JMIR Research Protocols,
Journal Year:
2025,
Volume and Issue:
14, P. e58567 - e58567
Published: April 22, 2025
Background
There
has
been
an
unprecedented
effort
to
sequence
the
SARS-CoV-2
virus
and
examine
its
molecular
evolution.
This
facilitated
by
availability
of
publicly
accessible
databases,
such
as
GISAID
(Global
Initiative
on
Sharing
All
Influenza
Data)
GenBank,
which
collectively
hold
millions
records.
Genomic
epidemiology,
however,
seeks
go
beyond
phylogenetic
(the
study
evolutionary
relationships
among
biological
entities)
analysis
linking
genetic
information
patient
characteristics
disease
outcomes,
enabling
a
comprehensive
understanding
transmission
dynamics
impact.
While
these
repositories
include
fields
reflecting
patient-related
metadata
for
given
sequence,
inclusion
demographic
clinical
details
is
scarce.
The
current
in
published
sequencing
studies
quality
remains
unexplored.
Objective
Our
review
aims
quantitatively
assess
extent
patient-reported
papers
reporting
original
whole
genome
analyze
publication
patterns
using
bibliometric
analysis.
Finally,
we
will
evaluate
efficacy
reliability
machine
learning
classifier
accurately
identifying
relevant
scoping
review.
Methods
National
Institutes
Health’s
LitCovid
collection
be
used
automated
classification
having
deposited
sequences
public
repositories,
while
independent
search
conducted
MEDLINE
PubMed
Central
validation.
Data
extraction
Covidence
(Veritas
Health
Innovation
Ltd).
extracted
data
synthesized
summarized
quantify
literature
studies.
For
analysis,
points,
author
affiliations,
citation
metrics,
keywords,
Medical
Subject
Headings
terms
extracted.
Results
expected
completed
early
2025.
model
developed
have
classified
publications
through
February
2023.
As
September
2024,
August
2024
are
being
prepared
processing.
Screening
underway
validated
from
classifier.
Direct
searches
screening
results
began
October
2024.
We
summarize
narratively
describe
our
findings
tables,
graphs,
charts
where
applicable.
Conclusions
report
types
reported
genomic
viral
SARS-CoV-2,
identify
gaps
metadata,
make
recommendations
improving
consistency
this
area.
uncover
trends
including
differences
based
or
geographic
regions.
insights
gained
may
help
improve
enhancing
utility
facilitating
future
research
infectious
diseases.
Trial
Registration
OSF
Registries
osf.io/wrh95;
https://doi.org/10.17605/OSF.IO/WRH95
International
Registered
Report
Identifier
(IRRID)
DERR1-10.2196/58567
Epidemiology and Health,
Journal Year:
2020,
Volume and Issue:
unknown, P. e2020038 - e2020038
Published: June 2, 2020
Transmission
of
infectious
diseases
is
often
prevented
by
quarantine
and
isolation
the
populations
at
risk.
These
approaches
restrict
mobility,
social
interactions,
daily
activities
affected
individuals.
In
recent
coronavirus
disease
2019
(COVID-19)
pandemic,
are
being
adopted
in
many
contexts,
which
necessitates
an
evaluation
global
evidence
on
how
such
measures
impact
mental
health
outcomes
among
populations.
This
umbrella
review
aimed
to
synthesize
available
for
preventing
diseases.We
searched
nine
major
databases
additional
sources
included
articles
if
they
were
systematically
conducted
reviews,
published
as
peer-reviewed
journal
articles,
reported
or
any
population.Among
1,364
citations,
only
eight
reviews
met
our
criteria.
Most
primary
studies
those
high-income
nations
hospital
settings.
a
high
burden
problems
patients,
informal
caregivers,
healthcare
providers
who
experienced
isolation.
Prevalent
individuals
include
depression,
anxiety,
mood
disorders,
psychological
distress,
posttraumatic
stress
disorder,
insomnia,
fear,
stigmatization,
low
self-esteem,
lack
self-control,
other
adverse
outcomes.This
found
severe
have
undergone
different
contexts.
multipronged
interventions
including
policy
strengthening
services
globally
promoting
psychosocial
wellbeing
high-risk
Psychiatria Danubina,
Journal Year:
2020,
Volume and Issue:
32(1), P. 6 - 14
Published: April 15, 2020
The
Coronavirus
disease
2019
pandemic
emerged
in
Wuhan,
China
and
has
spread
all
over
the
world
caused
huge
threats
to
health
lives.It
affected
different
frontiers
of
lives
induced
many
psychiatric
individual
collective
problems
such
as
panic,
anxiety,
depression,
post-traumatic
stress
disorders,
suspiciousness,
infodemia,
cacophony,
xenophobia,
racisms,
etc.The
COVID-19
outbreak
public
global
mental
crisis
well
a
psychosocial
experiment.Psychiatry
other
sciences
can
play
very
useful
role
supporting
well-being
patients
their
families,
healthcare
personnel
society.For
successful
fighting
with
present
future
pandemics
we
have
learn
more
about
psychological
aspects
from
perspectives
health.
Background:
Transmission
of
infectious
diseases
is
often
prevented
by
quarantine
and
isolation
the
populations
at
risk.
These
approaches
restrict
mobility,
social
interactions,
daily
activities
affected
individuals.
In
recent
novel
coronavirus
disease
(COVID-19)
pandemic,
are
being
adopted
in
many
contexts,
which
necessitates
an
evaluation
global
evidence
on
how
such
measures
impact
mental
health
outcomes
among
populations.
This
umbrella
review
aimed
to
synthesize
available
for
preventing
diseases.Materials
methods:
We
searched
nine
major
databases
additional
sources
included
articles
if
they
were
systematically
conducted
reviews,
published
as
peer-reviewed
journal
articles,
reported
or
any
population.Results:
Among
1364
citations,
only
eight
reviews
met
our
criteria.
Most
primary
studies
those
high-income
nations
hospital
settings.
a
high
burden
problems
patients,
informal
caregivers,
healthcare
providers
who
experienced
isolation.
Prevalent
individuals
include
depression,
anxiety,
mood
disorders,
psychological
distress,
posttraumatic
stress
disorder,
insomnia,
fear,
stigmatization,
low
self-esteem,
lack
self-control,
other
adverse
outcomes.Conclusion:
found
severe
have
undergone
different
contexts.
multipronged
interventions
including
policy
strengthening
services
globally
promoting
psychosocial
wellbeing
high-risk
Higher Education,
Journal Year:
2020,
Volume and Issue:
81(5), P. 949 - 966
Published: July 24, 2020
This
study
sought
to
understand
the
nature
of
scientific
globalism
during
a
global
crisis,
particularly
COVID-19.
Findings
show
that
occurs
differently
when
comparing
COVID-19
publications
with
non-COVID-19
as
well
before
pandemic.
Despite
tense
geopolitical
climate,
countries
increased
their
proportion
international
collaboration
and
open-access
However,
not
all
engaged
more
globally.
Countries
have
been
impacted
by
crisis
those
relatively
lower
GDPs
tended
participate
in
than
counterparts.
Sustainability,
Journal Year:
2020,
Volume and Issue:
12(21), P. 9132 - 9132
Published: Nov. 3, 2020
The
lack
of
knowledge
about
the
COVID-19
pandemic
has
encouraged
extensive
research
in
academic
sphere,
reflected
exponentially
growing
scientific
literature.
While
state
reveals
it
is
currently
an
early
stage
developing
knowledge,
a
comprehensive
and
in-depth
overview
still
missing.
Accordingly,
paper’s
main
aim
to
provide
bibliometric
analysis
across
science
social
landscape,
using
innovative
approaches
(e.g.,
Venn
diagram,
Biblioshiny
descriptive
statistics,
VOSviewer
co-occurrence
network
analysis,
Jaccard
distance
cluster
text
mining
based
on
binary
logistic
regression).
considers
Scopus
database,
including
all
relevant
information
related
publications
(n
=
16,866)
available
first
half
2020.
empirical
results
indicate
domination
health
sciences
terms
number
total
citations,
while
physical
humanities
lag
behind
significantly.
Nevertheless,
there
evidence
collaboration
within
between
different
subject
area
classifications
with
gradual
increase
importance
non-health
disciplines.
findings
emphasize
great
need
for
approach
that
various
disciplines
so
as
benefit
not
only
community
but
evidence-based
policymaking
part
efforts
properly
respond
pandemic.
PLoS ONE,
Journal Year:
2020,
Volume and Issue:
15(10), P. e0240123 - e0240123
Published: Oct. 6, 2020
The
COVID-19
pandemic
has
unleashed
a
deluge
of
publications.
For
this
cross-sectional
study
we
compared
the
amount
and
reporting
characteristics
COVID-19-related
academic
articles
preprints
number
ongoing
clinical
trials
systematic
reviews.
To
do
this,
searched
PubMed
database
citations
abstracts
for
published
life
science
journals
by
using
appropriate
combinations
medical
subject
headings
(MeSH
terms),
section
MedRxiv
BioRxiv
archives
up
to
20
May
2020
(21
weeks).
In
addition,
Clinicaltrial.gov,
Chinese
Clinical
Trial
Registry,
EU
Trials
Register,
15
other
trial
registers,
as
well
PROSPERO,
international
prospective
register
each
publication
were
extracted.
Regression
analyses
Z
tests
used
detect
trends
their
relative
proportions.
A
total
3635
publications
3805
retrieved.
Only
8.6%
(n
=
329)
already
in
indexed
journals.
preprint
increased
significantly
over
time
(p<0.001).
Case
reports
(6%
vs
0.9%
preprints;
p<0.001)
letters
(17.4%
0.5%
accounted
greater
share
Differently,
randomized
controlled
(0.22%
0.63%;
reviews
(0.08%
5%)
made
preprints.
proportion
studies
registered
at
Clinicaltrials.gov,
Register
was
57.9%,
49.5%,
98.9%,
respectively,
most
which
still
"recruiting".
PROSPERO
listed
962
review
protocols.
Preprints
slightly
more
prevalent
than
but
both
increasing
number.
void
left
lack
primary
filled
an
outpour
immediate
opinions
(i.e.,
editor)
PubMed-indexed
Summarizing,
have
gained
traction
publishing
response
demand
prompt
access
empirical,
albeit
not
peer-reviewed,
findings
during
present
pandemic.
PLoS ONE,
Journal Year:
2020,
Volume and Issue:
15(7), P. e0236464 - e0236464
Published: July 21, 2020
The
coronavirus
pandemic
has
rapidly
evolved
into
an
unprecedented
crisis.
susceptible-infectious-removed
(SIR)
model
and
its
variants
have
been
used
for
modeling
the
pandemic.
However,
time-independent
parameters
in
classical
models
may
not
capture
dynamic
transmission
removal
processes,
governed
by
virus
containment
strategies
taken
at
various
phases
of
epidemic.
Moreover,
few
account
possible
inaccuracies
reported
cases.
We
propose
a
Poisson
with
time-dependent
rates
to
random
errors
reporting
estimate
disease
reproduction
number,
which
reflect
effectiveness
control
strategies.
apply
our
method
study
several
severely
impacted
countries,
analyze
forecast
evolving
spread
coronavirus.
developed
interactive
web
application
facilitate
readers'
use
method.
El Profesional de la Informacion,
Journal Year:
2020,
Volume and Issue:
29(2)
Published: April 14, 2020
The
scientific
community
is
facing
one
of
its
greatest
challenges
in
solving
a
global
health
problem:
COVID-19
pandemic.
This
situation
has
generated
an
unprecedented
volume
publications.
What
the
volume,
terms
publications,
research
on
COVID-19?
general
objective
this
work
to
obtain
vision
daily
growth
production
different
databases
(Dimensions,
Web
Science
Core
Collection,
Scopus-Elsevier,
Pubmed
and
eight
repositories).
In
relation
results
obtained,
Dimensions
indexes
total
9435
publications
(69%
with
peer
review
2677
preprints)
well
above
Scopus
(1568)
WoS
(718).
classic
biliometric
phenomenon
exponential
(R2
=
0.92).
rate
500
doubles
every
15
days.
case
weekly
around
1000
Of
repositories
analysed,
Central,
Medrxiv
SSRN
are
leaders.
Despite
their
enormous
contribution,
journals
continue
be
core
communication.
Finally,
it
been
established
that
three
out
four
available
open
access.
information
explosion
demands
serious
coordinated
response
from
professionals,
which
places
us
at
centre
El Profesional de la Informacion,
Journal Year:
2020,
Volume and Issue:
29(3)
Published: June 3, 2020
Covid-19
represents
the
greatest
challenge
facing
mankind
today.
In
December
2019,
several
cases
of
pneumonia
unknown
etiology
were
reported
from
China.
This
coronavirus
infection
subsequently
identified
as
aroused
worldwide
concern.
As
a
result,
scientific
community
has
focused
attention
on
Covid-19,
revealed
by
recent
research
in
literature
based
holistic
approach.
this
regard,
study
conducts
bibliometric
analysis
with
an
emphasis
disease,
using
reference
publications
Web
Science
Core
Collection
1970
to
2020.
analyzes
12,571
(April
18)
2020
applying
advanced
techniques
SciMAT
software.
The
current
therefore
provides
complete
conceptual
main
types
and
strains
quantifying
performance
indicators,
identifying
authors,
organizations,
countries,
sources,
areas,
evaluating
development
field.
Furthermore,
science
map
is
constructed
understand
corresponding
intellectual
structure
lines
(themes).
thereby
offers
approach
field
evaluates
indicators
related
coronavirus,
focus
Covid-19.
Finally,
serves
framework
strengthen
existing
develop
new
ones,
establishing
synergistic
relationships
that
not
visible
without
maps
generated
herein.