Tiled amplicon sequencing of monkeypox virus from wastewater: a novel approach for clade and subclade level differentiation
Abstract
Wastewater-based
surveillance
(WBS)
has
modernized
in
recent
years
and
emerged
as
an
important
tool
for
the
monitoring
of
viral
pathogens,
including
monkeypox
virus
(MPXV).
Here
we
describe
a
novel
targeted
amplicon
sequencing
method
developed
clade
subclade
characterization
MPXV
from
municipal
wastewater.
This
new
addresses
limitations
PCR-based
methods
challenges
pathogen
displaying
low
load
wastewater
samples.
A
tiled
scheme
composed
11
primer
pairs
targeting
4.2
kb
portion
inverted
terminal
repeat
(ITR)
region
genome
was
designed
tested.
In
silico
analysis
demonstrated
high
accuracy
calls
using
full
target
region,
with
specific
amplicons
also
exhibiting
strong
performance
individually.
An
consensus
sequence
representing
entire
successfully
sequenced
sample
differentiated
positive
controls
by
distinct
deletion
within
short
homopolymeric
region.
Notably,
clade-informing
data
achieved
partial
sequences
recovered
lower
abundance
study
presents
enhanced
genomic
resolution
compared
to
existing
approaches,
providing
critical
genomic-level
information
informing
public
health
interventions.
Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown
Published: May 5, 2025
Language: Английский