coronavirus coronavirus 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. 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. orthocoronavirinae group member sars-cov-2 illustration key: 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 information: alphacoronavirus betacoronavirus gammacoronavirus deltacoronavirus synonyms coronavirinae coronaviruses constitute the subfamily orthocoronavirinae, in the family coronaviridae, order nidovirales and realm riboviria. 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 26 to 32 kilobases, one of the largest among rna viruses. 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. etymology the name "coronavirus" is derived from latin corona, meaning "crown" or "wreath", itself a borrowing from greek κορώνη korṓnē, "garland, wreath". the name was coined by june almeida and david tyrrell who first observed and studied human coronaviruses. 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. 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. this morphology is created by the viral spike peplomers, which are proteins on the surface of the virus. 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. as the number of new species increased, the genus was split into four genera, namely alphacoronavirus, betacoronavirus, deltacoronavirus, and gammacoronavirus in 2009. the common name coronavirus is used to refer to any member of the subfamily orthocoronavirinae. as of 2020, 45 species are officially recognised. 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. 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%. leland david bushnell and carl alfred brandly isolated the virus that caused the infection in 1933. 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. 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. it was not realized at the time that these three different viruses were related. human coronaviruses were discovered in the 1960s using two different methods in the united kingdom and the united states. 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. 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. the new cultivating method was introduced to the lab by bertil hoorn. the isolated virus when intranasally inoculated into volunteers caused a cold and was inactivated by ether which indicated it had a lipid envelope. dorothy hamre 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. 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. using electron microscopy the three viruses were shown to be morphologically related by their general shape and distinctive club-like spikes. 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). like b814, 229e, and ibv, the novel cold virus oc43 had distinctive club-like spikes when observed with the electron microscope. the ibv-like novel cold viruses were soon shown to be also morphologically related to the mouse hepatitis virus. this new group of viruses were named coronaviruses after their distinctive morphological appearance. human coronavirus 229e and human coronavirus oc43 continued to be studied in subsequent decades. the coronavirus strain b814 was lost. it is not known which present human coronavirus it was. 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. there have also been a large number of animal coronaviruses identified since the 1960s. microbiology structure structure of a coronavirus coronaviruses are large, roughly spherical particles with unique surface projections. their size is highly variable with average diameters of 80 to 120 nm. extreme sizes are known from 50 to 200 nm in diameter. the total molecular mass is on average 40,000 kda. they are enclosed in an envelope embedded with a number of protein molecules. the lipid bilayer envelope, membrane proteins, and nucleocapsid protect the virus when it is outside the host cell. the viral envelope is made up of a lipid bilayer in which the membrane (m), envelope (e) and spike (s) structural proteins are anchored. the molar ratio of e:s:m in the lipid bilayer is approximately 1:20:300. the e and m protein are the structural proteins that combined with the lipid bilayer to shape the viral envelope and maintain its size. 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. 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). 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. 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. the e proteins are minor structural proteins and highly variable in different species. there are only about 20 copies of the e protein molecule in a coronavirus particle. they are 8.4 to 12 kda in size and are composed of 76 to 109 amino acids. 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). 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. 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. 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. 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). a subset of coronaviruses (specifically the members of betacoronavirus subgroup a) also has a shorter spike-like surface protein called hemagglutinin esterase (he). 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. 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. 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. genome