whole
genome
Sanger
sequencing
spike
coding
region.
Phylogenetic
analysis
classified
traced
their
evolutionary
relationships.
Clusters
identified
using
70%
cut-off.
methods
yielded
comparable
results
terms
variant
classification.
In
2021,
we
several
variants,
including
B.1.258
(4/67),
B.1.177
(9/67),
Alpha
(B.1.1.7,
9/67),
Gamma
(P.1.1,
4/67),
Delta
(4/67).
only
Omicron
its
sub-lineage
observed
(37/67).
screened
detect
naturally
occurring
resistance
genomic
regions,
target
new
therapies,
comparing
them
Wuhan
Hu-1
reference
strain.
Interestingly,
2/30
non-Omicron
carried
G15S
3CLpro
substitution
responsible
reduced
susceptibility
protease
inhibitors.
On
other
hand,
unusual
substitutions
A1803V,
D1809N,
A949T
on
PLpro,
D216N
3CLpro.
Finally,
P323L
RdRp
regions
was
not
associated
with
mutational
pattern
related
polymerase
inhibitor
resistance.
This
study
highlights
importance
continuous
surveillance
monitor
evolution
general
population,
as
well
restricted
communities.
Язык: Английский
Navigating the New Norm: The FDA's Final Rule on Laboratory Developed Tests (LDTs) and Its Impact on Clinical Laboratory Operations
Clinical Microbiology Newsletter,
Год журнала:
2024,
Номер
unknown
Опубликована: Сен. 1, 2024
Язык: Английский
Dataset for a Validated Method of Non-Invasive Urine Collection Using Sodium Polyacrylate-Based Diapers for PCR Detection of Uropathogens
Data in Brief,
Год журнала:
2024,
Номер
57, С. 111036 - 111036
Опубликована: Окт. 18, 2024
Язык: Английский
Precision Metagenomic Next-Generation Sequencing Data of Respiratory Infection
Опубликована: Окт. 3, 2023
Understanding
microbial
composition
in
upper
respiratory
infections
(URIs)
is
critical
for
effective
diagnosis
and
treatment.
Precision
Metagenomic
next-generation
sequencing
p(mNGS)
can
provide
a
comprehensive
yet
clinically
relevant
profile
of
infection.
The
hybridization
capture-based
targeted
generated
precision
metagenomics
29
patients
with
acute
URIs.
Nasopharyngeal
samples
were
collected
from
the
subjects
suspected
infection,
was
performed
using
Illumina®/IDbyDNA
Respiratory
Pathogen
ID/AMR
Panel
(RPIP).
dataset
obtained
mNGS
analysis
contains
wealth
information
on
URI
microbiota,
including
relative
abundance
known
pathogens
potential
clinical
implications.
represents
valuable
resource
future
research
endeavors
medicine,
infectious
disease
epidemiology,
therapeutic
interventions.
In
addition,
offers
significant
reuse
integration
other
omics
datasets.
nature
data
allows
exploration
associations
between
microbiota
host
factors
such
as
outcomes,
immune
responses,
or
genetic
predisposition.
Combining
this
datasets,
transcriptomics
metabolomics,
could
deeper
understanding
complex
interactions
Язык: Английский
Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania
Genes,
Год журнала:
2024,
Номер
15(3), С. 361 - 361
Опубликована: Март 14, 2024
The
rapid
genetic
evolution
of
the
severe
acute
respiratory
syndrome
coronavirus
2
(SARS-CoV-2)
during
disease
2019
(COVID-19)
pandemic
has
greatly
challenged
public
health
authorities
worldwide,
including
in
Mauritania.
Despite
presence
virus
Mauritania,
only
one
study
described
its
genomic
variation
course
epidemic.
purpose
present
was
to
document
pattern
SARS-CoV-2
variants
from
clinical
isolates
COVID-19
outbreak
September
November
2021.
whole
genomes
54
strains
detected
nasopharyngeal
swabs
with
a
cycle
threshold
value
≤
30
were
successfully
sequenced
using
next-generation
sequencing
(NGS)
and
Illumina
protocol.
mean
genome
coverage
(±standard
deviation)
96.8%
(±3.7).
most
commonly
identified
clade
21J
(57.4%),
followed
by
21D
(16.7%),
20A
(11.1%),
20B
(9.2%).
At
level
lineages,
majority
samples
Delta
sub-lineage
AY.34
(or
B.1.617.2.34).
Among
that
sequenced,
33
(61.1%)
came
vaccinated
individuals,
21
(38.9%)
unvaccinated
individuals.
Several
Mauritania
between
As
like
many
West
African
countries,
is
resource-limited
regarding
viral
facilities,
establishment
mutualized
sub-regional
platforms
will
be
necessary
ensure
continuous
monitoring
mutations
track
potential
reduction
vaccine
efficacy,
increased
transmissibility,
severity.
Язык: Английский
A Low-cost High-throughput Targeted Sequencing for the Accurate Detection of Respiratory Tract Pathogen
Ju Changyan,
Zhou Chengbosen,
Deng Zhezhi
и другие.
International Journal of Clinical Virology,
Год журнала:
2024,
Номер
8(1), С. 001 - 007
Опубликована: Март 12, 2024
Introduction:
The
current
gold
standard
for
SARS-CoV-2
diagnosis
by
real-time
RT-PCR
has
limitations
of
gene
numbers
that
can
be
detected.
In
this
study,
we
developed
a
low-cost
and
high-throughput
next-generation
sequencing
technology
overcome
the
RT-PCR.
Methodology:
A
targeted
panel
(TSP)
consisting
approximately
500
amplicons
was
designed
simultaneously
detect
broad
range
loci
genes
most
common
viruses
respiratory
infectious
in
single
run
up
to
96
samples.
448
samples
31
control
were
examined
independently
with
both
TSP
RT-PCR,
results
compared
accuracy
other
indicators.
Results:
identified
50
positive
99.33%
match
results.
It
is
not
surprising
also
multiple
viral
infections
from
samples,
whereas
could
not.
demonstrated
its
ability
conclude
those
undecided
tests.
Conclusion:
Our
data
fast
accurate
test
detecting
pathogen
tract.
Язык: Английский