Frontiers in Microbiology,
Год журнала:
2022,
Номер
13
Опубликована: Апрель 6, 2022
Hepatitis
Delta
Virus
(HDV)
is
the
smallest
mammalian
single-stranded
RNA
virus.
It
requires
host
cells
and
hepatitis
B
virus
(HBV)
to
complete
its
unique
life
cycle.
The
present
review
summarizes
specific
regions
on
D
antigen
(HDAg)
surface
(HBsAg)
that
drive
HDV
utilize
cell
machinery
system
produce
three
types
of
two
forms
HDAg,
hijack
HBsAg
for
secretion
de
novo
entry.
Previously,
interferon-α
was
only
recommended
therapy
infection.
In
recent
years,
some
new
therapies
targeting
these
regions,
such
as
Bulevirtide,
Lonafarnib,
Nucleic
acid
polymers
have
appeared,
with
better
curative
effects
fewer
adverse
reactions.
Nature,
Год журнала:
2022,
Номер
602(7895), С. 142 - 147
Опубликована: Янв. 26, 2022
Public
databases
contain
a
planetary
collection
of
nucleic
acid
sequences,
but
their
systematic
exploration
has
been
inhibited
by
lack
efficient
methods
for
searching
this
corpus,
which
(at
the
time
writing)
exceeds
20
petabases
and
is
growing
exponentially1.
Here
we
developed
cloud
computing
infrastructure,
Serratus,
to
enable
ultra-high-throughput
sequence
alignment
at
petabase
scale.
We
searched
5.7
million
biologically
diverse
samples
(10.2
petabases)
hallmark
gene
RNA-dependent
RNA
polymerase
identified
well
over
105
novel
viruses,
thereby
expanding
number
known
species
roughly
an
order
magnitude.
characterized
viruses
related
coronaviruses,
hepatitis
delta
virus
huge
phages,
respectively,
analysed
environmental
reservoirs.
To
catalyse
ongoing
revolution
viral
discovery,
established
free
comprehensive
database
these
data
tools.
Expanding
diversity
can
reveal
evolutionary
origins
emerging
pathogens
improve
pathogen
surveillance
anticipation
mitigation
future
pandemics.
The Lancet Microbe,
Год журнала:
2022,
Номер
3(8), С. e625 - e637
Опубликована: Янв. 10, 2022
Despite
the
global
investment
in
One
Health
disease
surveillance,
it
remains
difficult
and
costly
to
identify
monitor
wildlife
reservoirs
of
novel
zoonotic
viruses.
Statistical
models
can
guide
sampling
target
prioritisation,
but
predictions
from
any
given
model
might
be
highly
uncertain;
moreover,
systematic
validation
is
rare,
drivers
performance
are
consequently
under-documented.
Here,
we
use
bat
hosts
betacoronaviruses
as
a
case
study
for
data-driven
process
comparing
validating
predictive
probable
reservoir
hosts.
In
early
2020,
generated
an
ensemble
eight
statistical
that
predicted
host–virus
associations
developed
priority
recommendations
potential
bridge
SARS-CoV-2.
During
time
frame
more
than
year,
tracked
discovery
47
new
betacoronaviruses,
validated
initial
predictions,
dynamically
updated
our
analytical
pipeline.
We
found
ecological
trait-based
performed
well
at
predicting
these
hosts,
whereas
network
methods
consistently
approximately
or
worse
expected
random.
These
findings
illustrate
importance
modelling
buffer
against
mixed-model
quality
highlight
value
including
host
ecology
models.
Our
revised
showed
improved
compared
with
ensemble,
400
species
globally
could
undetected
betacoronavirus
show,
through
validation,
machine
learning
help
optimise
undiscovered
viruses
illustrates
how
such
approaches
best
implemented
dynamic
prediction,
data
collection,
updating.
Cell,
Год журнала:
2023,
Номер
186(3), С. 646 - 661.e4
Опубликована: Янв. 24, 2023
Viroids
and
viroid-like
covalently
closed
circular
(ccc)
RNAs
are
minimal
replicators
that
typically
encode
no
proteins
hijack
cellular
enzymes
for
replication.
The
extent
diversity
of
agents
poorly
understood.
We
developed
a
computational
pipeline
to
identify
cccRNAs
applied
it
5,131
metatranscriptomes
1,344
plant
transcriptomes.
search
yielded
11,378
spanning
4,409
species-level
clusters,
5-fold
increase
compared
the
previously
identified
elements.
Within
this
diverse
collection,
we
discovered
numerous
putative
viroids,
satellite
RNAs,
retrozymes,
ribozy-like
viruses.
Diverse
ribozyme
combinations
unusual
ribozymes
within
were
identified.
Self-cleaving
in
ambiviruses,
some
mito-like
viruses
capsid-encoding
virus-like
cccRNAs.
broad
presence
transcriptomes
ecosystems
implies
their
host
range
is
far
broader
than
currently
known,
matches
CRISPR
spacers
suggest
replicate
prokaryotes.
Nearly
all
organisms
are
hosts
to
multiple
viruses
that
collectively
appear
be
the
most
abundant
biological
entities
in
biosphere.
With
recent
advances
metagenomics
and
metatranscriptomics,
known
diversity
of
substantially
expanded.
Comparative
analysis
these
using
advanced
computational
methods
culminated
reconstruction
evolution
major
groups
enabled
construction
a
virus
megataxonomy,
which
has
been
formally
adopted
by
International
Committee
on
Taxonomy
Viruses.
This
comprehensive
taxonomy
consists
six
realms,
aspired
monophyletic
assembled
based
conservation
hallmark
proteins
involved
capsid
structure
formation
or
genome
replication.
The
different
taxa
differ
host
range
accordingly
ecological
niches.
In
this
review
article,
we
outline
latest
developments
megataxonomy
discoveries
will
likely
lead
reassessment
some
taxa,
particular,
split
three
current
realms
into
two
more
independent
realms.
We
then
discuss
correspondence
between
distribution
among
niches,
as
well
abundance
versus
cells
habitats.
across
environments
appears
primarily
determined
ranges,
i.e.
virome
is
shaped
composition
biome
given
habitat,
itself
affected
abiotic
factors.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Янв. 21, 2024
Here,
we
describe
the
"Obelisks,"
a
previously
unrecognised
class
of
viroid-like
elements
that
first
identified
in
human
gut
metatranscriptomic
data.
"Obelisks"
share
several
properties:
(i)
apparently
circular
RNA
~1kb
genome
assemblies,
(ii)
predicted
rod-like
secondary
structures
encompassing
entire
genome,
and
(iii)
open
reading
frames
coding
for
novel
protein
superfamily,
which
call
"Oblins".
We
find
Obelisks
form
their
own
distinct
phylogenetic
group
with
no
detectable
sequence
or
structural
similarity
to
known
biological
agents.
Further,
are
prevalent
tested
microbiome
metatranscriptomes
representatives
detected
~7%
analysed
stool
(29/440)
~50%
oral
(17/32).
Obelisk
compositions
appear
differ
between
anatomic
sites
capable
persisting
individuals,
continued
presence
over
>300
days
observed
one
case.
Large
scale
searches
29,959
(clustered
at
90%
nucleotide
identity),
examples
from
all
seven
continents
diverse
ecological
niches.
From
this
search,
subset
code
Obelisk-specific
variants
hammerhead
type-III
self-cleaving
ribozyme.
Lastly,
case
bacterial
species
(Streptococcus
sanguinis)
defined
laboratory
strains
harboured
specific
population.
As
such,
comprise
RNAs
have
colonised,
gone
unnoticed
in,
human,
global
microbiomes.
Current Opinion in Virology,
Год журнала:
2021,
Номер
52, С. 192 - 202
Опубликована: Дек. 23, 2021
The
emergence
of
zoonotic
viral
diseases
in
humans
commonly
reflects
exposure
to
mammalian
wildlife.
Bats
(order
Chiroptera)
are
arguably
the
most
important
reservoir
for
viruses,
with
notable
examples
including
Severe
Acute
Respiratory
Syndrome
coronaviruses
1
and
2,
Middle
East
coronavirus,
henipaviruses
lyssaviruses.
Herein,
we
outline
our
current
knowledge
on
diversity
bat
viromes,
particularly
through
lens
metagenomic
next-generation
sequencing
context
disease
emergence.
A
key
conclusion
is
that
although
bats
harbour
abundant
virus
diversity,
vast
majority
viruses
have
not
emerged
cause
new
hosts
such
better
regarded
as
critical
but
endangered
components
global
ecosystems.
Annual Review of Virology,
Год журнала:
2022,
Номер
9(1), С. 173 - 192
Опубликована: Июнь 15, 2022
The
coronavirus
disease
2019
(COVID-19)
pandemic
has
had
a
profound
impact
on
human
health,
economic
well-being,
and
societal
function.
It
is
essential
that
we
use
this
generational
experience
to
better
understand
the
processes
underpin
emergence
of
COVID-19
other
zoonotic
diseases.
Herein,
I
review
mechanisms
determine
why
how
viruses
emerge
in
new
hosts,
as
well
barriers
process.
show
traditional
studies
virus
have
an
inherent
anthropocentric
bias,
with
humans
considered
inevitable
outcome
emergence,
when
reality
are
integral
components
global
ecosystem
characterized
by
continual
host
jumping
also
transmitting
their
animals.
illustrate
these
points
using
coronaviruses,
including
severe
acute
respiratory
syndrome
2,
case
study.
outline
potential
steps
can
be
followed
help
mitigate
prevent
future
pandemics,
combating
climate
change
central
component.
Biomolecules,
Год журнала:
2022,
Номер
12(8), С. 1073 - 1073
Опубликована: Авг. 4, 2022
Virus
discovery
has
been
fueled
by
new
technologies
ever
since
the
first
viruses
were
discovered
at
end
of
19th
century.
Starting
with
mechanical
devices
that
provided
evidence
for
virus
presence
in
sick
hosts,
gradually
transitioned
into
a
sequence-based
scientific
discipline,
which,
nowadays,
can
characterize
identity
and
explore
viral
diversity
an
unprecedented
resolution
depth.
Sequencing
are
now
being
used
routinely
ever-increasing
scales,
producing
avalanche
novel
sequences
found
multitude
organisms
environments.
In
this
perspective
article,
we
argue
started
to
undergo
another
transformation
prompted
emergence
approaches
sequence
data-centered
primarily
computational,
setting
them
apart
from
previous
technology-driven
innovations.
The
data-driven
approach
is
largely
uncoupled
collection
processing
biological
samples,
exploits
availability
massive
amounts
publicly
freely
accessible
data
sequencing
archives.
We
discuss
open
challenges
be
solved
order
unlock
full
potential
discovery,
highlight
benefits
it
bring
classical
(mostly
molecular)
virology
molecular
biology
general.
Microbiology and Molecular Biology Reviews,
Год журнала:
2021,
Номер
85(4)
Опубликована: Сен. 1, 2021
Originally,
viruses
were
defined
as
miniscule
infectious
agents
that
passed
through
filters
retain
even
the
smallest
cells.
Subsequently,
considered
obligate
intracellular
parasites
whose
reproduction
depends
on
their
cellular
hosts
for
energy
supply
and
molecular
building
blocks.