Species of coronavirus causing SARS and COVID-19
This article is about a species of coronavirus comprising multiple strains. For the strain that causes SARS, see
SARS-CoV-1
. For the strain that causes COVID-19, see
SARS-CoV-2
.
Betacoronavirus pandemicum
[2]
(also known as
Severe acute respiratory syndrome?related coronavirus
, abbreviated as
SARSr-CoV
or
SARS-CoV
)
[note 1]
is a species of virus consisting of many known strains. Two
strains
of the virus have caused
outbreaks
of severe
respiratory diseases
in humans:
severe acute respiratory syndrome coronavirus 1
(SARS-CoV or SARS-CoV-1), the cause of
the 2002?2004 outbreak
of
severe acute respiratory syndrome
(SARS), and
severe acute respiratory syndrome coronavirus 2
(SARS-CoV-2), the cause of
the pandemic
of
COVID-19
.
[3]
[4]
There are hundreds of other strains of SARSr-CoV, which are only known to infect non-human mammal species:
bats are a major reservoir
of many strains of SARSr-CoV; several strains have been identified in
Himalayan palm civets
, which were likely ancestors of SARS-CoV-1.
[3]
[5]
[6]
[7]
These
enveloped
,
positive-sense single-stranded RNA viruses
enter host cells by binding to the
angiotensin-converting enzyme 2
(ACE2) receptor.
[8]
The SARSr-CoV species is a member of the genus
Betacoronavirus
and the only species of the subgenus
Sarbecovirus
(
SAR
S
Be
ta
co
rona
virus
).
[9]
[10]
The SARS-related coronavirus was one of several viruses identified by the
World Health Organization
(WHO) in 2016 as a likely cause of a future
epidemic
in a new plan developed after the
Ebola epidemic
for urgent research and development before and during an epidemic towards
diagnostic tests
,
vaccines
and
medicines
. This prediction came to pass with the
COVID-19 pandemic
.
[11]
[12]
Classification
[
edit
]
SARS-related coronavirus is a member of the genus
Betacoronavirus
(group 2) and
monotypic
of the subgenus
Sarbecovirus
(subgroup B).
[13]
Sarbecoviruses, unlike
embecoviruses
or
alphacoronaviruses
, have only one
papain-like proteinase
(PLpro) instead of two in the
open reading frame
ORF1ab
.
[14]
SARSr-CoV was determined to be an early split-off from the betacoronaviruses based on a set of conserved domains that it shares with the group.
[15]
[16]
Bats serve as the main host reservoir species for the SARS-related coronaviruses like SARS-CoV-1 and SARS-CoV-2. The virus has coevolved in the
bat host reservoir
over a long period of time.
[17]
Only recently have strains of SARS-related coronavirus been observed to have evolved into having been able to make the
cross-species jump
from bats to humans, as in the case of the strains
SARS-CoV-1
and
SARS-CoV-2
.
[18]
[8]
Both of these strains descended from a single ancestor but made the cross-species jump into humans separately. SARS-CoV-2 is not a direct descendant of SARS-CoV-1.
[3]
Genome
[
edit
]
The SARS-related
coronavirus
is an enveloped,
positive-sense, single-stranded RNA virus
. Its genome is about 30
kb
, which is one of the largest among RNA viruses. The virus has 14
open reading frames
which overlap in some cases.
[19]
The genome has the usual
5′ methylated cap
and a
3′ polyadenylated tail
.
[20]
There are 265
nucleotides
in the
5'UTR
and 342 nucleotides in the
3'UTR
.
[19]
The 5' methylated cap and 3' polyadenylated tail allows the
positive-sense RNA genome
to be directly
translated
by the host cell's
ribosome
on
viral entry
.
[21]
SARSr-CoV is similar to other coronaviruses in that its genome expression starts with translation by the host cell's ribosomes of its initial two large overlapping open reading frames (ORFs), 1a and 1b, both of which produce
polyproteins
.
[19]
Function of SARSr-CoV
genome proteins
|
Protein
|
Function
[22]
[23]
[24]
[25]
|
ORF1ab
P0C6X7
|
Replicase/transcriptase polyprotein (pp1ab)
(
nonstructural proteins
)
|
ORF2
P59594
|
Spike
(S) protein, virus binding and entry
(
structural protein
)
|
ORF3a
P59632
|
Interacts with S, E, M structural proteins;
Ion channel
activity;
Upregulates
cytokines
and
chemokines
such as
IL-8
and
RANTES
;
Upregulates
NF-κB
and
JNK
;
Induces
apoptosis
and
cell cycle arrest
, via
Caspase 8
and
-9
,
and by
Bax
,
p53
, and
p38 MAP kinase
|
ORF3b
P59633
|
Upregulates
cytokines
and
chemokines
by
RUNX1b
;
Inhibits
Type I IFN
production and signaling;
Induces apoptosis and
cell cycle arrest
;
|
ORF3c
P0DTG1
|
Unknown; first identified in SARS-CoV-2 but also present in SARS-CoV
|
ORF3d
P0DTG0
|
Novel gene in SARS-CoV-2, of unknown function
|
ORF4
P59637
|
Envelope
(E) protein, virus assembly and budding
(
structural protein
)
|
ORF5
P59596
|
Membrane
(M) protein, virus assembly and budding
(
structural protein
)
|
ORF6
P59634
|
Enhances cellular DNA synthesis;
Inhibits Type I IFN production and signaling
|
ORF7a
P59635
|
Inhibits cellular protein synthesis;
Induces inflammatory response by
NF-kappaB
and
IL-8 promotor
;
Upregulate chemokines such as IL-8 and RANTES;
Upregulates JNK, p38 MAP kinase;
Induces apoptosis and cell cycle arrest
|
ORF7b
Q7TFA1
|
Unknown
|
ORF8a
Q7TFA0
|
Induces apoptosis through
mitochondria
pathway
|
ORF8b
Q80H93
|
Enhances cellular DNA synthesis, also known as X5.
|
ORF9a
P59595
|
Nucleocapsid
(N) protein, viral RNA packaging
(
structural protein
)
|
ORF9b
P59636
|
Induces apoptosis
|
ORF9c
Q7TLC7
|
Also known as ORF14; function unknown and may not be protein-coding
|
ORF10
A0A663DJA2
|
Novel gene in SARS-CoV-2, of unknown function; may not be protein-coding
|
UniProt
identifiers shown for
SARS-CoV
proteins unless they are specific to SARS-CoV-2
|
The functions of several of the viral proteins are known.
[26]
ORFs 1a and 1b encode the replicase/transcriptase polyprotein, and later ORFs 2, 4, 5, and 9a encode, respectively, the four major structural proteins:
spike
(S),
envelope
(E),
membrane
(M), and
nucleocapsid
(N).
[27]
The later ORFs also encode for eight unique proteins (orf3a to orf9b), known as the
accessory proteins
, many with no known homologues. The different functions of the accessory proteins are not well understood.
[26]
SARS coronaviruses have been genetically engineered in several laboratories.
[28]
Phylogenetics
[
edit
]
Phylogenetic analysis
showed that the evolutionary branch composed of Bat coronavirus BtKY72 and BM48-31 was the base group of SARS?related CoVs evolutionary tree, which separated from other SARS?related CoVs earlier than SARS-CoV-1 and SARS-CoV-2.
[29]
[3]
SARSr‑CoV
|
|
|
|
|
|
|
|
|
SARS-CoV-1 related coronavirus
|
|
|
|
|
|
|
|
|
|
|
|
SARS-CoV-2 related coronavirus
|
|
|
|
|
|
|
|
|
|
|
|
SARS-CoV-1 related
[
edit
]
A phylogenetic tree based on whole-genome sequences of SARS-CoV-1 and related coronaviruses is:
SARS-CoV-2 related
[
edit
]
A phylogenetic tree based on whole-genome sequences of SARS-CoV-2 and related coronaviruses is:
[39]
[40]
SARS‑CoV‑2 related coronavirus
|
|
(
Bat
)
Rc-o319
, 81% to SARS-CoV-2,
Rhinolophus cornutus
,
Iwate
, Japan
[41]
|
|
|
|
|
|
|
|
Pangolin
SARSr-CoV-GX, 85.3% to SARS-CoV-2,
Manis javanica
, smuggled from Southeast Asia
[43]
|
|
|
|
Pangolin SARSr-CoV-GD, 90.1% to SARS-CoV-2,
Manis javanica
, smuggled from Southeast Asia
[44]
|
|
|
|
|
|
|
|
|
|
|
|
|
|
SARS-CoV-1
, 79% to SARS-CoV-2
|
|
Morphology
[
edit
]
The morphology of the SARS-related coronavirus is characteristic of the coronavirus family as a whole. The viruses are large
pleomorphic
spherical particles with bulbous surface projections that form a corona around the particles in electron micrographs.
[50]
The size of the virus particles is in the 80?90 nm range. The envelope of the virus in electron micrographs appears as a distinct pair of electron dense shells.
[51]
The
viral envelope
consists of a
lipid bilayer
where the
membrane
(M),
envelope
(E) and
spike
(S) proteins are anchored.
[52]
The spike proteins provide the virus with its bulbous surface projections, known as
peplomers
. The spike protein's interaction with its complement
host cell receptor
is central in determining the
tissue tropism
,
infectivity
, and
species range
of the virus.
[53]
[54]
Inside the envelope, there is the
nucleocapsid
, which is formed from multiple copies of the
nucleocapsid
(N) protein, which are bound to the positive-sense single-stranded (~30
kb
) RNA genome in a continuous
beads-on-a-string
type conformation.
[55]
[56]
The lipid bilayer envelope, membrane proteins, and nucleocapsid protect the virus when it is outside the host.
[57]
Life cycle
[
edit
]
SARS-related coronavirus follows the replication strategy typical of all coronaviruses.
[20]
[58]
Attachment and entry
[
edit
]
The attachment of the SARS-related coronavirus to the host cell is mediated by the spike protein and its receptor.
[59]
The spike protein receptor binding domain (RBD) recognizes and attaches to the
angiotensin-converting enzyme 2
(ACE2) receptor.
[8]
Following attachment, the virus can enter the host cell by two different paths. The path the virus takes depends on the host
protease
available to cleave and activate the receptor-attached spike protein.
[60]
The attachment of sarbecoviruses to ACE2 has been shown to be an
evolutionarily conserved
feature, present in many species of the taxon.
[61]
The first path the SARS coronavirus can take to enter the host cell is by
endocytosis
and uptake of the virus in an
endosome
. The receptor-attached spike protein is then activated by the host's pH-dependent
cysteine protease
cathepsin L
. Activation of the receptor-attached spike protein causes a
conformational change
, and the subsequent fusion of the viral envelope with the
endosomal wall
.
[60]
Alternatively, the virus can enter the host cell directly by
proteolytic
cleavage of the receptor-attached spike protein by the host's
TMPRSS2
or
TMPRSS11D
serine proteases
at the cell surface.
[62]
[63]
In the SARS coronavirus, the activation of the
C-terminal part
of the spike protein triggers the fusion of the viral envelope with the host cell membrane by inducing conformational changes which are not fully understood.
[64]
Genome translation
[
edit
]
After fusion the nucleocapsid passes into the
cytoplasm
, where the viral genome is released.
[59]
The genome
acts as a messenger RNA
, and the cell's ribosome
translates
two-thirds of the genome, which corresponds to the open reading frame
ORF1a
and
ORF1b
, into two large overlapping polyproteins, pp1a and pp1ab.
The larger polyprotein pp1ab is a result of a
-1 ribosomal frameshift
caused by a
slippery sequence
(UUUAAAC) and a downstream
RNA pseudoknot
at the end of open reading frame ORF1a.
[67]
The ribosomal frameshift allows for the continuous translation of ORF1a followed by ORF1b.
[68]
The polyproteins contain their own
proteases
,
PLpro
and
3CLpro
, which cleave the polyproteins at different specific sites. The cleavage of polyprotein pp1ab yields 16 nonstructural proteins (nsp1 to nsp16). Product proteins include various replication proteins such as
RNA-dependent RNA polymerase
(RdRp),
RNA helicase
, and
exoribonuclease
(ExoN).
[68]
The two SARS-CoV-2 proteases (PLpro and 3CLpro) also interfere with the immune system response to the viral infection by cleaving three immune system proteins. PLpro cleaves
IRF3
and 3CLpro cleaves both
NLRP12
and
TAB1
. "Direct cleavage of IRF3 by NSP3 could explain the blunted Type-I IFN response seen during SARS-CoV-2 infections while NSP5 mediated cleavage of NLRP12 and TAB1 point to a molecular mechanism for enhanced production of IL-6 and inflammatory response observed in COVID-19 patients."
[69]
Replication and transcription
[
edit
]
A number of the nonstructural replication proteins coalesce to form a
multi-protein
replicase-transcriptase complex (RTC).
[68]
The main replicase-transcriptase protein is the
RNA-dependent RNA polymerase
(RdRp). It is directly involved in the
replication
and
transcription
of RNA from an RNA strand. The other nonstructural proteins in the complex assist in the replication and transcription process.
[65]
The protein nsp14 is a
3'-5' exoribonuclease
which provides extra fidelity to the replication process. The exoribonuclease provides a
proofreading
function to the complex which the RNA-dependent RNA polymerase lacks. Similarly, proteins nsp7 and nsp8 form a hexadecameric sliding clamp as part of the complex which greatly increases the
processivity
of the RNA-dependent RNA polymerase.
[65]
The coronaviruses require the increased fidelity and processivity during RNA synthesis because of the relatively large genome size in comparison to other RNA viruses.
[70]
One of the main functions of the replicase-transcriptase complex is to transcribe the viral genome. RdRp directly mediates the
synthesis
of negative-sense
subgenomic RNA
molecules from the positive-sense genomic RNA. This is followed by the transcription of these negative-sense subgenomic RNA molecules to their corresponding positive-sense
mRNAs
.
[71]
The other important function of the replicase-transcriptase complex is to replicate the viral genome. RdRp directly mediates the
synthesis
of negative-sense genomic RNA from the positive-sense genomic RNA. This is followed by the replication of positive-sense genomic RNA from the negative-sense genomic RNA.
[71]
The replicated positive-sense genomic RNA becomes the genome of the
progeny viruses
. The various smaller mRNAs are transcripts from the last third of the virus genome which follows the reading frames ORF1a and ORF1b. These mRNAs are translated into the four structural proteins (S, E, M, and N) that will become part of the progeny virus particles and also eight other accessory proteins (orf3 to orf9b) which assist the virus.
[72]
Recombination
[
edit
]
When two SARS-CoV
genomes
are present in a host cell, they may interact with each other to form recombinant genomes that can be transmitted to progeny viruses. Recombination likely occurs during genome replication when the
RNA polymerase
switches from one template to another (copy choice recombination).
[73]
Human SARS-CoV appears to have had a complex history of
recombination
between ancestral
coronaviruses
that were hosted in several different animal groups.
[73]
[74]
Assembly and release
[
edit
]
RNA translation
occurs inside the
endoplasmic reticulum
. The viral structural proteins S, E and M move along the secretory pathway into the
Golgi intermediate compartment
. There, the M proteins direct most protein-protein interactions required for assembly of viruses following its binding to the nucleocapsid.
[75]
Progeny viruses are released from the host cell by
exocytosis
through secretory vesicles.
[75]
See also
[
edit
]
Notes
[
edit
]
- ^
The terms
SARSr-CoV
and
SARS-CoV
are sometimes used interchangeably, especially prior to the discovery of SARS-CoV-2. This may cause confusion when some publications refer to SARS-CoV-1 as
SARS-CoV
.
References
[
edit
]
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Further reading
[
edit
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- Snijder EJ, Bredenbeek PJ, Dobbe JC, Thiel V, Ziebuhr J, Poon LL, et al. (August 2003).
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- Enjuanes L, Sola I, Zuniga S, Almazan F (2008). "Coronavirus Replication and Interaction with Host". In Mettenleiter TC, Sobrino F (eds.).
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. Caister Academic Press.
ISBN
978-1-904455-22-6
.
External links
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General topics
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People
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In popular culture
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