Online dashboards for SARS-CoV-2 wastewater-based epidemiology
Future Microbiology,
Journal Year:
2024,
Volume and Issue:
19(9), P. 761 - 769
Published: May 23, 2024
Aim:
Wastewater-based
epidemiology
(WBE)
is
increasingly
used
to
monitor
pandemics.
In
this
manuscript,
we
review
methods
and
limitations
of
WBE,
as
well
their
online
dashboards.
Materials
&
methods:
Online
dashboards
were
retrieved
using
PubMed
search
engines,
annotated
for
timeliness,
availability
English
version,
details
on
SARS-CoV-2
sublineages,
normalization
by
population
PPMoV
load,
case/hospitalization
count
charts
raw
data
export.
Results:
We
51
web
portals,
half
them
from
Europe.
Africa
represented
South
only,
only
seven
portals
are
available
Asia.
Conclusion:
WBS
provides
near-real-time
cost-effective
monitoring
analytes
across
space
time
in
populations.
However,
tremendous
heterogeneity
still
persists
the
WBE
literature.
Language: Английский
Monitoring pathogens in wastewater
Nature Reviews Microbiology,
Journal Year:
2024,
Volume and Issue:
22(5), P. 261 - 261
Published: Feb. 27, 2024
Language: Английский
Wastewater Surveillance of SARS-CoV-2 in Zambia: An Early Warning Tool
Published: June 26, 2024
Wastewater-based
surveillance
has
emerged
as
an
important
method
for
monitoring
SARS-CoV-2.
This
study
investigated
the
presence
of
SARS-CoV-2
in
wastewater
Zambia.
We
conducted
a
longitudinal
Copperbelt
and
Eastern
provinces
Zambia
from
October
2023
to
December
during
which
155
samples
were
collected.
The
subjected
three
different
concentration
methods,
namely
bag-mediated
filtration,
skimmed
milk
flocculation,
polythene
glycol-based
assays.
Molecular
detection
nucleic
acid
was
using
real-time
PCR.
Whole
genome
sequencing
Illumina
COVIDSEQ
assay.
Of
samples,
62
(40%)
tested
positive
these,
13
sequences
sufficient
length
determine
lineages
obtained
two
phylogenetically
analyzed.
Various
Omicron
subvariants
detected
including
BA.5,
XBB.1.45,
BA.2.86,
JN.1.
Some
these
have
been
clinical
cases
Interestingly,
phylogenetic
analysis
positioned
sequence
Province
B.1.1.529
clade,
suggesting
that
earlier
variants
late
2021
could
still
be
circulating
may
not
wholly
replaced
by
newer
subvariants.
stresses
need
integrating
into
mainstream
strategies
circulation
Language: Английский
The consequences of SARS-CoV-2 within-host persistence
Nature Reviews Microbiology,
Journal Year:
2024,
Volume and Issue:
unknown
Published: Nov. 25, 2024
Language: Английский
Wastewater Surveillance of SARS-CoV-2 in Zambia: An Early Warning Tool
International Journal of Molecular Sciences,
Journal Year:
2024,
Volume and Issue:
25(16), P. 8839 - 8839
Published: Aug. 14, 2024
Wastewater-based
surveillance
has
emerged
as
an
important
method
for
monitoring
the
Severe
Acute
Respiratory
Syndrome
Coronavirus
2
(SARS-CoV-2).
This
study
investigated
presence
of
SARS-CoV-2
in
wastewater
Zambia.
We
conducted
a
longitudinal
Copperbelt
and
Eastern
provinces
Zambia
from
October
2023
to
December
during
which
155
samples
were
collected.
The
subjected
three
different
concentration
methods,
namely
bag-mediated
filtration,
skimmed
milk
flocculation,
polythene
glycol-based
assays.
Molecular
detection
nucleic
acid
was
using
real-time
Polymerase
Chain
Reaction
(PCR).
Whole
genome
sequencing
Illumina
COVIDSEQ
assay.
Of
samples,
62
(40%)
tested
positive
SARS-CoV-2.
these,
13
sequences
sufficient
length
determine
lineages
obtained
phylogenetically
analyzed.
Various
Omicron
subvariants
detected
including
BA.5,
XBB.1.45,
BA.2.86,
JN.1.
Some
these
have
been
clinical
cases
Interestingly,
phylogenetic
analysis
positioned
sequence
Province
B.1.1.529
clade,
suggesting
that
earlier
variants
late
2021
could
still
be
circulating
may
not
wholly
replaced
by
newer
subvariants.
stresses
need
integrating
into
mainstream
strategies
circulation
Language: Английский
Wastewater sequencing from a rural community enables identification of widespread adaptive mutations in a SARS-CoV-2 Alpha variant
Michael J. Conway,
No information about this author
Michael P. Novay,
No information about this author
Carsten M. Pusch
No information about this author
et al.
medRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Nov. 11, 2024
Abstract
Background
Central
Michigan
University
(CMU)
participated
in
a
state-wide
wastewater
monitoring
program
starting
2021.
One
rural
site
consistently
produced
higher
concentrations
of
SARS-CoV-2
genome
copies.
Samples
from
this
were
sequenced
retrospectively
and
exclusively
contained
derivative
Alpha
variant
lineage
B.1.1.7
that
shed
the
same
for
20-28
months.
Results
Complete
reconstruction
each
open
reading
frame
(ORF)
alignment
to
an
early
clinical
isolate
identified
novel
mutations
selected
non-structural
(nsp1,
nsp2,
nsp3,
nsp4,
nsp5/3CLpro,
nsp6,
RdRp,
nsp15,
nsp16,
ORF3a,
ORF6,
ORF7a,
ORF7b)
structural
genes
(Spike,
M,
N).
These
rare
have
not
accumulated
samples
worldwide.
Mutational
analysis
revealed
divergence
reference
sequence
over
time.
We
present
on
available
models
discuss
potential
role
these
during
chronic
infection.
Conclusions
This
study
further
supports
small
treatment
plants
can
enhance
resolution
events
facilitate
viral
genomes
due
relative
lack
contaminating
sequences
identifies
may
be
associated
with
infections.
Language: Английский