Science,
Journal Year:
2022,
Volume and Issue:
376(6599), P. 1327 - 1332
Published: May 24, 2022
Repeated
emergence
of
severe
acute
respiratory
syndrome
coronavirus
2
(SARS-CoV-2)
variants
with
increased
fitness
underscores
the
value
rapid
detection
and
characterization
new
lineages.
We
have
developed
PyR
0
,
a
hierarchical
Bayesian
multinomial
logistic
regression
model
that
infers
relative
prevalence
all
viral
lineages
across
geographic
regions,
detects
increasing
in
prevalence,
identifies
mutations
relevant
to
fitness.
Applying
publicly
available
SARS-CoV-2
genomes,
we
identify
numerous
substitutions
increase
fitness,
including
previously
identified
spike
many
nonspike
within
nucleocapsid
nonstructural
proteins.
forecasts
growth
from
their
mutational
profile,
ranks
as
sequences
become
available,
prioritizes
biological
public
health
concern
for
functional
characterization.
Nature,
Journal Year:
2022,
Volume and Issue:
603(7902), P. 679 - 686
Published: Jan. 7, 2022
Abstract
The
SARS-CoV-2
epidemic
in
southern
Africa
has
been
characterized
by
three
distinct
waves.
first
was
associated
with
a
mix
of
lineages,
while
the
second
and
third
waves
were
driven
Beta
(B.1.351)
Delta
(B.1.617.2)
variants,
respectively
1–3
.
In
November
2021,
genomic
surveillance
teams
South
Botswana
detected
new
variant
rapid
resurgence
infections
Gauteng
province,
Africa.
Within
days
genome
being
uploaded,
it
designated
concern
(Omicron,
B.1.1.529)
World
Health
Organization
and,
within
weeks,
had
identified
87
countries.
Omicron
is
exceptional
for
carrying
over
30
mutations
spike
glycoprotein,
which
are
predicted
to
influence
antibody
neutralization
function
4
Here
we
describe
profile
early
transmission
dynamics
Omicron,
highlighting
spread
regions
high
levels
population
immunity.
Nature,
Journal Year:
2022,
Volume and Issue:
608(7923), P. 593 - 602
Published: June 17, 2022
Abstract
Severe
acute
respiratory
syndrome
coronavirus
2
(SARS-CoV-2)
Omicron
sublineages
BA.2.12.1,
BA.4
and
BA.5
exhibit
higher
transmissibility
than
the
BA.2
lineage
1
.
The
receptor
binding
immune-evasion
capability
of
these
recently
emerged
variants
require
immediate
investigation.
Here,
coupled
with
structural
comparisons
spike
proteins,
we
show
that
(BA.4
are
hereafter
referred
collectively
to
as
BA.4/BA.5)
similar
affinities
for
angiotensin-converting
enzyme
(ACE2)
receptor.
Of
note,
BA.2.12.1
BA.4/BA.5
display
increased
evasion
neutralizing
antibodies
compared
against
plasma
from
triple-vaccinated
individuals
or
who
developed
a
BA.1
infection
after
vaccination.
To
delineate
underlying
antibody-evasion
mechanism,
determined
escape
mutation
profiles
,
epitope
distribution
3
Omicron-neutralization
efficiency
1,640
directed
receptor-binding
domain
viral
protein,
including
614
isolated
people
had
recovered
infection.
vaccination
predominantly
recalls
humoral
immune
memory
ancestral
(hereafter
wild-type
(WT))
SARS-CoV-2
protein.
resulting
elicited
could
neutralize
both
WT
enriched
on
epitopes
do
not
bind
ACE2.
However,
most
cross-reactive
evaded
by
mutants
L452Q,
L452R
F486V.
can
also
induce
new
clones
BA.1-specific
potently
BA.1.
Nevertheless,
largely
owing
D405N
F486V
mutations,
react
weakly
pre-Omicron
variants,
exhibiting
narrow
neutralization
breadths.
therapeutic
bebtelovimab
4
cilgavimab
5
effectively
BA.4/BA.5,
whereas
S371F,
R408S
mutations
undermine
broadly
sarbecovirus-neutralizing
antibodies.
Together,
our
results
indicate
may
evolve
evade
immunity
infection,
suggesting
BA.1-derived
vaccine
boosters
achieve
broad-spectrum
protection
variants.
Nature,
Journal Year:
2021,
Volume and Issue:
602(7898), P. 654 - 656
Published: Dec. 23, 2021
Abstract
The
emergence
of
the
SARS-CoV-2
variant
concern
Omicron
(Pango
lineage
B.1.1.529),
first
identified
in
Botswana
and
South
Africa,
may
compromise
vaccine
effectiveness
lead
to
re-infections
1
.
Here
we
investigated
escape
from
neutralization
by
antibodies
African
individuals
vaccinated
with
Pfizer
BNT162b2.
We
used
blood
samples
taken
soon
after
vaccination
who
were
previously
infected
or
no
evidence
previous
infection.
isolated
sequence-confirmed
live
virus
an
person
observed
that
requires
angiotensin-converting
enzyme
2
(ACE2)
receptor
infect
cells.
compared
plasma
relative
ancestral
strain
found
was
much
higher
vaccinated-only
participants.
However,
both
groups
showed
a
22-fold
reduction
vaccine-elicited
variant.
Participants
had
been
exhibited
residual
similar
level
vaccination-only
group.
These
data
support
notion
reasonable
protection
against
be
maintained
using
approaches.
Nature Reviews Microbiology,
Journal Year:
2023,
Volume and Issue:
unknown
Published: Jan. 18, 2023
In
late
2020,
after
circulating
for
almost
a
year
in
the
human
population,
severe
acute
respiratory
syndrome
coronavirus
2
(SARS-CoV-2)
exhibited
major
step
change
its
adaptation
to
humans.
These
highly
mutated
forms
of
SARS-CoV-2
had
enhanced
rates
transmission
relative
previous
variants
and
were
termed
'variants
concern'
(VOCs).
Designated
Alpha,
Beta,
Gamma,
Delta
Omicron,
VOCs
emerged
independently
from
one
another,
turn
each
rapidly
became
dominant,
regionally
or
globally,
outcompeting
variants.
The
success
VOC
previously
dominant
variant
was
enabled
by
altered
intrinsic
functional
properties
virus
and,
various
degrees,
changes
antigenicity
conferring
ability
evade
primed
immune
response.
increased
fitness
associated
with
is
result
complex
interplay
biology
context
changing
immunity
due
both
vaccination
prior
infection.
this
Review,
we
summarize
literature
on
transmissibility
variants,
role
mutations
at
furin
spike
cleavage
site
non-spike
proteins,
potential
importance
recombination
success,
evolution
T
cells,
innate
population
immunity.
shows
complicated
relationship
among
antigenicity,
virulence,
which
has
unpredictable
implications
future
trajectory
disease
burden
COVID-19.
JAMA,
Journal Year:
2022,
Volume and Issue:
327(7), P. 639 - 639
Published: Jan. 21, 2022
Importance
Assessing
COVID-19
vaccine
performance
against
the
rapidly
spreading
SARS-CoV-2
Omicron
variant
is
critical
to
inform
public
health
guidance.
Objective
To
estimate
association
between
receipt
of
3
doses
Pfizer-BioNTech
BNT162b2
or
Moderna
mRNA-1273
and
symptomatic
infection,
stratified
by
(Omicron
Delta).
Design,
Setting,
Participants
A
test-negative
case-control
analysis
among
adults
18
years
older
with
COVID-like
illness
tested
December
10,
2021,
through
January
1,
2022,
a
national
pharmacy-based
testing
program
(4666
sites
across
49
US
states).
Exposures
Three
mRNA
(third
dose
≥14
days
before
test
≥6
months
after
second
dose)
vs
unvaccinated
2
6
more
(ie,
eligible
for
booster
dose).
Main
Outcomes
Measures
Association
infection
(stratified
Delta
variants
defined
usingS-gene
target
failure)
vaccination
(3
doses).
Associations
were
measured
multivariable
multinomial
regression.
Among
cases,
secondary
outcome
was
median
cycle
threshold
values
(inversely
proportional
amount
nucleic
acid
present)
viral
genes,
status.
individuals
seeking
(compared
doses)
less
likely
compared
controls.
These
findings
suggest
that
vaccine,
relative
doses,
associated
protection
variants,
although
ratios
than
Nature,
Journal Year:
2022,
Volume and Issue:
603(7902), P. 700 - 705
Published: Feb. 1, 2022
Abstract
The
emergence
of
the
Omicron
variant
SARS-CoV-2
is
an
urgent
global
health
concern
1
.
In
this
study,
our
statistical
modelling
suggests
that
has
spread
more
rapidly
than
Delta
in
several
countries
including
South
Africa.
Cell
culture
experiments
showed
to
be
less
fusogenic
and
ancestral
strain
SARS-CoV-2.
Although
spike
(S)
protein
efficiently
cleaved
into
two
subunits,
which
facilitates
cell–cell
fusion
2,3
,
S
was
compared
proteins
Furthermore,
a
hamster
model,
decreased
lung
infectivity
pathogenic
Our
multiscale
investigations
reveal
virological
characteristics
Omicron,
rapid
growth
human
population,
lower
fusogenicity
attenuated
pathogenicity.
