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Coronavirus

May 20, 2023

This article is about the group of viruses. For the disease involved in the ongoing COVID-19 pandemic, see COVID-19. For the virus that causes this disease, see SARS-CoV-2.

Coronaviruses are a group of related RNA viruses that cause diseases in mammals and birds. In humans and birds, they cause respiratory tract infections that can range from mild to lethal. Mild illnesses in humans include some cases of the common cold (which is also caused by other viruses, predominantly rhinoviruses), while more lethal varieties can cause SARS, MERS and COVID-19, which is causing the ongoing pandemic. In cows and pigs they cause diarrhea, while in mice they cause hepatitis and encephalomyelitis.

Orthocoronavirinae
Group member SARS-CoV-2
  •   Blue: lipid bilayer envelope
      Light blue: spike (S) glycoprotein
      Red: envelope (E) proteins
      Green: membrane (M) proteins .
      Orange: glycan
Virus classification
(unranked): Virus
Realm: Riboviria
Kingdom: Orthornavirae
Phylum: Pisuviricota
Class: Pisoniviricetes
Order: Nidovirales
Family: Coronaviridae
Subfamily: Orthocoronavirinae
Genera[1]
Synonyms[2][3]
  • Coronavirinae

Coronaviruses constitute the subfamily Orthocoronavirinae, in the family Coronaviridae, order Nidovirales and realm Riboviria.[3][4] They are enveloped viruses with a positive-sense single-stranded RNA genome and a nucleocapsid of helical symmetry.[5] The genome size of coronaviruses ranges from approximately 26 to 32 kilobases, one of the largest among RNA viruses.[6] They have characteristic club-shaped spikes that project from their surface, which in electron micrographs create an image reminiscent of the stellar corona, from which their name derives.[7]

Etymology

The name "coronavirus" is derived from Latin corona, meaning "crown" or "wreath", itself a borrowing from Greek κορώνη korṓnē, "garland, wreath".[8][9] The name was coined by June Almeida and David Tyrrell who first observed and studied human coronaviruses.[10] The word was first used in print in 1968 by an informal group of virologists in the journal Nature to designate the new family of viruses.[7] 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 the solar corona or halo.[7][10] This morphology is created by the viral spike peplomers, which are proteins on the surface of the virus.[11]

The scientific name Coronavirus was accepted as a genus name by the International Committee for the Nomenclature of Viruses (later renamed International Committee on Taxonomy of Viruses) in 1971.[12] As the number of new species increased, the genus was split into four genera, namely Alphacoronavirus, Betacoronavirus, Deltacoronavirus, and Gammacoronavirus in 2009.[13] The common name coronavirus is used to refer to any member of the subfamily Orthocoronavirinae.[4] As of 2020, 45 species are officially recognised.[14]

History

Main article: History of coronavirus
 
Colorized transmission electron micrograph of coronavirus 229E

The earliest reports of a coronavirus infection in animals occurred in the late 1920s, when an acute respiratory infection of domesticated chickens emerged in North America.[15] Arthur Schalk and M.C. Hawn in 1931 made the first detailed report which described a new respiratory infection of chickens in North Dakota. The infection of new-born chicks was characterized by gasping and listlessness with high mortality rates of 40–90%.[16] Leland David Bushnell and Carl Alfred Brandly isolated the virus that caused the infection in 1933.[17] The virus was then known as infectious bronchitis virus (IBV). Charles D. Hudson and Fred Robert Beaudette cultivated the virus for the first time in 1937.[18] The specimen came to be known as the Beaudette strain. In the late 1940s, two more animal coronaviruses, JHM that causes brain disease (murine encephalitis) and mouse hepatitis virus (MHV) that causes hepatitis in mice were discovered.[19] It was not realized at the time that these three different viruses were related.[20][12]

Human coronaviruses were discovered in the 1960s[21][22] using two different methods in the United Kingdom and the United States.[23] E.C. Kendall, Malcolm Bynoe, and David Tyrrell working at the Common Cold Unit of the British Medical Research Council collected a unique common cold virus designated B814 in 1961.[24][25][26] The virus could not be cultivated using standard techniques which had successfully cultivated rhinoviruses, adenoviruses and other known common cold viruses. In 1965, Tyrrell and Bynoe successfully cultivated the novel virus by serially passing it through organ culture of human embryonic trachea.[27] The new cultivating method was introduced to the lab by Bertil Hoorn.[28] The isolated virus when intranasally inoculated into volunteers caused a cold and was inactivated by ether which indicated it had a lipid envelope.[24][29] Dorothy Hamre[30] and John Procknow at the University of Chicago isolated a novel cold from medical students in 1962. They isolated and grew the virus in kidney tissue culture, designating it 229E. The novel virus caused a cold in volunteers and, like B814, was inactivated by ether.[31]

 
Transmission electron micrograph of organ cultured coronavirus OC43

Scottish virologist June Almeida at St Thomas' Hospital in London, collaborating with Tyrrell, compared the structures of IBV, B814 and 229E in 1967.[32][33] Using electron microscopy the three viruses were shown to be morphologically related by their general shape and distinctive club-like spikes.[34] A research group at the National Institute of Health the same year was able to isolate another member of this new group of viruses using organ culture and named one of the samples OC43 (OC for organ culture).[35] Like B814, 229E, and IBV, the novel cold virus OC43 had distinctive club-like spikes when observed with the electron microscope.[36][37]

The IBV-like novel cold viruses were soon shown to be also morphologically related to the mouse hepatitis virus.[19] This new group of viruses were named coronaviruses after their distinctive morphological appearance.[7] Human coronavirus 229E and human coronavirus OC43 continued to be studied in subsequent decades.[38][39] The coronavirus strain B814 was lost. It is not known which present human coronavirus it was.[40] Other human coronaviruses have since been identified, including SARS-CoV in 2003, HCoV NL63 in 2003, HCoV HKU1 in 2004, MERS-CoV in 2013, and SARS-CoV-2 in 2019.[41] There have also been a large number of animal coronaviruses identified since the 1960s.[42]

Microbiology

Structure

 
Structure of a coronavirus

Coronaviruses are large, roughly spherical particles with unique surface projections.[43] Their size is highly variable with average diameters of 80 to 120 nm. Extreme sizes are known from 50 to 200 nm in diameter.[44] The total molecular mass is on average 40,000 kDa. They are enclosed in an envelope embedded with a number of protein molecules.[45] The lipid bilayer envelope, membrane proteins, and nucleocapsid protect the virus when it is outside the host cell.[46]

The viral envelope is made up of a lipid bilayer in which the membrane (M), envelope (E) and spike (S) structural proteins are anchored.[47] The molar ratio of E:S:M in the lipid bilayer is approximately 1:20:300.[48] The E and M protein are the structural proteins that combined with the lipid bilayer to shape the viral envelope and maintain its size.[49] S proteins are needed for interaction with the host cells. But human coronavirus NL63 is peculiar in that its M protein has the binding site for the host cell, and not its S protein.[50] The diameter of the envelope is 85 nm. The envelope of the virus in electron micrographs appears as a distinct pair of electron-dense shells (shells that are relatively opaque to the electron beam used to scan the virus particle).[51][49]

The M protein is the main structural protein of the envelope that provides the overall shape and is a type III membrane protein. It consists of 218 to 263 Amino acid residues and forms a layer 7.8 nm thick.[45] It has three domains, a short N-terminal ectodomain, a triple-spanning transmembrane domain, and a C-terminal endodomain. The C-terminal domain forms a matrix-like lattice that adds to the extra-thickness of the envelope. Different species can have either N- or O-linked glycans in their protein amino-terminal domain. The M protein is crucial during the assembly, budding, envelope formation, and pathogenesis stages of the virus lifecycle.[52]

The E proteins are minor structural proteins and highly variable in different species.[44] There are only about 20 copies of the E protein molecule in a coronavirus particle.[48] They are 8.4 to 12 kDa in size and are composed of 76 to 109 amino acids.[44] They are integral proteins (i.e. embedded in the lipid layer) and have two domains namely a transmembrane domain and an extramembrane C-terminal domain. They are almost fully α-helical, with a single α-helical transmembrane domain, and form pentameric (five-molecular) ion channels in the lipid bilayer. They are responsible for virion assembly, intracellular trafficking and morphogenesis (budding).[45]

 
Diagram of the genome and functional domains of the S protein for SARS-CoV and MERS-CoV

The spikes are the most distinguishing feature of coronaviruses and are responsible for the corona- or halo-like surface. On average a coronavirus particle has 74 surface spikes.[53] Each spike is about 20 nm long and is composed of a trimer of the S protein. The S protein is in turn composed of an S1 and S2 subunit. The homotrimeric S protein is a class I fusion protein which mediates the receptor binding and membrane fusion between the virus and host cell. The S1 subunit forms the head of the spike and has the receptor-binding domain (RBD). The S2 subunit forms the stem which anchors the spike in the viral envelope and on protease activation enables fusion. The two subunits remain noncovalently linked as they are exposed on the viral surface until they attach to the host cell membrane.[45] In a functionally active state, three S1 are attached to two S2 subunits. The subunit complex is split into individual subunits when the virus binds and fuses with the host cell under the action of proteases such as cathepsin family and transmembrane protease serine 2 (TMPRSS2) of the host cell.[54]

 
After binding of the ACE2 receptor, SARS-CoV spike is activated and cleaved at the S1/S2 level

S1 proteins are the most critical components in terms of infection. They are also the most variable components as they are responsible for host cell specificity. They possess two major domains named N-terminal domain (S1-NTD) and C-terminal domain (S1-CTD), both of which serve as the receptor-binding domains. The NTDs recognize and bind sugars on the surface of the host cell. An exception is the MHV NTD that binds to a protein receptor carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1). S1-CTDs are responsible for recognizing different protein receptors such as angiotensin-converting enzyme 2 (ACE2), aminopeptidase N (APN), and dipeptidyl peptidase 4 (DPP4).[45]

A subset of coronaviruses (specifically the members of betacoronavirus subgroup A) also has a shorter spike-like surface protein called hemagglutinin esterase (HE).[42] The HE proteins occur as homodimers composed of about 400 amino acid residues and are 40 to 50 kDa in size. They appear as tiny surface projections of 5 to 7 nm long embedded in between the spikes. They help in the attachment to and detachment from the host cell.[55]

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.[49][56] N protein is a phosphoprotein of 43 to 50 kDa in size, and is divided into three conserved domains. The majority of the protein is made up of domains 1 and 2, which are typically rich in arginines and lysines. Domain 3 has a short carboxy terminal end and has a net negative charge due to excess of acidic over basic amino acid residues.[44]

Genome

See also: Severe acute respiratory syndrome–related coronavirus § Genome
 
SARS-CoV genome and proteins

Coronaviruses contain a positive-sense, single-stranded RNA genome. The genome size for coronaviruses ranges from 26.4 to 31.7 kilobases.[6] The genome size is one of the largest among RNA viruses. The genome has a 5′ methylated cap and a 3′ polyadenylated tail.[49]

The genome organization for a coronavirus is 5′-leader-UTR-replicase (ORF1ab)-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 polyprotein (pp1ab). The replicase polyprotein self cleaves to form 16 nonstructural proteins (nsp1–nsp16).[49]

The later reading frames encode the four major structural proteins: spike, envelope, membrane, and nucleocapsid.[57] 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.[49]

Replication cycle

Cell entry

 
The life cycle of a coronavirus

Infection begins when the viral 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 the virus to enter the host cell by endocytosis or direct fusion of the viral envelope with the host membrane.[58]

Coronaviruses can enter cells by either fusing to their lipid envelope with the cell membrane on the cell surface or by internalization via endocytosis.[59]

Genome translation

On entry into the host cell, the virus particle is uncoated, and its genome enters the cell cytoplasm. The coronavirus RNA genome has a 5′ methylated cap and a 3′ polyadenylated tail, which allows it to act like a messenger RNA and be directly translated by the host cell's ribosomes. The host ribosomes translate the initial overlapping open reading frames ORF1a and ORF1b of the virus genome into two large overlapping polyproteins, pp1a and pp1ab.[49]

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.[60] The ribosomal frameshift allows for the continuous translation of ORF1a followed by ORF1b.[49]

The polyproteins have their own proteases, PLpro (nsp3) and 3CLpro (nsp5), 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 (nsp12), RNA helicase (nsp13), and exoribonuclease (nsp14).[49]

Replicase-transcriptase

 
Replicase-transcriptase complex

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 nonstructural protein, for instance, provides extra fidelity to replication by providing a proofreading function which the RNA-dependent RNA polymerase lacks.[61]

Replication – 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.[49]

 
Transcription of nested mRNAs
 
Nested set of subgenomic mRNAs

Transcription – 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 process is followed by the transcription of these negative-sense subgenomic RNA molecules to their corresponding positive-sense mRNAs.[49] The subgenomic mRNAs form a "nested set" which have a common 5'-head and partially duplicate 3'-end.[62]

Recombination – The replicase-transcriptase complex is also capable of genetic recombination when at least two viral genomes are present in the same infected cell.[62] RNA recombination appears to be a major driving force in determining genetic variability within a coronavirus species, the capability of a coronavirus species to jump from one host to another and, infrequently, in determining the emergence of novel coronaviruses.[63] The exact mechanism of recombination in coronaviruses is unclear, but likely involves template switching during genome replication.[63]

Assembly and 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 many accessory proteins.[49] 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 the assembly of viruses following its binding to the nucleocapsid. Progeny viruses are then released from the host cell by exocytosis through secretory vesicles. Once released the viruses can infect other host cells.[64]

Transmission

Infected carriers are able to shed viruses into the environment. The interaction of the coronavirus spike protein with its complementary cell receptor is central in determining the tissue tropism, infectivity, and species range of the released virus.[65][66] Coronaviruses mainly target epithelial cells.[42] They are transmitted from one host to another host, depending on the coronavirus species, by either an aerosol, fomite, or fecal-oral route.[67]

Human coronaviruses infect the epithelial cells of the respiratory tract, while animal coronaviruses generally infect the epithelial cells of the digestive tract.[42] SARS coronavirus, for example, infects the human epithelial cells of the lungs via an aerosol route[68] by binding to the angiotensin-converting enzyme 2 (ACE2) receptor.[69] Transmissible gastroenteritis coronavirus (TGEV) infects the pig epithelial cells of the digestive tract via a fecal-oral route[67] by binding to the Alanine aminopeptidase (APN) receptor.[49]

Classification

For a more detailed list of members, see Coronaviridae.
 
Phylogenetic tree of coronaviruses

Coronaviruses form the subfamily Orthocoronavirinae,[2][3][4] which is one of two sub-families in the family Coronaviridae, order Nidovirales, and realm Riboviria.[42][70] They are divided into the four genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus and Deltacoronavirus. Alphacoronaviruses and betacoronaviruses infect mammals, while gammacoronaviruses and deltacoronaviruses primarily infect birds.[71][72]

Origin

 
Origins of human coronaviruses with possible intermediate hosts

The most recent common ancestor (MRCA) of all coronaviruses is estimated to have existed as recently as 8000 BCE, although some models place the common ancestor as far back as 55 million years or more, implying long term coevolution with bat and avian species.[73] The most recent common ancestor of the alphacoronavirus line has been placed at about 2400 BCE, of the betacoronavirus line at 3300 BCE, of the gammacoronavirus line at 2800 BCE, and the deltacoronavirus line at about 3000 BCE. Bats and birds, as warm-blooded flying vertebrates, are an ideal natural reservoir for the coronavirus gene pool (with bats the reservoir for alphacoronaviruses and betacoronavirus – and birds the reservoir for gammacoronaviruses and deltacoronaviruses). The large number and global range of bat and avian species that host viruses have enabled extensive evolution and dissemination of coronaviruses.[74]

Many human coronaviruses have their origin in bats.[75] The human coronavirus NL63 shared a common ancestor with a bat coronavirus (ARCoV.2) between 1190 and 1449 CE.[76] The human coronavirus 229E shared a common ancestor with a bat coronavirus (GhanaGrp1 Bt CoV) between 1686 and 1800 CE.[77] More recently, alpaca coronavirus and human coronavirus 229E diverged sometime before 1960.[78] MERS-CoV emerged in humans from bats through the intermediate host of camels.[79] MERS-CoV, although related to several bat coronavirus species, appears to have diverged from these several centuries ago.[80] The most closely related bat coronavirus and SARS-CoV diverged in 1986.[81] The ancestors of SARS-CoV first infected leaf-nose bats of the genus Hipposideridae; subsequently, they spread to horseshoe bats in the species Rhinolophidae, then to Asian palm civets, and finally to humans.[82][83]

Unlike other betacoronaviruses, bovine coronavirus of the species Betacoronavirus 1 and subgenus Embecovirus is thought to have originated in rodents and not in bats.[75][84] In the 1790s, equine coronavirus diverged from the bovine coronavirus after a cross-species jump.[85] Later in the 1890s, human coronavirus OC43 diverged from bovine coronavirus after another cross-species spillover event.[86][85] It is speculated that the flu pandemic of 1890 may have been caused by this spillover event, and not by the influenza virus, because of the related timing, neurological symptoms, and unknown causative agent of the pandemic.[87] Besides causing respiratory infections, human coronavirus OC43 is also suspected of playing a role in neurological diseases.[88] In the 1950s, the human coronavirus OC43 began to diverge into its present genotypes.[89] Phylogenetically, mouse hepatitis virus (Murine coronavirus), which infects the mouse's liver and central nervous system,[90] is related to human coronavirus OC43 and bovine coronavirus. Human coronavirus HKU1, like the aforementioned viruses, also has its origins in rodents.[75]

Infection in humans

 
Transmission and life-cycle of SARS-CoV-2 causing COVID-19

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.[49] Coronaviruses can cause colds with major symptoms, such as fever, and a sore throat from swollen adenoids.[91] Coronaviruses can cause pneumonia (either direct viral pneumonia or secondary bacterial pneumonia) and bronchitis (either direct viral bronchitis or secondary bacterial bronchitis).[92] The 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.[92]

Six species of human coronaviruses are known, with one species subdivided into two different strains, making seven strains of human coronaviruses altogether.

 
Seasonal distribution of HCoV-NL63 in Germany shows a preferential detection from November to March

Four human coronaviruses produce symptoms that are generally mild, even though it is contended they might have been more aggressive in the past:[93]

  1. Human coronavirus OC43 (HCoV-OC43), β-CoV
  2. Human coronavirus HKU1 (HCoV-HKU1), β-CoV
  3. Human coronavirus 229E (HCoV-229E), α-CoV
  4. Human coronavirus NL63 (HCoV-NL63), α-CoV–

Three human coronaviruses produce potentially severe symptoms:

  1. Severe acute respiratory syndrome coronavirus (SARS-CoV), β-CoV (identified in 2003)
  2. Middle East respiratory syndrome-related coronavirus (MERS-CoV), β-CoV (identified in 2012)
  3. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), β-CoV (identified in 2019)

These cause the diseases commonly called SARS, MERS, and COVID-19 respectively.

Common cold

Main article: Common cold

Although the common cold is usually caused by rhinoviruses,[94] in about 15% of cases the cause is a coronavirus.[95] The human coronaviruses HCoV-OC43, HCoV-HKU1, HCoV-229E, and HCoV-NL63 continually circulate in the human population in adults and children worldwide and produce the generally mild symptoms of the common cold.[88] The four mild coronaviruses have a seasonal incidence occurring in the winter months in temperate climates.[96][97] There is no preponderance in any season in tropical climates.[98]

Severe acute respiratory syndrome (SARS)

Main article: SARS
Characteristics of zoonotic coronavirus strains
MERS-CoV, SARS-CoV, SARS-CoV-2,
and related diseases
MERS-CoV SARS-CoV SARS-CoV-2
Disease MERS SARS COVID-19
Outbreaks 2012, 2015,
2018		 2002–2004 2019–2021
pandemic
Epidemiology
Date of first
identified case		 June
2012		 November
2002		 December
2019[99]
Location of first
identified case		 Jeddah,
Saudi Arabia		 Shunde,
China		 Wuhan,
China
Age average 56 44[100][a] 56[101]
Sex ratio (M:F) 3.3:1 0.8:1[102] 1.6:1[101]
Confirmed cases 2494 8096[103] 676,609,955[104][b]
Deaths 858 774[103] 6,881,955[104][b]
Case fatality rate 37% 9.2% 1.02%[104]
Symptoms
Fever 98% 99–100% 87.9%[105]
Dry cough 47% 29–75% 67.7%[105]
Dyspnea 72% 40–42% 18.6%[105]
Diarrhea 26% 20–25% 3.7%[105]
Sore throat 21% 13–25% 13.9%[105]
Ventilatory use 24.5%[106] 14–20% 4.1%[107]
Notes
  1. ^ Based on data from Hong Kong.
  2. ^ a b Data as of 10 March 2023.

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 several laboratories was the causative agent for SARS. The virus was officially named the SARS coronavirus (SARS-CoV). More than 8,000 people from 29 countries and territories were infected, and at least 774 died.[108][69]

Middle East respiratory syndrome (MERS)

Main article: 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).[109][110] The World Health Organization issued a global alert soon after.[111] The WHO update on 28 September 2012 said the virus did not seem to pass easily from person to person.[112] 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.[113] 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.[114] By 30 October 2013, there were 124 cases and 52 deaths in Saudi Arabia.[115]

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). The only U.S. cases (both survived) were recorded in May 2014.[116]

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 four hospitals in the Seoul area to treat his illness. This caused one of the largest outbreaks of MERS-CoV outside the Middle East.[117] 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%.[118]

Coronavirus disease 2019 (COVID-19)

Main article: COVID-19

In December 2019, a pneumonia outbreak was reported in Wuhan, China.[119] On 31 December 2019, the outbreak was traced to a novel strain of coronavirus,[120] which was given the interim name 2019-nCoV by the World Health Organization,[121][122][123] later renamed SARS-CoV-2 by the International Committee on Taxonomy of Viruses.

As of 10 March 2023, there have been at least 6,881,955[104] confirmed deaths and more than 676,609,955[104] confirmed cases in the COVID-19 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.[124] The virus has a 96% similarity to a bat coronavirus, so it is widely suspected to originate from bats as well.[125][126]

Coronavirus HuPn-2018

Main article: Canine coronavirus HuPn-2018

During a surveillance study of archived samples of Malaysian viral pneumonia patients, virologists identified a strain of canine coronavirus which has infected humans in 2018.

Infection in animals

Coronaviruses have been recognized as causing pathological conditions in veterinary medicine since the 1930s.[19] They infect a range of animals including swine, cattle, horses, camels, cats, dogs, rodents, birds and bats.[127] The majority of animal related coronaviruses infect the intestinal tract and are transmitted by a fecal-oral route.[128] Significant research efforts have been focused on elucidating the viral pathogenesis of these animal coronaviruses, especially by virologists interested in veterinary and zoonotic diseases.[129]

Farm animals

Coronaviruses infect domesticated birds.[130] Infectious bronchitis virus (IBV), a type of coronavirus, causes avian infectious bronchitis.[131] The virus is of concern to the poultry industry because of the high mortality from infection, its rapid spread, and its effect on production.[127] The virus affects both meat production and egg production and causes substantial economic loss.[132] In chickens, infectious bronchitis virus targets not only the respiratory tract but also the urogenital tract. The virus can spread to different organs throughout the chicken.[131] The virus is transmitted by aerosol and food contaminated by feces. Different vaccines against IBV exist and have helped to limit the spread of the virus and its variants.[127] Infectious bronchitis virus is one of a number of strains of the species Avian coronavirus.[133] Another strain of avian coronavirus is turkey coronavirus (TCV) which causes enteritis in turkeys.[127]

Coronaviruses also affect other branches of animal husbandry such as pig farming and the Cattle raising.[127] Swine acute diarrhea syndrome coronavirus (SADS-CoV), which is related to bat coronavirus HKU2, causes diarrhea in pigs.[134] Porcine epidemic diarrhea virus (PEDV) is a coronavirus that has recently emerged and similarly causes diarrhea in pigs.[135] Transmissible gastroenteritis virus (TGEV), which is a member of the species Alphacoronavirus 1,[136] is another coronavirus that causes diarrhea in young pigs.[137][138] In the cattle industry bovine coronavirus (BCV), which is a member of the species Betacoronavirus 1 and related to HCoV-OC43,[139] is responsible for severe profuse enteritis in young calves.[127]

Domestic pets

Coronaviruses infect domestic pets such as cats, dogs, and ferrets.[130] There are two forms of feline coronavirus which are both members of the species Alphacoronavirus 1.[136] 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 with high mortality.[127] There are two different coronaviruses that infect dogs. Canine coronavirus (CCoV), which is a member of the species Alphacoronavirus 1,[136] causes mild gastrointestinal disease.[127] Canine respiratory coronavirus (CRCoV), which is a member of the species Betacoronavirus 1 and related to HCoV-OC43,[139] cause respiratory disease.[127] Similarly, there are two types of coronavirus that infect ferrets.[140] 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).[141][142]

Laboratory animals

Coronaviruses infect laboratory animals.[127] Mouse hepatitis virus (MHV), which is a member of the species Murine coronavirus,[143] causes an epidemic murine illness with high mortality, especially among colonies of laboratory mice.[144] Prior to the discovery of SARS-CoV, MHV was 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.[129] Sialodacryoadenitis virus (SDAV), which is a strain of the species Murine coronavirus,[143] is highly infectious coronavirus of laboratory rats, which can be transmitted between individuals by direct contact and indirectly by aerosol. Rabbit enteric coronavirus causes acute gastrointestinal disease and diarrhea in young European rabbits.[127] Mortality rates are high.[145]

Prevention and treatment

A number of vaccines using different methods have been developed against human coronavirus SARS-CoV-2.[146][147] Antiviral targets against human coronaviruses have also been identified such as viral proteases, polymerases, and entry proteins. Drugs are in development which target these proteins and the different steps of viral replication.[148][147]

Vaccines are available for animal coronaviruses IBV, TGEV, and Canine CoV, although their effectiveness is limited. In the case of outbreaks of highly contagious animal coronaviruses, such as PEDV, measures such as destruction of entire herds of pigs may be used to prevent transmission to other herds.[49]

See also

References

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Further reading

 
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May 20, 2023
coronavirus, this, article, about, group, viruses, disease, involved, ongoing, covid, pandemic, covid, virus, that, causes, this, disease, sars, group, related, viruses, that, cause, diseases, mammals, birds, humans, birds, they, cause, respiratory, tract, inf. This article is about the group of viruses For the disease involved in the ongoing COVID 19 pandemic see COVID 19 For the virus that causes this disease see SARS CoV 2 Coronaviruses are a group of related RNA viruses that cause diseases in mammals and birds In humans and birds they cause respiratory tract infections that can range from mild to lethal Mild illnesses in humans include some cases of the common cold which is also caused by other viruses predominantly rhinoviruses while more lethal varieties can cause SARS MERS and COVID 19 which is causing the ongoing pandemic In cows and pigs they cause diarrhea while in mice they cause hepatitis and encephalomyelitis OrthocoronavirinaeGroup member SARS CoV 2 Blue lipid bilayer envelope Light blue spike S glycoprotein Red envelope E proteins Green membrane M proteins Orange glycanVirus classification unranked VirusRealm RiboviriaKingdom OrthornaviraePhylum PisuviricotaClass PisoniviricetesOrder NidoviralesFamily CoronaviridaeSubfamily OrthocoronavirinaeGenera 1 AlphacoronavirusBetacoronavirusGammacoronavirusDeltacoronavirusSynonyms 2 3 CoronavirinaeCoronaviruses constitute the subfamily Orthocoronavirinae in the family Coronaviridae order Nidovirales and realm Riboviria 3 4 They are enveloped viruses with a positive sense single stranded RNA genome and a nucleocapsid of helical symmetry 5 The genome size of coronaviruses ranges from approximately 26 to 32 kilobases one of the largest among RNA viruses 6 They have characteristic club shaped spikes that project from their surface which in electron micrographs create an image reminiscent of the stellar corona from which their name derives 7 Contents 1 Etymology 2 History 3 Microbiology 3 1 Structure 3 2 Genome 3 3 Replication cycle 3 3 1 Cell entry 3 3 2 Genome translation 3 3 3 Replicase transcriptase 3 3 4 Assembly and release 3 4 Transmission 4 Classification 5 Origin 6 Infection in humans 6 1 Common cold 6 2 Severe acute respiratory syndrome SARS 6 3 Middle East respiratory syndrome MERS 6 4 Coronavirus disease 2019 COVID 19 6 5 Coronavirus HuPn 2018 7 Infection in animals 7 1 Farm animals 7 2 Domestic pets 7 3 Laboratory animals 8 Prevention and treatment 9 See also 10 References 11 Further readingEtymologyThe name coronavirus is derived from Latin corona meaning crown or wreath itself a borrowing from Greek korwnh korṓne garland wreath 8 9 The name was coined by June Almeida and David Tyrrell who first observed and studied human coronaviruses 10 The word was first used in print in 1968 by an informal group of virologists in the journal Nature to designate the new family of viruses 7 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 the solar corona or halo 7 10 This morphology is created by the viral spike peplomers which are proteins on the surface of the virus 11 The scientific name Coronavirus was accepted as a genus name by the International Committee for the Nomenclature of Viruses later renamed International Committee on Taxonomy of Viruses in 1971 12 As the number of new species increased the genus was split into four genera namely Alphacoronavirus Betacoronavirus Deltacoronavirus and Gammacoronavirus in 2009 13 The common name coronavirus is used to refer to any member of the subfamily Orthocoronavirinae 4 As of 2020 45 species are officially recognised 14 HistoryMain article History of coronavirus Colorized transmission electron micrograph of coronavirus 229E The earliest reports of a coronavirus infection in animals occurred in the late 1920s when an acute respiratory infection of domesticated chickens emerged in North America 15 Arthur Schalk and M C Hawn in 1931 made the first detailed report which described a new respiratory infection of chickens in North Dakota The infection of new born chicks was characterized by gasping and listlessness with high mortality rates of 40 90 16 Leland David Bushnell and Carl Alfred Brandly isolated the virus that caused the infection in 1933 17 The virus was then known as infectious bronchitis virus IBV Charles D Hudson and Fred Robert Beaudette cultivated the virus for the first time in 1937 18 The specimen came to be known as the Beaudette strain In the late 1940s two more animal coronaviruses JHM that causes brain disease murine encephalitis and mouse hepatitis virus MHV that causes hepatitis in mice were discovered 19 It was not realized at the time that these three different viruses were related 20 12 Human coronaviruses were discovered in the 1960s 21 22 using two different methods in the United Kingdom and the United States 23 E C Kendall Malcolm Bynoe and David Tyrrell working at the Common Cold Unit of the British Medical Research Council collected a unique common cold virus designated B814 in 1961 24 25 26 The virus could not be cultivated using standard techniques which had successfully cultivated rhinoviruses adenoviruses and other known common cold viruses In 1965 Tyrrell and Bynoe successfully cultivated the novel virus by serially passing it through organ culture of human embryonic trachea 27 The new cultivating method was introduced to the lab by Bertil Hoorn 28 The isolated virus when intranasally inoculated into volunteers caused a cold and was inactivated by ether which indicated it had a lipid envelope 24 29 Dorothy Hamre 30 and John Procknow at the University of Chicago isolated a novel cold from medical students in 1962 They isolated and grew the virus in kidney tissue culture designating it 229E The novel virus caused a cold in volunteers and like B814 was inactivated by ether 31 Transmission electron micrograph of organ cultured coronavirus OC43 Scottish virologist June Almeida at St Thomas Hospital in London collaborating with Tyrrell compared the structures of IBV B814 and 229E in 1967 32 33 Using electron microscopy the three viruses were shown to be morphologically related by their general shape and distinctive club like spikes 34 A research group at the National Institute of Health the same year was able to isolate another member of this new group of viruses using organ culture and named one of the samples OC43 OC for organ culture 35 Like B814 229E and IBV the novel cold virus OC43 had distinctive club like spikes when observed with the electron microscope 36 37 The IBV like novel cold viruses were soon shown to be also morphologically related to the mouse hepatitis virus 19 This new group of viruses were named coronaviruses after their distinctive morphological appearance 7 Human coronavirus 229E and human coronavirus OC43 continued to be studied in subsequent decades 38 39 The coronavirus strain B814 was lost It is not known which present human coronavirus it was 40 Other human coronaviruses have since been identified including SARS CoV in 2003 HCoV NL63 in 2003 HCoV HKU1 in 2004 MERS CoV in 2013 and SARS CoV 2 in 2019 41 There have also been a large number of animal coronaviruses identified since the 1960s 42 MicrobiologyStructure Structure of a coronavirus Coronaviruses are large roughly spherical particles with unique surface projections 43 Their size is highly variable with average diameters of 80 to 120 nm Extreme sizes are known from 50 to 200 nm in diameter 44 The total molecular mass is on average 40 000 kDa They are enclosed in an envelope embedded with a number of protein molecules 45 The lipid bilayer envelope membrane proteins and nucleocapsid protect the virus when it is outside the host cell 46 The viral envelope is made up of a lipid bilayer in which the membrane M envelope E and spike S structural proteins are anchored 47 The molar ratio of E S M in the lipid bilayer is approximately 1 20 300 48 The E and M protein are the structural proteins that combined with the lipid bilayer to shape the viral envelope and maintain its size 49 S proteins are needed for interaction with the host cells But human coronavirus NL63 is peculiar in that its M protein has the binding site for the host cell and not its S protein 50 The diameter of the envelope is 85 nm The envelope of the virus in electron micrographs appears as a distinct pair of electron dense shells shells that are relatively opaque to the electron beam used to scan the virus particle 51 49 The M protein is the main structural protein of the envelope that provides the overall shape and is a type III membrane protein It consists of 218 to 263 Amino acid residues and forms a layer 7 8 nm thick 45 It has three domains a short N terminal ectodomain a triple spanning transmembrane domain and a C terminal endodomain The C terminal domain forms a matrix like lattice that adds to the extra thickness of the envelope Different species can have either N or O linked glycans in their protein amino terminal domain The M protein is crucial during the assembly budding envelope formation and pathogenesis stages of the virus lifecycle 52 The E proteins are minor structural proteins and highly variable in different species 44 There are only about 20 copies of the E protein molecule in a coronavirus particle 48 They are 8 4 to 12 kDa in size and are composed of 76 to 109 amino acids 44 They are integral proteins i e embedded in the lipid layer and have two domains namely a transmembrane domain and an extramembrane C terminal domain They are almost fully a helical with a single a helical transmembrane domain and form pentameric five molecular ion channels in the lipid bilayer They are responsible for virion assembly intracellular trafficking and morphogenesis budding 45 Diagram of the genome and functional domains of the S protein for SARS CoV and MERS CoV The spikes are the most distinguishing feature of coronaviruses and are responsible for the corona or halo like surface On average a coronavirus particle has 74 surface spikes 53 Each spike is about 20 nm long and is composed of a trimer of the S protein The S protein is in turn composed of an S1 and S2 subunit The homotrimeric S protein is a class I fusion protein which mediates the receptor binding and membrane fusion between the virus and host cell The S1 subunit forms the head of the spike and has the receptor binding domain RBD The S2 subunit forms the stem which anchors the spike in the viral envelope and on protease activation enables fusion The two subunits remain noncovalently linked as they are exposed on the viral surface until they attach to the host cell membrane 45 In a functionally active state three S1 are attached to two S2 subunits The subunit complex is split into individual subunits when the virus binds and fuses with the host cell under the action of proteases such as cathepsin family and transmembrane protease serine 2 TMPRSS2 of the host cell 54 After binding of the ACE2 receptor SARS CoV spike is activated and cleaved at the S1 S2 level S1 proteins are the most critical components in terms of infection They are also the most variable components as they are responsible for host cell specificity They possess two major domains named N terminal domain S1 NTD and C terminal domain S1 CTD both of which serve as the receptor binding domains The NTDs recognize and bind sugars on the surface of the host cell An exception is the MHV NTD that binds to a protein receptor carcinoembryonic antigen related cell adhesion molecule 1 CEACAM1 S1 CTDs are responsible for recognizing different protein receptors such as angiotensin converting enzyme 2 ACE2 aminopeptidase N APN and dipeptidyl peptidase 4 DPP4 45 A subset of coronaviruses specifically the members of betacoronavirus subgroup A also has a shorter spike like surface protein called hemagglutinin esterase HE 42 The HE proteins occur as homodimers composed of about 400 amino acid residues and are 40 to 50 kDa in size They appear as tiny surface projections of 5 to 7 nm long embedded in between the spikes They help in the attachment to and detachment from the host cell 55 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 49 56 N protein is a phosphoprotein of 43 to 50 kDa in size and is divided into three conserved domains The majority of the protein is made up of domains 1 and 2 which are typically rich in arginines and lysines Domain 3 has a short carboxy terminal end and has a net negative charge due to excess of acidic over basic amino acid residues 44 Genome See also Severe acute respiratory syndrome related coronavirus Genome SARS CoV genome and proteins Coronaviruses contain a positive sense single stranded RNA genome The genome size for coronaviruses ranges from 26 4 to 31 7 kilobases 6 The genome size is one of the largest among RNA viruses The genome has a 5 methylated cap and a 3 polyadenylated tail 49 The genome organization for a coronavirus is 5 leader UTR replicase ORF1ab 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 polyprotein pp1ab The replicase polyprotein self cleaves to form 16 nonstructural proteins nsp1 nsp16 49 The later reading frames encode the four major structural proteins spike envelope membrane and nucleocapsid 57 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 49 Replication cycle Cell entry The life cycle of a coronavirus Infection begins when the viral 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 the virus to enter the host cell by endocytosis or direct fusion of the viral envelope with the host membrane 58 Coronaviruses can enter cells by either fusing to their lipid envelope with the cell membrane on the cell surface or by internalization via endocytosis 59 Genome translation On entry into the host cell the virus particle is uncoated and its genome enters the cell cytoplasm The coronavirus RNA genome has a 5 methylated cap and a 3 polyadenylated tail which allows it to act like a messenger RNA and be directly translated by the host cell s ribosomes The host ribosomes translate the initial overlapping open reading frames ORF1a and ORF1b of the virus genome into two large overlapping polyproteins pp1a and pp1ab 49 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 60 The ribosomal frameshift allows for the continuous translation of ORF1a followed by ORF1b 49 The polyproteins have their own proteases PLpro nsp3 and 3CLpro nsp5 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 nsp12 RNA helicase nsp13 and exoribonuclease nsp14 49 Replicase transcriptase Replicase transcriptase complex 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 nonstructural protein for instance provides extra fidelity to replication by providing a proofreading function which the RNA dependent RNA polymerase lacks 61 Replication 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 49 Transcription of nested mRNAs Nested set of subgenomic mRNAs Transcription 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 process is followed by the transcription of these negative sense subgenomic RNA molecules to their corresponding positive sense mRNAs 49 The subgenomic mRNAs form a nested set which have a common 5 head and partially duplicate 3 end 62 Recombination The replicase transcriptase complex is also capable of genetic recombination when at least two viral genomes are present in the same infected cell 62 RNA recombination appears to be a major driving force in determining genetic variability within a coronavirus species the capability of a coronavirus species to jump from one host to another and infrequently in determining the emergence of novel coronaviruses 63 The exact mechanism of recombination in coronaviruses is unclear but likely involves template switching during genome replication 63 Assembly and 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 many accessory proteins 49 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 the assembly of viruses following its binding to the nucleocapsid Progeny viruses are then released from the host cell by exocytosis through secretory vesicles Once released the viruses can infect other host cells 64 Transmission Infected carriers are able to shed viruses into the environment The interaction of the coronavirus spike protein with its complementary cell receptor is central in determining the tissue tropism infectivity and species range of the released virus 65 66 Coronaviruses mainly target epithelial cells 42 They are transmitted from one host to another host depending on the coronavirus species by either an aerosol fomite or fecal oral route 67 Human coronaviruses infect the epithelial cells of the respiratory tract while animal coronaviruses generally infect the epithelial cells of the digestive tract 42 SARS coronavirus for example infects the human epithelial cells of the lungs via an aerosol route 68 by binding to the angiotensin converting enzyme 2 ACE2 receptor 69 Transmissible gastroenteritis coronavirus TGEV infects the pig epithelial cells of the digestive tract via a fecal oral route 67 by binding to the Alanine aminopeptidase APN receptor 49 ClassificationFor a more detailed list of members see Coronaviridae Phylogenetic tree of coronaviruses Coronaviruses form the subfamily Orthocoronavirinae 2 3 4 which is one of two sub families in the family Coronaviridae order Nidovirales and realm Riboviria 42 70 They are divided into the four genera Alphacoronavirus Betacoronavirus Gammacoronavirus and Deltacoronavirus Alphacoronaviruses and betacoronaviruses infect mammals while gammacoronaviruses and deltacoronaviruses primarily infect birds 71 72 Genus Alphacoronavirus 67 Species Alphacoronavirus 1 TGEV Feline coronavirus Canine coronavirus 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 68 Species Betacoronavirus 1 Bovine Coronavirus Human coronavirus OC43 Hedgehog coronavirus 1 Human coronavirus HKU1 Middle East respiratory syndrome related coronavirus Murine coronavirus Pipistrellus bat coronavirus HKU5 Rousettus bat coronavirus HKU9 Severe acute respiratory syndrome related coronavirus SARS CoV SARS CoV 2 Tylonycteris bat coronavirus HKU4 Genus Gammacoronavirus 18 Species Avian coronavirus Beluga whale coronavirus SW1 Genus Deltacoronavirus Species Bulbul coronavirus HKU11 Porcine coronavirus HKU15Origin Origins of human coronaviruses with possible intermediate hosts The most recent common ancestor MRCA of all coronaviruses is estimated to have existed as recently as 8000 BCE although some models place the common ancestor as far back as 55 million years or more implying long term coevolution with bat and avian species 73 The most recent common ancestor of the alphacoronavirus line has been placed at about 2400 BCE of the betacoronavirus line at 3300 BCE of the gammacoronavirus line at 2800 BCE and the deltacoronavirus line at about 3000 BCE Bats and birds as warm blooded flying vertebrates are an ideal natural reservoir for the coronavirus gene pool with bats the reservoir for alphacoronaviruses and betacoronavirus and birds the reservoir for gammacoronaviruses and deltacoronaviruses The large number and global range of bat and avian species that host viruses have enabled extensive evolution and dissemination of coronaviruses 74 Many human coronaviruses have their origin in bats 75 The human coronavirus NL63 shared a common ancestor with a bat coronavirus ARCoV 2 between 1190 and 1449 CE 76 The human coronavirus 229E shared a common ancestor with a bat coronavirus GhanaGrp1 Bt CoV between 1686 and 1800 CE 77 More recently alpaca coronavirus and human coronavirus 229E diverged sometime before 1960 78 MERS CoV emerged in humans from bats through the intermediate host of camels 79 MERS CoV although related to several bat coronavirus species appears to have diverged from these several centuries ago 80 The most closely related bat coronavirus and SARS CoV diverged in 1986 81 The ancestors of SARS CoV first infected leaf nose bats of the genus Hipposideridae subsequently they spread to horseshoe bats in the species Rhinolophidae then to Asian palm civets and finally to humans 82 83 Unlike other betacoronaviruses bovine coronavirus of the species Betacoronavirus 1 and subgenus Embecovirus is thought to have originated in rodents and not in bats 75 84 In the 1790s equine coronavirus diverged from the bovine coronavirus after a cross species jump 85 Later in the 1890s human coronavirus OC43 diverged from bovine coronavirus after another cross species spillover event 86 85 It is speculated that the flu pandemic of 1890 may have been caused by this spillover event and not by the influenza virus because of the related timing neurological symptoms and unknown causative agent of the pandemic 87 Besides causing respiratory infections human coronavirus OC43 is also suspected of playing a role in neurological diseases 88 In the 1950s the human coronavirus OC43 began to diverge into its present genotypes 89 Phylogenetically mouse hepatitis virus Murine coronavirus which infects the mouse s liver and central nervous system 90 is related to human coronavirus OC43 and bovine coronavirus Human coronavirus HKU1 like the aforementioned viruses also has its origins in rodents 75 Infection in humans Transmission and life cycle of SARS CoV 2 causing COVID 19 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 49 Coronaviruses can cause colds with major symptoms such as fever and a sore throat from swollen adenoids 91 Coronaviruses can cause pneumonia either direct viral pneumonia or secondary bacterial pneumonia and bronchitis either direct viral bronchitis or secondary bacterial bronchitis 92 The 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 92 Six species of human coronaviruses are known with one species subdivided into two different strains making seven strains of human coronaviruses altogether Seasonal distribution of HCoV NL63 in Germany shows a preferential detection from November to March Four human coronaviruses produce symptoms that are generally mild even though it is contended they might have been more aggressive in the past 93 Human coronavirus OC43 HCoV OC43 b CoV Human coronavirus HKU1 HCoV HKU1 b CoV Human coronavirus 229E HCoV 229E a CoV Human coronavirus NL63 HCoV NL63 a CoV Three human coronaviruses produce potentially severe symptoms Severe acute respiratory syndrome coronavirus SARS CoV b CoV identified in 2003 Middle East respiratory syndrome related coronavirus MERS CoV b CoV identified in 2012 Severe acute respiratory syndrome coronavirus 2 SARS CoV 2 b CoV identified in 2019 These cause the diseases commonly called SARS MERS and COVID 19 respectively Common cold Main article Common cold Although the common cold is usually caused by rhinoviruses 94 in about 15 of cases the cause is a coronavirus 95 The human coronaviruses HCoV OC43 HCoV HKU1 HCoV 229E and HCoV NL63 continually circulate in the human population in adults and children worldwide and produce the generally mild symptoms of the common cold 88 The four mild coronaviruses have a seasonal incidence occurring in the winter months in temperate climates 96 97 There is no preponderance in any season in tropical climates 98 Severe acute respiratory syndrome SARS Main article SARS Characteristics of zoonotic coronavirus strainsMERS CoV SARS CoV SARS CoV 2 and related diseases MERS CoV SARS CoV SARS CoV 2Disease MERS SARS COVID 19Outbreaks 2012 2015 2018 2002 2004 2019 2021 pandemicEpidemiologyDate of first identified case June 2012 November 2002 December 2019 99 Location of first identified case Jeddah Saudi Arabia Shunde China Wuhan ChinaAge average 56 44 100 a 56 101 Sex ratio M F 3 3 1 0 8 1 102 1 6 1 101 Confirmed cases 2494 8096 103 676 609 955 104 b Deaths 858 774 103 6 881 955 104 b Case fatality rate 37 9 2 1 02 104 SymptomsFever 98 99 100 87 9 105 Dry cough 47 29 75 67 7 105 Dyspnea 72 40 42 18 6 105 Diarrhea 26 20 25 3 7 105 Sore throat 21 13 25 13 9 105 Ventilatory use 24 5 106 14 20 4 1 107 Notes Based on data from Hong Kong a b Data as of 10 March 2023 vteIn 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 several laboratories was the causative agent for SARS The virus was officially named the SARS coronavirus SARS CoV More than 8 000 people from 29 countries and territories were infected and at least 774 died 108 69 Middle East respiratory syndrome MERS Main article 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 109 110 The World Health Organization issued a global alert soon after 111 The WHO update on 28 September 2012 said the virus did not seem to pass easily from person to person 112 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 113 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 114 By 30 October 2013 there were 124 cases and 52 deaths in Saudi Arabia 115 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 The only U S cases both survived were recorded in May 2014 116 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 four hospitals in the Seoul area to treat his illness This caused one of the largest outbreaks of MERS CoV outside the Middle East 117 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 5 118 Coronavirus disease 2019 COVID 19 Main article COVID 19 In December 2019 a pneumonia outbreak was reported in Wuhan China 119 On 31 December 2019 the outbreak was traced to a novel strain of coronavirus 120 which was given the interim name 2019 nCoV by the World Health Organization 121 122 123 later renamed SARS CoV 2 by the International Committee on Taxonomy of Viruses As of 10 March 2023 there have been at least 6 881 955 104 confirmed deaths and more than 676 609 955 104 confirmed cases in the COVID 19 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 124 The virus has a 96 similarity to a bat coronavirus so it is widely suspected to originate from bats as well 125 126 Coronavirus HuPn 2018 Main article Canine coronavirus HuPn 2018 During a surveillance study of archived samples of Malaysian viral pneumonia patients virologists identified a strain of canine coronavirus which has infected humans in 2018 Infection in animalsCoronaviruses have been recognized as causing pathological conditions in veterinary medicine since the 1930s 19 They infect a range of animals including swine cattle horses camels cats dogs rodents birds and bats 127 The majority of animal related coronaviruses infect the intestinal tract and are transmitted by a fecal oral route 128 Significant research efforts have been focused on elucidating the viral pathogenesis of these animal coronaviruses especially by virologists interested in veterinary and zoonotic diseases 129 Farm animals Coronaviruses infect domesticated birds 130 Infectious bronchitis virus IBV a type of coronavirus causes avian infectious bronchitis 131 The virus is of concern to the poultry industry because of the high mortality from infection its rapid spread and its effect on production 127 The virus affects both meat production and egg production and causes substantial economic loss 132 In chickens infectious bronchitis virus targets not only the respiratory tract but also the urogenital tract The virus can spread to different organs throughout the chicken 131 The virus is transmitted by aerosol and food contaminated by feces Different vaccines against IBV exist and have helped to limit the spread of the virus and its variants 127 Infectious bronchitis virus is one of a number of strains of the species Avian coronavirus 133 Another strain of avian coronavirus is turkey coronavirus TCV which causes enteritis in turkeys 127 Coronaviruses also affect other branches of animal husbandry such as pig farming and the Cattle raising 127 Swine acute diarrhea syndrome coronavirus SADS CoV which is related to bat coronavirus HKU2 causes diarrhea in pigs 134 Porcine epidemic diarrhea virus PEDV is a coronavirus that has recently emerged and similarly causes diarrhea in pigs 135 Transmissible gastroenteritis virus TGEV which is a member of the species Alphacoronavirus 1 136 is another coronavirus that causes diarrhea in young pigs 137 138 In the cattle industry bovine coronavirus BCV which is a member of the species Betacoronavirus 1 and related to HCoV OC43 139 is responsible for severe profuse enteritis in young calves 127 Domestic pets Coronaviruses infect domestic pets such as cats dogs and ferrets 130 There are two forms of feline coronavirus which are both members of the species Alphacoronavirus 1 136 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 with high mortality 127 There are two different coronaviruses that infect dogs Canine coronavirus CCoV which is a member of the species Alphacoronavirus 1 136 causes mild gastrointestinal disease 127 Canine respiratory coronavirus CRCoV which is a member of the species Betacoronavirus 1 and related to HCoV OC43 139 cause respiratory disease 127 Similarly there are two types of coronavirus that infect ferrets 140 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 141 142 Laboratory animals Coronaviruses infect laboratory animals 127 Mouse hepatitis virus MHV which is a member of the species Murine coronavirus 143 causes an epidemic murine illness with high mortality especially among colonies of laboratory mice 144 Prior to the discovery of SARS CoV MHV was 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 129 Sialodacryoadenitis virus SDAV which is a strain of the species Murine coronavirus 143 is highly infectious coronavirus of laboratory rats which can be transmitted between individuals by direct contact and indirectly by aerosol Rabbit enteric coronavirus causes acute gastrointestinal disease and diarrhea in young European rabbits 127 Mortality rates are high 145 Prevention and treatmentA number of vaccines using different methods have been developed against human coronavirus SARS CoV 2 146 147 Antiviral targets against human coronaviruses have also been identified such as viral proteases polymerases and entry proteins Drugs are in development which target these proteins and the different steps of viral replication 148 147 Vaccines are available for animal coronaviruses IBV TGEV and Canine CoV although their effectiveness is limited In the case of outbreaks of highly contagious animal coronaviruses such as PEDV measures such as destruction of entire herds of pigs may be used to prevent transmission to other herds 49 See alsoCoronavirus diseases ZoonosisReferences Virus Taxonomy 2018b Release International Committee on Taxonomy of Viruses ICTV March 2019 Archived from the original on 2018 03 04 Retrieved 2020 01 24 a b 2017 012 015S xlsx International Committee on Taxonomy of Viruses ICTV October 2018 Archived from the original on 2019 05 14 Retrieved 2020 01 24 a b c ICTV Taxonomy history Orthocoronavirinae International Committee on Taxonomy of Viruses ICTV Retrieved 2020 01 24 a b c Fan Y Zhao K Shi ZL Zhou P March 2019 Bat Coronaviruses in China Viruses 11 3 210 doi 10 3390 v11030210 PMC 6466186 PMID 30832341 Cherry J Demmler Harrison GJ 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resistance and its influence on the development of new antiseptic strategies Viruses 4 11 3044 68 doi 10 3390 v4113044 PMC 3509683 PMID 23202515 Corman VM Jores J Meyer B Younan M Liljander A Said MY et al August 2014 Antibodies against MERS coronavirus in dromedary camels Kenya 1992 2013 Emerging Infectious Diseases 20 8 1319 22 doi 10 1007 978 1 4899 7448 8 10 ISBN 978 1 4899 7447 1 PMC 7122465 PMID 25075637 The other OC strains and B814 that could not be adapted to mouse brain resisted adaptation to cell culture as well these distinct viruses have since been lost and may actually have been rediscovered recently Zhu N Zhang D Wang W Li X Yang B Song J et al February 2020 A Novel Coronavirus from Patients with Pneumonia in China 2019 The New England Journal of Medicine 382 8 727 733 doi 10 1056 NEJMoa2001017 PMC 7092803 PMID 31978945 a b c d e de Groot RJ Baker SC Baric R Enjuanes L Gorbalenya AE Holmes KV Perlman S Poon L Rottier PJ Talbot PJ Woo PC Ziebuhr J 2011 Family Coronaviridae In King AM Lefkowitz E Adams MJ Carstens EB International Committee on Taxonomy of Viruses International Union of Microbiological Societies Virology Division eds Ninth Report of the International Committee on Taxonomy of Viruses Oxford Elsevier pp 806 28 doi 10 1016 B978 0 12 384684 6 00068 9 ISBN 978 0 12 384684 6 S2CID 212719285 Goldsmith CS Tatti KM Ksiazek TG Rollin PE Comer JA Lee WW et al February 2004 Ultrastructural characterization of SARS coronavirus Emerging Infectious Diseases 10 2 320 6 doi 10 3201 eid1002 030913 PMC 3322934 PMID 15030705 Virions acquired an envelope by budding into the cisternae and formed mostly spherical sometimes pleomorphic particles that averaged 78 nm in diameter Figure 1A a b c d Masters PS 2006 The molecular biology of coronaviruses Advances in Virus Research 66 193 292 doi 10 1016 S0065 3527 06 66005 3 ISBN 9780120398690 PMC 7112330 PMID 16877062 a b c d e Lalchhandama K 2020 The chronicles of coronaviruses the electron microscope the doughnut and the spike Science Vision 20 2 78 92 doi 10 33493 scivis 20 02 03 Neuman BW Kiss G Kunding AH Bhella D Baksh MF Connelly S et al April 2011 A structural analysis of M protein in coronavirus assembly and morphology Journal of Structural Biology 174 1 11 22 doi 10 1016 j jsb 2010 11 021 PMC 4486061 PMID 21130884 See Figure 10 Lai MM Cavanagh D 1997 The molecular biology of coronaviruses Advances in Virus Research 48 1 100 doi 10 1016 S0065 3527 08 60286 9 ISBN 9780120398485 PMC 7130985 PMID 9233431 a b Godet M L Haridon R Vautherot JF Laude H 1992 TGEV corona virus ORF4 encodes a membrane protein that is incorporated into virions Virology 188 2 666 75 doi 10 1016 0042 6822 92 90521 p PMC 7131960 PMID 1316677 a b c d e f g h i j k l m n o Fehr AR Perlman S 2015 Coronaviruses an overview of their replication and pathogenesis In Maier HJ Bickerton E Britton P eds Coronaviruses Methods in Molecular Biology Vol 1282 Springer pp 1 23 doi 10 1007 978 1 4939 2438 7 1 ISBN 978 1 4939 2438 7 PMC 4369385 PMID 25720466 See section Virion Structure Naskalska A Dabrowska A Szczepanski A Milewska A Jasik KP Pyrc K October 2019 Membrane Protein of Human Coronavirus NL63 Is Responsible for Interaction with the Adhesion Receptor Journal of Virology 93 19 doi 10 1128 JVI 00355 19 PMC 6744225 PMID 31315999 Neuman BW Adair BD Yoshioka C Quispe JD Orca G Kuhn P et al August 2006 Supramolecular architecture of severe acute respiratory syndrome coronavirus revealed by electron cryomicroscopy Journal of Virology 80 16 7918 28 doi 10 1128 JVI 00645 06 PMC 1563832 PMID 16873249 Particle diameters ranged from 50 to 150 nm excluding the spikes with mean particle diameters of 82 to 94 nm Also See Figure 1 for double shell Schoeman D Fielding BC May 2019 Coronavirus envelope protein current knowledge Virology Journal 16 1 69 doi 10 1186 s12985 019 1182 0 PMC 6537279 PMID 31133031 Neuman BW Kiss G Kunding AH Bhella D Baksh MF Connelly S et al April 2011 A structural analysis of M protein in coronavirus assembly and morphology Journal of Structural Biology 174 1 11 22 doi 10 1016 j jsb 2010 11 021 PMC 4486061 PMID 21130884 J Alsaadi EA Jones IM April 2019 Membrane binding proteins of coronaviruses Future Virology 14 4 275 286 doi 10 2217 fvl 2018 0144 PMC 7079996 PMID 32201500 Zeng Q Langereis MA van Vliet AL Huizinga EG de Groot RJ July 2008 Structure of coronavirus hemagglutinin esterase offers insight into corona and influenza virus evolution Proceedings of the National Academy of Sciences of the United States of America 105 26 9065 9 Bibcode 2008PNAS 105 9065Z doi 10 1073 pnas 0800502105 PMC 2449365 PMID 18550812 Chang CK Hou MH Chang CF Hsiao CD Huang TH March 2014 The SARS coronavirus nucleocapsid protein forms and functions Antiviral Research 103 39 50 doi 10 1016 j antiviral 2013 12 009 PMC 7113676 PMID 24418573 See Figure 4c Snijder EJ Bredenbeek PJ Dobbe JC Thiel V Ziebuhr J Poon LL et al August 2003 Unique and conserved features of genome and proteome of SARS coronavirus an early split off from the coronavirus group 2 lineage Journal of Molecular Biology 331 5 991 1004 doi 10 1016 S0022 2836 03 00865 9 PMC 7159028 PMID 12927536 See Figure 1 Simmons G Zmora P Gierer S Heurich A Pohlmann S December 2013 Proteolytic activation of the SARS coronavirus spike protein cutting enzymes at the cutting edge of antiviral research Antiviral Research 100 3 605 14 doi 10 1016 j antiviral 2013 09 028 PMC 3889862 PMID 24121034 See Figure 2 Szlachcic Wojciech J Dabrowska Agnieszka Milewska Aleksandra Ziojla Natalia Blaszczyk Katarzyna Barreto Duran Emilia Sanak Marek Surmiak Marcin Owczarek Katarzyna Grzanka Dariusz Durzynska Julia Pyrc Krzysztof Borowiak Malgorzata July 2022 SARS CoV 2 infects an in vitro model of the human developing pancreas through endocytosis iScience 25 7 104594 doi 10 1016 j isci 2022 104594 Masters PS 2006 01 01 The molecular biology of coronaviruses Advances in Virus Research Academic Press 66 193 292 doi 10 1016 S0065 3527 06 66005 3 ISBN 9780120398690 PMC 7112330 PMID 16877062 See Figure 8 Sexton NR Smith EC Blanc H Vignuzzi M Peersen OB Denison MR August 2016 Homology Based Identification of a Mutation in the Coronavirus RNA Dependent RNA Polymerase That Confers Resistance to Multiple Mutagens Journal of Virology 90 16 7415 28 doi 10 1128 JVI 00080 16 PMC 4984655 PMID 27279608 Finally these results combined with those from previous work 33 44 suggest that CoVs encode at least three proteins involved in fidelity nsp12 RdRp nsp14 ExoN and nsp10 supporting the assembly of a multiprotein replicase fidelity complex as described previously 38 a b Payne S 2017 01 01 Chapter 17 Family Coronaviridae Viruses Academic Press pp 149 158 doi 10 1016 B978 0 12 803109 4 00017 9 ISBN 978 0 12 803109 4 S2CID 91572610 a b Su S Wong G Shi W Liu J Lai AC Zhou J Liu W Bi Y Gao GF June 2016 Epidemiology Genetic Recombination and Pathogenesis of Coronaviruses Trends in Microbiology 24 6 490 502 doi 10 1016 j tim 2016 03 003 PMC 7125511 PMID 27012512 Fehr AR Perlman S 2015 Coronaviruses an overview of their replication and pathogenesis In Maier HJ Bickerton E Britton P eds Coronaviruses Methods in Molecular Biology Vol 1282 Springer pp 1 23 doi 10 1007 978 1 4939 2438 7 1 ISBN 978 1 4939 2438 7 PMC 4369385 PMID 25720466 See section Coronavirus Life Cycle Assembly and Release Masters PS 2006 01 01 The molecular biology of coronaviruses Advances in Virus Research Academic Press 66 193 292 doi 10 1016 S0065 3527 06 66005 3 ISBN 978 0120398690 PMC 7112330 PMID 16877062 Nevertheless the interaction between S protein and receptor remains the principal if not sole determinant of coronavirus host species range and tissue tropism Cui J Li F Shi ZL March 2019 Origin and evolution of pathogenic coronaviruses Nature Reviews Microbiology 17 3 181 92 doi 10 1038 s41579 018 0118 9 PMC 7097006 PMID 30531947 Different SARS CoV strains isolated from several hosts vary in their binding affinities for human ACE2 and 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gastroenteritis virus Veterinary Microbiology 23 1 4 147 54 doi 10 1016 0378 1135 90 90144 K PMC 7117338 PMID 2169670 Sola I Alonso S Zuniga S Balasch M Plana Duran 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 fur die Gesamte Virusforschung 29 1 105 08 doi 10 1007 BF01253886 PMC 7086923 PMID 4195092 S2CID 42104521 Portals COVID 19 Medicine Viruses Retrieved from https en wikipedia org w index php title Coronavirus amp oldid 1153784581, wikipedia, wiki, book, books, library,

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