Coronavirus
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Coronaviruses are a group of related
viruses that cause diseases in
mammals and
birds. In humans, coronaviruses cause
respiratory tract infections that can be mild, such as some cases of the
common cold (among other possible causes, predominantly
rhinoviruses), and others that can be lethal, such as
SARS,
MERS, and
COVID-19. Symptoms in other species vary: in chickens, they cause an
upper respiratory tract disease, while in cows and pigs they cause
diarrhea. There are yet to be
vaccines or
antiviral drugs to prevent or treat human coronavirus infections.
Coronaviruses constitute the
subfamily Orthocoronavirinae, in the family
Coronaviridae, order
Nidovirales, and realm
Riboviria.
[5][6] They are
enveloped viruses with a
positive-sense single-stranded RNA genome and a
nucleocapsid of helical symmetry. The
genome size of coronaviruses ranges from approximately 27 to 34
kilobases, the largest among known
RNA viruses.
[7] The name
coronavirus is derived from the Latin
corona, meaning "crown" or "halo", which refers to the characteristic appearance reminiscent of a crown or a
solar corona around the virions (virus particles) when viewed under two-dimensional
transmission electron microscopy, due to the surface being covered in club-shaped protein spikes.
Discovery
Human coronaviruses were first discovered in the late 1960s.
[8] The earliest ones discovered were an
infectious bronchitis virus in chickens and two in human patients with the
common cold (later named
human coronavirus 229E and
human coronavirus OC43).
[9] Other members of this family have since been identified, including
SARS-CoV in 2003,
HCoV NL63 in 2004,
HKU1 in 2005,
MERS-CoV in 2012, and
SARS-CoV-2 (formerly known as 2019-nCoV) in 2019. Most of these have involved serious
respiratory tract infections.
Etymology
The name "coronavirus" is derived from Latin
corona, meaning "crown" or "wreath", itself a borrowing from
Greek κορώνη korṓnē, "garland, wreath". The name refers to the characteristic appearance of
virions (the infective form of the virus) by
electron microscopy, which have a fringe of large, bulbous surface projections creating an image reminiscent of a crown or of a
solar corona. This
morphology is created by the viral spike
peplomers, which are
proteins on the surface of the virus.
[10][11]
Morphology
Cross-sectional model of a coronavirus
Coronaviruses are large
pleomorphic spherical particles with bulbous surface projections.
[12] The diameter of the virus particles is around 120 nm.
[13] The envelope of the virus in electron micrographs appears as a distinct pair of electron dense shells.
[14]
The
viral envelope consists of a
lipid bilayer where the membrane (M), envelope (E) and
spike (S) structural proteins are anchored.
[15] A subset of coronaviruses (specifically the members of
betacoronavirus subgroup A) also have a shorter spike-like surface protein called
hemagglutinin esterase (HE).
[5]
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
RNA genome in a continuous
beads-on-a-string type conformation.
[13][16] The lipid bilayer envelope, membrane proteins, and nucleocapsid protect the virus when it is outside the host cell.
[17]
Genome
Schematic representation of the genome organization and functional domains of S protein for SARS-CoV and MERS-CoV.
Coronaviruses contain a
positive-sense, single-stranded RNA genome. The
genome size for coronaviruses ranges from approximately 27 to 34
kilobases.
[7] The genome size is one of the largest among RNA viruses. The genome has a
5′ methylated cap and a
3′ polyadenylated tail.
[18]
The genome organization for a coronavirus is
5′-leader-UTR-replicase/transcriptase-spike (S)-envelope (E)-membrane (M)-nucleocapsid (N)-
3′UTR-poly
(A) tail. The open reading frames 1a and 1b, which occupy the first
two-thirds of the genome, encode the replicase/transcriptase
polyprotein. The replicase/transcriptase polyprotein self cleaves to
form the nonstructural proteins (nsps).
[19]
The later reading frames encode the four major structural proteins: spike, envelope, membrane, and nucleocapsid.
[20]
Interspersed between these reading frames are the reading frames for
the accessory proteins. The number of accessory proteins and their
function is unique depending on the specific coronavirus.
[19]
Life cycle
Entry
The life cycle of a coronavirus
Infection begins when the viral spike (S) glycoprotein attaches to its complementary host cell receptor. After attachment, a
protease
of the host cell cleaves and activates the receptor-attached spike
protein. Depending on the host cell protease available, cleavage and
activation allows the
virus to enter the host cell by
endocytosis or direct fusion of the viral envelop with the
host membrane.
[21]
On entry into the
host cell, the virus particle is
uncoated, and its
genome enters the
cell cytoplasm.
[22] The coronavirus RNA genome has a
5′ methylated cap and a
3′ polyadenylated tail, which allows the RNA to attach to the host cell's
ribosome for translation.
[23] The host ribosome translates the initial overlapping
open reading frame of the virus genome and forms a long
polyprotein. The polyprotein has its own
proteases which
cleave the polyprotein into multiple nonstructural proteins.
[19]
Replication
A number of the nonstructural proteins coalesce to form a
multi-protein replicase-transcriptase complex (RTC). 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. The
exoribonuclease non-structural protein, for instance, provides extra fidelity to replication by providing a
proofreading function which the RNA-dependent RNA polymerase lacks.
[24]
One of the main functions of the 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.
[19] The other important function of the 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.
[19]
Release
The replicated positive-sense genomic RNA becomes the genome of the
progeny viruses.
The mRNAs are gene transcripts of the last third of the virus genome
after the initial overlapping reading frame. These mRNAs are translated
by the host's ribosomes into the structural proteins and a number of
accessory proteins.
[19] 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.
[25] Progeny viruses are then released from the host cell by
exocytosis through secretory vesicles.
[25]
Transmission
Human to human transmission of coronaviruses is primarily thought to occur among close contacts via
respiratory droplets generated by sneezing and coughing.
[26] The interaction of the coronavirus spike protein with its complement
host cell receptor is central in determining the
tissue tropism,
infectivity, and
species range of the virus.
[27][28] The
SARS coronavirus, for example, infects human cells by attaching to the
angiotensin-converting enzyme 2 (ACE2) receptor.
[29]
Taxonomy
Phylogenetic tree of coronaviruses
The scientific name for coronavirus is
Orthocoronavirinae or
Coronavirinae.
[2][3][4] Coronavirus belongs to the family of
Coronaviridae.
Evolution
The
most recent common ancestor (MRCA) of all coronaviruses has been estimated to have existed as recently as 8000
BCE, though some models place the MRCA as far back as 55 million years or more, implying long term coevolution with bats.
[30]
The MRCAs of the alphacoronavirus line has been placed at about 2400
BCE, the betacoronavirus line at 3300 BCE, the gammacoronavirus line at
2800 BCE, and the deltacoronavirus line at about 3000 BCE. It appears
that bats and birds, as warm-blooded flying vertebrates, are ideal hosts
for the coronavirus gene source (with
bats
for alphacoronavirus and betacoronavirus, and birds for
gammacoronavirus and deltacoronavirus) to fuel coronavirus evolution and
dissemination.
[31]
Bovine coronavirus and canine respiratory coronaviruses diverged from a common ancestor recently (~ 1950).
[32]
Bovine coronavirus and human coronavirus OC43 diverged around the
1890s. Bovine coronavirus diverged from the equine coronavirus species
at the end of the 18th century.
[33]
The MRCA of human coronavirus OC43 has been dated to the 1950s.
[34]
MERS-CoV, although related to several bat coronavirus species, appears to have diverged from these several centuries ago.
[35] The human coronavirus NL63 and a bat coronavirus shared an MRCA 563–822 years ago.
[36]
The most closely related bat coronavirus and SARS-CoV diverged in 1986.
[37]
A path of evolution of the SARS virus and keen relationship with bats
have been proposed. The authors suggest that the coronaviruses have been
coevolved with bats for a long time and the ancestors of SARS-CoV first
infected the species of the genus
Hipposideridae, subsequently spread to species of the
Rhinolophidae and then to
civets, and finally to humans.
[38][39]
Alpaca coronavirus and human coronavirus 229E diverged before 1960.
[40]
Human coronaviruses
Illustration of SARSr-CoV virion
Coronaviruses vary significantly in risk factor. Some can kill more than 30% of those infected (such as
MERS-CoV), and some are relatively harmless, such as the common cold.
[19] Coronaviruses cause colds with major symptoms, such as
fever, and
sore throat from swollen
adenoids, occurring primarily in the winter and early spring seasons.
[41] Coronaviruses can cause
pneumonia (either direct
viral pneumonia or a secondary
bacterial pneumonia) and
bronchitis (either direct viral bronchitis or a secondary bacterial bronchitis).
[42] The much publicized human coronavirus discovered in 2003,
SARS-CoV, which causes
severe acute respiratory syndrome (SARS), has a unique pathogenesis because it causes both
upper and
lower respiratory tract infections.
[42]
Seven strains of human coronaviruses are known, of which four produce the generally mild symptoms of the
common cold:
- Human coronavirus OC43 (HCoV-OC43), Betacoronavirus
- Human coronavirus HKU1, Betacoronavirus, its genome has 75% similarity to OC43[43]
- Human coronavirus 229E (HCoV-229E), Alphacoronavirus
- Human coronavirus NL63 (HCoV-NL63, New Haven coronavirus), Alphacoronavirus
– and three, symptoms that are potentially severe:
- Middle East respiratory syndrome-related coronavirus (MERS-CoV), previously known as novel coronavirus 2012 and HCoV-EMC
- Severe acute respiratory syndrome coronavirus (SARS-CoV or "SARS-classic")
- Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), previously known as 2019-nCoV or "novel coronavirus 2019"
The coronaviruses HCoV-229E, -NL63, -OC43, and -HKU1 continually
circulate in the human population and cause respiratory infections in
adults and children world-wide.
[44]
Outbreaks of coronavirus-related diseases
Outbreaks of coronavirus types of relatively high mortality are as follows:
Severe acute respiratory syndrome (SARS)
Characteristics of patients who have been
infected with coronaviruses of the types
SARS-CoV-2, MERS-CoV, or SARS-CoV[50] (
)
|
SARS-CoV-2 |
MERS-CoV |
SARS-CoV
|
| Demographic
|
Date of first
identified case |
December
2019 |
June
2012 |
November
2002
|
Location of first
identified case |
Wuhan,
China |
Jeddah,
Saudi Arabia |
Shunde,
China
|
| Age average |
56[51] |
56 |
39.9
|
| Age range |
all ages |
14–94 |
1–91
|
| Male:female ratio |
1.6:1[51] |
3.3:1 |
1:1.25
|
| Confirmed cases |
713,171[49][a] |
2494 |
8096
|
| Deaths |
33,597[49][a] |
858 |
744
|
| Case fatality rate |
3.4% |
37% |
10%
|
| Health-care workers |
8%[52] |
9.8% |
23.1%
|
| Symptoms
|
| Fever |
87.9%[53] |
98% |
99–100%
|
| Dry cough |
67.7%[53] |
47% |
29–75%
|
| Dyspnea |
18.6%[53] |
72% |
40–42%
|
| Diarrhea |
3.7%[53] |
26% |
20–25%
|
| Sore throat |
13.9%[53] |
21% |
13–25%
|
| Ventilatory support |
4.1%[54] |
24.5%[55] |
14–20%
|
Notes
|
- Data as of 29 March 2020.
|
In 2003, following the outbreak of severe acute respiratory syndrome
(SARS) which had begun the prior year in Asia, and secondary cases
elsewhere in the world, the
World Health Organization
(WHO) issued a press release stating that a novel coronavirus
identified by a number of laboratories was the causative agent for SARS.
The virus was officially named the SARS coronavirus (SARS-CoV). More
than 8,000 people were infected, about ten percent of whom died.
[29]
Middle East respiratory syndrome (MERS)
In September 2012, a new type of coronavirus was identified,
initially called Novel Coronavirus 2012, and now officially named Middle
East respiratory syndrome coronavirus (MERS-CoV).
[56][57] The World Health Organization issued a global alert soon after.
[58] The WHO update on 28 September 2012 said the virus did not seem to pass easily from person to person.
[59]
However, on 12 May 2013, a case of human-to-human transmission in
France was confirmed by the French Ministry of Social Affairs and
Health.
[60] In addition, cases of human-to-human transmission were reported by the Ministry of Health in
Tunisia.
Two confirmed cases involved people who seemed to have caught the
disease from their late father, who became ill after a visit to Qatar
and Saudi Arabia. Despite this, it appears the virus had trouble
spreading from human to human, as most individuals who are infected do
not transmit the virus.
[61] By 30 October 2013, there were 124 cases and 52 deaths in Saudi Arabia.
[62]
After the Dutch
Erasmus Medical Centre
sequenced the virus, the virus was given a new name, Human
Coronavirus–Erasmus Medical Centre (HCoV-EMC). The final name for the
virus is Middle East respiratory syndrome coronavirus (MERS-CoV). In May
2014, the only two United States cases of MERS-CoV infection were
recorded, both occurring in healthcare workers who worked in Saudi
Arabia and then travelled to the U.S. One was treated in Indiana and one
in Florida. Both were hospitalized temporarily and then discharged.
[63]
In May 2015, an outbreak of MERS-CoV occurred in the
Republic of Korea,
when a man who had traveled to the Middle East, visited 4 hospitals in
the Seoul area to treat his illness. This caused one of the largest
outbreaks of MERS-CoV outside the Middle East.
[64]
As of December 2019, 2,468 cases of MERS-CoV infection had been
confirmed by laboratory tests, 851 of which were fatal, a mortality rate
of approximately 34.5%.
[65]
Coronavirus disease 2019 (COVID-19)
In December 2019, a pneumonia outbreak was reported in
Wuhan,
China.
[66] On 31 December 2019, the outbreak was traced to a novel strain of coronavirus,
[67] which was given the interim name 2019-nCoV by the
World Health Organization (WHO),
[68][69][70] later renamed
SARS-CoV-2 by the
International Committee on Taxonomy of Viruses. Some researchers have suggested that the
Huanan Seafood Wholesale Market may not be the original source of viral transmission to humans.
[71][72]
As of 29 March 2020, there have been at least 33,597
[49] confirmed deaths and more than 713,171
[49] confirmed cases in the
coronavirus pneumonia pandemic. The Wuhan strain has been identified as a new strain of
Betacoronavirus from group 2B with approximately 70% genetic similarity to the SARS-CoV.
[73] The virus has a 96% similarity to a bat coronavirus, so it is widely suspected to originate from bats as well.
[71][74]
The pandemic has resulted in travel restrictions and nationwide lockdowns in several countries.
Other animals
Coronaviruses have been recognized as causing pathological conditions in
veterinary medicine since the early 1970s. Except for
avian infectious bronchitis, the major related diseases have mainly an
intestinal location.
[75]
Diseases caused
Coronaviruses primarily infect the
upper respiratory and
gastrointestinal tract
of mammals and birds. They also cause a range of diseases in farm
animals and domesticated pets, some of which can be serious and are a
threat to the farming industry. In chickens, the
infectious bronchitis virus (IBV), a coronavirus, targets not only the respiratory tract but also the
urogenital tract. The virus can spread to different organs throughout the chicken.
[76] Economically significant coronaviruses of farm animals include
porcine coronavirus (
transmissible gastroenteritis coronavirus, TGE) and
bovine coronavirus, which both result in
diarrhea in young animals.
Feline coronavirus: two forms, feline enteric coronavirus is a pathogen of minor clinical significance, but spontaneous
mutation of this virus can result in
feline infectious peritonitis
(FIP), a disease associated with high mortality. Similarly, there are
two types of coronavirus that infect ferrets: Ferret enteric coronavirus
causes a gastrointestinal syndrome known as epizootic catarrhal
enteritis (ECE), and a more lethal systemic version of the virus (like
FIP in cats) known as ferret systemic coronavirus (FSC).
[77] There are two types of
canine coronavirus (CCoV), one that causes mild gastrointestinal disease and one that has been found to cause respiratory disease.
Mouse hepatitis virus (MHV) is a coronavirus that causes an epidemic
murine illness with high mortality, especially among colonies of laboratory mice.
[78]
Sialodacryoadenitis virus (SDAV) is highly infectious coronavirus of
laboratory rats, which can be transmitted between individuals by direct
contact and indirectly by aerosol. Acute infections have high
morbidity and
tropism for the salivary, lachrymal and
harderian glands.
[79]
A HKU2-related bat coronavirus called
swine acute diarrhea syndrome coronavirus (SADS-CoV) causes diarrhea in pigs.
[80]
Prior to the discovery of SARS-CoV, MHV had been the best-studied coronavirus both
in vivo and
in vitro
as well as at the molecular level. Some strains of MHV cause a
progressive demyelinating encephalitis in mice which has been used as a
murine model for
multiple sclerosis. Significant research efforts have been focused on elucidating the
viral pathogenesis of these animal coronaviruses, especially by
virologists interested in veterinary and
zoonotic diseases.
[81]
In domestic animals
Genomic cis-acting elements
In common with the genomes of all other RNA viruses, coronavirus genomes contain
cis-acting
RNA elements that ensure the specific replication of viral RNA by a
virally encoded RNA-dependent RNA polymerase. The embedded cis-acting
elements devoted to coronavirus replication constitute a small fraction
of the total genome, but this is presumed to be a reflection of the fact
that coronaviruses have the largest genomes of all RNA viruses. The
boundaries of cis-acting elements essential to replication are fairly
well-defined, and the
RNA secondary structures
of these regions are understood. However, how these cis-acting
structures and sequences interact with the viral replicase and host cell
components to allow RNA synthesis is not well understood.
[87][5]
Genome packaging
The assembly of infectious coronavirus particles requires the
selection of viral genomic RNA from a cellular pool that contains an
abundant excess of non-viral and viral RNAs. Among the seven to ten
specific viral mRNAs synthesized in virus-infected cells, only the
full-length genomic RNA is packaged efficiently into coronavirus
particles. Studies have revealed cis-acting elements and trans-acting
viral factors involved in the coronavirus genome
encapsidation
and packaging. Understanding the molecular mechanisms of genome
selection and packaging is critical for developing antiviral strategies
and viral expression vectors based on the coronavirus genome.
[87][5]
See also
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Further reading
 |
Look up coronavirus in Wiktionary, the free dictionary. |
- Alwan A, Mahjour J, Memish ZA (2013). "Novel coronavirus infection: time to stay ahead of the curve". Eastern Mediterranean Health Journal. 19 Suppl 1: S3-4. doi:10.26719/2013.19.supp1.S3. PMID 23888787.
- Laude H, Rasschaert D, Delmas B,
Godet M, Gelfi J, Charley B (June 1990). "Molecular biology of
transmissible gastroenteritis virus". Veterinary Microbiology. 23 (1–4): 147–54. doi:10.1016/0378-1135(90)90144-K. PMID 2169670.
- Sola I, Alonso S, Zúñiga S, Balasch M, Plana-Durán J, Enjuanes L (April 2003). "Engineering the transmissible gastroenteritis virus genome as an expression vector inducing lactogenic immunity". Journal of Virology. 77 (7): 4357–69. doi:10.1128/JVI.77.7.4357-4369.2003. PMC 150661. PMID 12634392.
- Tajima M (1970). "Morphology of transmissible gastroenteritis virus of pigs. A possible member of coronaviruses. Brief report". Archiv für die Gesamte Virusforschung. 29 (1): 105–8. doi:10.1007/BF01253886. PMID 4195092.
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