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Coronavirus

Subfamily of viruses in the family Coronaviridae
This article is about the group of viruses. For the specific coronavirus causing the 2019–20 coronavirus pandemic, see Severe acute respiratory syndrome coronavirus 2. For the disease caused by this strain, see Coronavirus disease 2019.
Orthocoronavirinae

Source:From Wikipedia, the free encyclopedia

Electron micrograph of avian infectious bronchitis virus

Illustration of the morphology of coronaviruses; the club-shaped viral spike peplomers, coloured red, create the look of a corona surrounding the virion, when viewed electron microscopically
Virus classification
(unranked): Virus
Realm: Riboviria
Phylum: incertae sedis
Order: Nidovirales
Family: Coronaviridae
Subfamily: Orthocoronavirinae
Genera[1]
Alphacoronavirus
Betacoronavirus
Gammacoronavirus
Deltacoronavirus
Synonyms

Coronavirinae

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 covering in club-shaped protein spikes.

Contents
1 Discovery
2 Etymology
3 Morphology
4 Replication
5 Transmission
6 Taxonomy
7 Evolution
8 Human coronaviruses
8.1 Coronavirus survival times and transmission efficiency in warm and wet air
8.2 Coronavirus survival times on stainless steel
9 Outbreaks of coronavirus-related diseases
9.1 Severe acute respiratory syndrome (SARS)
9.2 Middle East respiratory syndrome (MERS)
9.3 Coronavirus disease 2019 (COVID-19)
10 Other animals
10.1 Diseases caused
10.2 In domestic animals
11 Genomic cis-acting elements
12 Genome packaging
13 See also
14 References
15 Further reading

Discovery
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 ?????? kor?n?, “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.[citation needed] This morphology is created by the viral spike peplomers, which are proteins on the surface of the virus.
Morphology

Cross-sectional model of a coronavirus
Coronaviruses are large pleomorphic spherical particles with bulbous surface projections.[10] The diameter of the virus particles is around 120 nm.[11] The envelope of the virus in electron micrographs appears as a distinct pair of electron dense shells.[12]
The viral envelope consists of a lipid bilayer where the membrane (M), envelope (E) and spike (S) structural proteins are anchored.[13] 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.[11][14] The genome size for coronaviruses ranges from approximately 27 to 34 kilobases.[7] The lipid bilayer envelope, membrane proteins, and nucleocapsid protect the virus when it is outside the host cell.[15]
Replication

The infection cycle of a coronavirus
Infection begins when the virus enters the host organism and the spike protein 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 cell entry through endocytosis or direct fusion of the viral envelop with the host membrane.[16]
On entry into the host cell, the virus particle is uncoated, and its genome enters the cell cytoplasm.[17] 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.[18] 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]
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.[20]
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]
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.[21] Progeny viruses are then released from the host cell by exocytosis through secretory vesicles.[21]
Transmission
Human to human transmission of coronaviruses is primarily thought to occur among close contacts via respiratory droplets generated by sneezing and coughing.[22] 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.[23][24] The SARS coronavirus, for example, infects human cells by attaching to the angiotensin-converting enzyme 2 (ACE2) receptor.[25]
Taxonomy
For a more detailed list of members, see Coronaviridae.

Phylogenetic tree of coronaviruses
The scientific name for coronavirus is Orthocoronavirinae or Coronavirinae.[2][3][4] Coronavirus belongs to the family of Coronaviridae.
Genus: Alphacoronavirus
Species: Human coronavirus 229E, Human coronavirus NL63, Miniopterus bat coronavirus 1, Miniopterus bat coronavirus HKU8, Porcine epidemic diarrhea virus, Rhinolophus bat coronavirus HKU2, Scotophilus bat coronavirus 512
Genus Betacoronavirus; type species: Murine coronavirus
Species: Betacoronavirus 1, Human coronavirus HKU1, Murine coronavirus, Pipistrellus bat coronavirus HKU5, Rousettus bat coronavirus HKU9, Severe acute respiratory syndrome-related coronavirus, Severe acute respiratory syndrome coronavirus 2, Tylonycteris bat coronavirus HKU4, Middle East respiratory syndrome-related coronavirus, Human coronavirus OC43, Hedgehog coronavirus 1 (EriCoV)
Genus Gammacoronavirus; type species: Infectious bronchitis virus
Species: Beluga whale coronavirus SW1, Infectious bronchitis virus
Genus Deltacoronavirus; type species: Bulbul coronavirus HKU11
Species: Bulbul coronavirus HKU11, Porcine coronavirus HKU15
Evolution
The most recent common ancestor (MRCA) of all coronaviruses has been placed at around 8000 BCE.[26] 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.[27]
Bovine coronavirus and canine respiratory coronaviruses diverged from a common ancestor in 1951.[28] 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.[29]
The MRCA of human coronavirus OC43 has been dated to the 1950s.[30]
MERS-CoV, although related to several bat coronavirus species, appears to have diverged from these several centuries ago.[31] The human coronavirus NL63 and a bat coronavirus shared an MRCA 563–822 years ago.[32]
The most closely related bat coronavirus and SARS-CoV diverged in 1986.[33] 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.[34][35]
Alpaca coronavirus and human coronavirus 229E diverged before 1960.[36]
Human coronaviruses
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.[37] Coronaviruses can cause pneumonia (either direct viral pneumonia or a secondary bacterial pneumonia) and bronchitis (either direct viral bronchitis or a secondary bacterial bronchitis).[38] 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.[38]
Seven strains of human coronaviruses are known:
Human coronavirus 229E (HCoV-229E)
Human coronavirus OC43 (HCoV-OC43)
Severe acute respiratory syndrome coronavirus (SARS-CoV)
Human coronavirus NL63 (HCoV-NL63, New Haven coronavirus)
Human coronavirus HKU1
Middle East respiratory syndrome-related coronavirus (MERS-CoV), previously known as novel coronavirus 2012 and HCoV-EMC
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.[39]
Coronavirus survival times and transmission efficiency in warm and wet air

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