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=== ''Porcine epidemic diarrhea virus'' ===
=== ''Porcine epidemic diarrhea virus'' ===
An acute infectious diarrhoea was first reported from England in 1971. The infection was specifically among fattening pigs and sows. It eventually spread throughout Europe. ICTV gave named the virus ''Porcine epidemic diarrhea virus'' in 1995.<ref>{{Cite web|last=|first=|date=|title=ICTV Taxonomy history: Porcine epidemic diarrhea virus|url=https://talk.ictvonline.org/taxonomy/p/taxonomy-history?taxnode_id=201901857|url-status=live|archive-url=|archive-date=|access-date=2020-08-20|website=International Committee on Taxonomy of Viruses (ICTV)|language=en}}</ref> An epidemic broke out from China in 2010 that spread throughout the world. A virulent strain emerged in US between 2013 and 2015. It affected pigs of all ages, and mortality was as high as 95% among the the suckling piglets. Another severe outbreak occurred in Germany in 2014 that spread to other European countries.<ref>{{Cite journal|last=Antas|first=Marta|last2=Woźniakowski|first2=Grzegorz|date=2019|title=Current status of porcine epidemic diarrhoea (PED) in European pigs|url=https://www.ncbi.nlm.nih.gov/pubmed/31934654|journal=Journal of Veterinary Research|volume=63|issue=4|pages=465–470|doi=10.2478/jvetres-2019-0064|pmc=6950429|pmid=31934654|via=}}</ref>
An acute infectious diarrhoea was first known in England in 1971. The infection was specifically among fattening pigs and sows. It was first reported by J. Oldham in ''Pig Farming'' in 1972.<ref>{{Cite journal|last=Oldham|first=J|date=1972|title=Letter to the editor|url=|journal=Pig Farming|volume=72|issue=October Suppl|pages=72–73|via=}}</ref><ref>{{Cite journal|last=Pensaert|first=Maurice B.|last2=Martelli|first2=Paolo|date=2016|title=Porcine epidemic diarrhea: A retrospect from Europe and matters of debate|url=https://www.ncbi.nlm.nih.gov/pubmed/27317168|journal=Virus Research|volume=226|pages=1–6|doi=10.1016/j.virusres.2016.05.030|pmc=7132433|pmid=27317168|via=}}</ref> M. B. Pensaert and P. de Bouck at the University of Gent, Begium isolated and identified the new coronavirus in 1978, and designated it CV777.<ref>{{Cite journal|last=Pensaert|first=M. B.|last2=de Bouck|first2=P.|date=1978|title=A new coronavirus-like particle associated with diarrhea in swine|url=https://www.ncbi.nlm.nih.gov/pubmed/83132|journal=Archives of Virology|volume=58|issue=3|pages=243–247|doi=10.1007/BF01317606|pmc=7086830|pmid=83132|via=}}</ref> It eventually spread throughout Europe. ICTV gave named the virus ''Porcine epidemic diarrhea virus'' in 1995.<ref>{{Cite web|last=|first=|date=|title=ICTV Taxonomy history: Porcine epidemic diarrhea virus|url=https://talk.ictvonline.org/taxonomy/p/taxonomy-history?taxnode_id=201901857|url-status=live|archive-url=|archive-date=|access-date=2020-08-20|website=International Committee on Taxonomy of Viruses (ICTV)|language=en}}</ref> An epidemic broke out from China in 2010 that spread throughout the world. A virulent strain emerged in US between 2013 and 2015. It affected pigs of all ages, and mortality was as high as 95% among the the suckling piglets. Another severe outbreak occurred in Germany in 2014 that spread to other European countries.<ref>{{Cite journal|last=Antas|first=Marta|last2=Woźniakowski|first2=Grzegorz|date=2019|title=Current status of porcine epidemic diarrhoea (PED) in European pigs|url=https://www.ncbi.nlm.nih.gov/pubmed/31934654|journal=Journal of Veterinary Research|volume=63|issue=4|pages=465–470|doi=10.2478/jvetres-2019-0064|pmc=6950429|pmid=31934654|via=}}</ref>


=== Bat coronaviruses ===
=== Bat coronaviruses ===

Revision as of 08:07, 20 August 2020

The history of coronaviruses reflects the discovery of the diseases caused by coronaviruses and identification of the viruses. The first record of the disease was in 1931 when a new type of upper-respiratory tract disease was found in chickens in North Dakota. In 1933, the causative agent was identified as a virus. By 1936, it was recognised that the disease and the virus were unique from other viral diseases. The virus was named infectious bronchitis virus (IBV).[1]

A new brain disease of mice (murine encephalomyelitis) was discovered in 1947 at Harvard Medical School in Boston. The virus causing the disease was called JHM (after Harvard pathologist John Howard Mueller). Three years later a new mouse hepatitis was reported from National Institute for Medical Research in London. The causative virus was named mouse hepatitis virus (MHV).[2][3]

In 1961, a virus was obtained from a school boy in Epsom, England, who was suffering from common cold. The sample designated B814 was confirmed as novel virus in 1965. New common cold viruses (assigned 229E) collected from medical students at the University of Chicago were also reported in 1966. Structural analyses of IBV, MHV, B18 and 229E using transmission electron microscopy revealed that they all belong to the same group of viruses. June Almeida and David Tyrrell who made the comparative studies invented the collective name coronavirus for the viruses, as they are all characterised by solar corona-like projection on their surfaces.[4]

Discovery of chicken coronavirus

Arthur Frederick Schalk and Merle C. Fawn at the North Dakota Agricultural College were the first to report what was later identified as coronavirus disease in chickens.[1] Their publication in the Journal of the American Veterinary Medical Association in 1931 indicates that there was a new respiratory disease that mostly affected 2-day-old to 3-week-old chickens. They referred to the disease as "an apparently new respiratory disease of baby chicks."[5] The symptoms included severe shortness of breath and physical weakness. The infection was contagious and virulent. It was easily transmitted through direct contact between chickens or experimental transfer of the bronchial exudates from infected to healthy chickens. Maximum mortality recorded was 90%.[6]

The causative pathogen was not known. Charles D. Hudson and Fred Robert Beaudette at the New Jersey Agricultural Experiment Station in New Brunswick, Canada, put forth a hypothesis in 1932 that virus could be the cause and introduced the name as "virus of the infectious bronchitis."[7] But this was a misattribution because at the time another related disease was reported, known as infectious laryngotracheitis, which exhibited almost similar symptoms but mostly affect adult chickens.[3] As Beaudette later recalled in 1937, the disease he described was infectious layngotracheitis, saying: "Infectious laryngotracheitis is said to be the correct name for this disease rather than infectious bronchitis… Moreover, the gasping symptom ordinarily accepted as typical of the disease is also a prominent symptom in infectious bronchitis (gasping disease, chick bronchitis)."[8] The names infectious bronchitis and infectious laryngotracheitis were till then used synonymously and interchangably.

Unaware of the developments, Leland David Bushnell and Carl Alfred Brandly at the Kansas Agricultural Experiment Station studied a similar case which they called "gasping disease" due to the apparent symptom. They had known the disease since 1928. Their report in 1933 titled "Laryngotracheitis in chicks" published in the Poultry Science indicated a clear distinction of infectious bronchitis from infectious laryngotracheitis as the main organ affected was the bronchi.[9] The bronchi infection resulted in severe gasping and swift death due to inability to eat food. They also discovered that the pathogens could not be bacteria or protozoans as they passed through membranes (Berkefield filter) that would block those pathogens.[3] They therefore identified the pathogen as a virus, stating:

In several experiments we have reproduced the disease in chicks by the intratracheal, subcutaneous and intraperitoneal injection of Berkefeld filtered material. The chicks developed typical gasping symptoms after various periods of incubation, different groups of chicks first showing symptoms in six, seventeen, nineteen, etc., days after receiving the filtrate... The disease may also be transferred by means of filtrates of spleen, liver, and kidney tissues and by the transfer of bacteriologically sterile blood.[9]

This was the discovery of infectious bronchitis virus (IBV), later renamed Avian coronavirus. Yet, Bushnell and Brandy made an erroneous remark by saying, "The symptoms and lesions in the chicks [caused by IBV] are similar to those seen in so-called laryngotracheitis of adult birds and are probably due to the same agent."[9]

In 1936, Jerry Raymond Beach and Oscar William Schalm at the University of California, Berkeley, reexamined Bushnell and Brady's experiment with a conclusion that infectious laryngotracheitis and infectious bronchitis with their causative viruses were different. (Beach had discovered infectious laryngotracheitis virus in 1931.[10]) They concluded that:

  • It was found that chickens that recovered from an infection with one of the two strains of virus were refractory to further infection with either strain. It was also found that the sera from chickens that have recovered from an infection with one strain of the virus would neutralize virus of either strain. These results show the identity of the two strains of virus.
  • Chickens refractory to infection with this virus were shown to be susceptible to the virus of laryngotracheitis. Likewise, chickens refractory to the latter virus were susceptible to the former. These results demonstrate that the two viruses are distinct from one another.[11]

Hudson and Beaudette later in 1937 were able to culture IBV for the first time using chicken embryos.[12][6] This specimen, known as the Beaudette strain, became the first coronavirus to have its genome completely sequenced in 1987.[13]

Discovery of mouse coronaviruses

Francis Sargent Cheevers, Joan B. Daniels, Alwin M. Pappenheimer and Orville T. Bailey investigated the case of brain disease (murine encephalitis) at the Department of Bacteriology and Immunology of Harvard Medical School in Boston in 1949. Two laboratory mice (Schwenktker strains) of 17 and 18 days old had flaccid paralysis and died.[14] By then it was known that murine encephalitis was caused by a picornavirus, called Theiler's virus, which was discovered by Max Theiler at the Rockefeller Foundation in New York in 1937.[15] But the Harvard scientists found that the two mice had unusual symptoms other than brain damage (demyelination). The mice had no visible illness or diarrhoea, which usually accompany murine encephalitis. In addition, the causative virus was isolated from different organs including liver, spleen, lungs, and kidneys.[16] This indicated that brain was not the primary target organ. Liver was particularly affected with severe necrosis, indicating hepatitis. The new virus was named JHM, after the initials of John Howard Mueller.[17]

In the autumn of 1950 there was a sudden outbreak of fatal hepatitis among laboratory mice (Parkes or P strains) at the National Institute for Medical Research, Mill Hill, London.[18] Alan Watson Gledhill and Christopher Howard Andrewes isolated the causative virus, which experimentally was highly infectious to healthy mice. They named the virus as "mouse hepatitis virus (MHV)."[19] Gledhill called the experiments on the highly infectious nature of the virus as a "bizarre discovery".[20]

John A. Morris at the National Institutes of Health, Bethesda, discovered a new mouse virus, named H747, in 1959 from samples in Japan. When he compared the virus with JHM and MHV using serological tests he found that they were both antigenically related Convinced of their relatedness he created a common name as "hepatoencephalitis group of murine viruses."[21]

Discovery of human coronaviruses

Human coronaviruses were discovered as one of the many causative viruses of common cold. The research originated when the British Medical Research Council and the Ministry of Health established the Common Cold Research Unit (CCRU) at Salisbury in 1946.[22] Directed by Andrewes, the research laboratory discovered several viruses such as influenza viruses, parainfluenza viruses and rhinoviruses that cause common cold.[23][24]

David Arthur John Tyrrell joined CCRU in 1957 and succeeded Andrewes in 1962.[25] He developed a technique for growing rhinoviruses using nasal epithelial cells for the first time in 1960.[26][27][28] His team soon after developed a concept of broad categorisation of common cold viruses into two groups: one group, called H strain, could be maintained only in human-embryo-kidney cell culture, and another group, designated M strain, could be maintained both in human-embryo-kidney cell culture and monkey-embryo-kidney cell culture.[29] By then many common cold viruses could be grown in any of these cell cultures and designated as either M or H strain.[30][31]

During 1960-1961, Tyrrell's team collected throat swabs from 170 school boys having common cold at boarding school in Epsom, Surrey. England. Among few samples that could not be cultured in any of the culture media, a specimen designated B814, collected on 17 February 1961, was particularly infectious among healthy volunteers.[32] There was no evidence whether the pathogen in B814 was a bacterium or a virus as all bacterial and viral culture methods available showed negative results. It could only be maintained in human tracheal culture and experimentally passed on to healthy volunteers by nasal inoculation.[33] In 1965, they were able to confirm that the pathogen was a filter-passing virus, susceptible to ether treatment (indicating a lipid envelope of the virus), able to induce cold in antibiotic-treated volunteers (indicating it was not a bacterium), and cultured in human-embryo-trachea epithelial cell culture. Serological tests (antigen-antibody reactions) further indicated that the virus was not related (not reactive) to antibodies (serotypes) of any known viruses at the time.[3] In their report in the British Medical Journal, Tyrrell and Malcolm L. Bynoe wrote their conclusion as:

After considerable initial doubts we now believe that the B814 strain is a virus virtually unrelated to any other known virus of the human respiratory tract, although, since it is ether-labile, it may be a myxovirus.[34]

But they contradicted themselves regarding the identity of the virus as they mentioned in the experimental results, saying:

It was concluded that B814 did not belong to any of the serotypes of myxovirus used, but might be distantly related to influenza C or Sendai viruses.[34]

In an independent research in US, Dorothy Hamre and John J. Procknow studied respiratory tract infection among medical students at the University of Chicago.[35] In 1962, they obtained five samples that were associated with very different symptoms, causing mild cold only, and could be cultured only in secondary human kidney tissue in contrast to other cold viruses which they could maintain in monkey-embryo-kidney cell culture. Serological test indicated they were not myxoviruses (Orthomyxoviridae). They presented their discovery as "A new virus isolated from the human respiratory tract" in the Proceedings of the Society for Experimental Biology and Medicine in 1966.[36] They further studied one sample, designated 229E, grown in human diploid cell culture (Wi-38) and described its developmental stages using transmission electron microscopy.[37]

Discovery of the structure

Viruses cannot be seen normally seen with light microscopes. It was only with the development of electron microscope that viruses could be visualised. Reginald L. Reagan, Jean E. Hauser, Mary G. Lillie, and Arthur H. Craige Jr. of the University of Maryland were the first to describe the structure of coronavirus using the transmission electron microscopy. In 1948, they reported in The Cornell Veterinarian that IBV was spherical in shape and some of them had filamentous projections.[38] But the images were difficult to interpret owing to poor resolution and low magnification (at × 28,000).[3] Their subsequent studies did not show any striking properties from other viruses.[39][40] An important advancement was made by Charles Henry Domermuth and O.F. Edwards at the University of Kentucky in 1957 when they observed IBVs as "ring or doughnut-shaped structures."[41]

D.M. Berry at the Glaxo Laboratories, Middlesex, UK, with J.G. Cruickshank, H.P. Chu and R.J.H. Wells at the University of Cambridge published a more comprehensive and better electron microscopic images in 1964. Four strains of IBV, including Beaudette strain, were compared with influenza virus, with which they share most resemblance. In contrast to influenza virus in which the projections were small and straight, all IBV strains had "pear-shaped projections", which were names the "spikes" and described as:

These “spikes” were often seen over part of the surface only and were less densely packed than those seen in influenza viruses. They varied considerably in shape. Commonly they appeared to be attached to the virus by a very narrow neck and to thicken towards their distal ends, sometimes forming a bulbous mass 90-110 Å in diameter.[42]

J. F. David-Ferreira and R. A. Manaker from the National Cancer Institute, Bethesda, were the first to study the structure of MHV in 1965. They also observed the surface projections as on IBV, stating, "The outer surface of the particle is covered by 'spicules'."[43] In 1966, Tyrrell sought the help of Anthony Peter Waterson at the St Thomas's Hospital Medical School in London who had recruited June Dalziel Almeida as an electron microscopist. Almeida had studied IBV and MHV finding them as structurally distinct viruses, but her manuscript was rejected upon a referee's decision that the microscopic images were of influenza virus and lacked novelty.[4] Tyrrell supplied the human virus samples from which it was possible to ascertain the viral structure. Almeida and Tyrrell published their findings in the April 1967 issue of the Journal of General Virology, in which they concluded:

Probably the most interesting finding from these experiments was that two human respiratory viruses, 229 E and B814 are morphologically identical with avian infectious bronchitis. Their biological properties, as far as they are known, are consistent with this. Both the human viruses are ether sensitive as is avian infectious bronchitis 229 E, have a similar size by filtration and multiply in the presence of an inhibitor of DNA synthesis.[44]

In 1967, Kenneth McIntosh and co-workers at the National Institute of Health, Bethesda, reported the structure of common cold viruses they collected from fellow workers during 1965-1966. They found six of their samples had common characters with B814. They compared the structure of one of their samples numbered 501 (subsequently designated OC43 as the number of specimen in organ culture[2]) with those of 229E, IBV and influenza virus. It was so identical to IBV that they called the human viruses as "IBV-like viruses".[45] They made a definitive description as:

All "IBV-like" viruses, 229E, and IBV itself show the following characteristics: (1) an over-all diameter of 160 mμ with a variation of ± 440 mμ; (2) a moderate pleomorphism with resultant elliptical, round, or tear-drop shapes but no filamentous or "tailed" forms; (3) characteristic spikes 20 mμ long, usually club- or pear-shaped narrow at the base and 10 mμ wide at the outer edge, spaced widely apart and distributed fairly uniformly about the circumference of the particle.[45]

Invention of the name and origin of the taxonomy

By mid-1967 it was recognised that IBV, MHV, B814 and 229E were structurally and biologically similar so that they form a distinct group.[46][47] Tyrrell met Waterson and Almeida in London to decide on the name of the viruses. Almeida had earlier suggested the term "influenza-like" because of their resemblance, but Tyrrell thought it inappropriate.[4] Almeida came up with a novel name "coronavirus".[48] Tyrrell wrote of his recollection in Cold Wars: The Fight Against the Common Cold in 2002:

Even though we could only base our judgement on the electron microscope images we were quite certain that we had identified a previously unrecognised group of viruses. So what should we call them? 'Influenza-like' seem a bit feeble, somewhat vague, and probably misleading. We looked more closely at the appearance of the new viruses and noticed that they had a kind of halo surrounding them. Recourse to a dictionary produced the Latin equivalent, corona, and so the name coronavirus was born.[4]

Proposal of the new name was submitted to and accepted by the International Committee for the Nomenclature of Viruses (ICNV, established in 1966).[3] 16 November 1968 issue of Nature reported the justification by Almeida, Berry, C.H. Cunningham, Hamre, M.S. Hofstad, L. Mallucci, McIntosh and Tyrrell as:

Particles [of IBV] are more or less rounded in profile; although there is a certain amount of polymorphism, there is also a characteristic "fringe" of projections 200 Å long, which are rounded or petal shaped, rather than sharp or pointed, as in the myxoviruses. This appearance, recalling the solar corona, is shared by mouse hepatitis virus and several viruses recently recovered from man, namely strain B814, 229E and several others... In the opinion of the eight virologists these viruses are members of a previously unrecognized group which they suggest should be called the coronaviruses, to recall the characteristic appearance by which these viruses are identified in the electron microscope.[49]

Coronavirus was accepted as a genus name by ICNV in its first report in 1971.[50] IBV was then officially designated the type species as Avian infectious bronchitis virus (but renamed to Avian coronavirus in 2009).[51] Mouse hepatitis virus approved in 1971 was merged with Rat coronavirus (discovered in 1970[52]) as Murine coronavirus in 2009.[53] 229E and OC43 were collectively named Human respiratory virus but merged as Human coronavirus 229E (HCoV-229E) in 2009.[54] The first discovered human coronavirus B814 was antigenically different from 229E and OC43,[55] but it could not be propagated in culture and was exhausted during experiments in 1968,[56] thus, was excluded in taxonomy. Coroniviridae was adopted as the family name in the ICNV (soon after renamed International Committee on Taxonomy of Viruses, ICTV) second report in 1975.[57][58]

Other animal coronaviruses

Due to increasing number and diversity of new species, CTV split the genus Coronavirus in 2009 into four genera, Alphacoronavirus, Betacoronavirus, Deltacoronavirus, and Gammacoronavirus.[59][60] As of 2020, there are 39 species of coronaviruses under the family Coronaviridae.[61] There are 7 human coronaviruses while 32 species are those of pigs, dogs, cats, rodents, cows, horses, camels, Beluga whales, birds and bats.[1]

Feline infectious peritonitis virus

A viral infection in pigs, called transmissible gastroenteritis, which was characterised mainly by diarrhoea and vomitting, and associated with high mortality was first recognised by Leo P. Doyle and L. M. Hutchings in 1946.[62] A. W. McClurkin isolated and identified the virus in 1965.[63] The virus was named Transmissible gastro-enteritis virus of swine in the ICNV first report, and changed to Porcine transmissible gastroenteritis virus (PTGV) in the second report in 1976.[64] A new disease that caused inflammation of the abdomen (peritonitis) in cats was reported in 1966,[65] the virus was identified in 1968,[66] and was named by ICTV in 1991 as Feline infectious peritonitis virus. In 1974 a new coronavirus was discovered from US military dogs,[67] and was named by ICTV in 1991 as Canine coronavirus. As the molecular and antigenic relationship of the three viruses were later established,[68][69] ICTV merged the three viruses into Alphacoronavirus 1 in 2009.[64][70]

Porcine epidemic diarrhea virus

An acute infectious diarrhoea was first known in England in 1971. The infection was specifically among fattening pigs and sows. It was first reported by J. Oldham in Pig Farming in 1972.[71][72] M. B. Pensaert and P. de Bouck at the University of Gent, Begium isolated and identified the new coronavirus in 1978, and designated it CV777.[73] It eventually spread throughout Europe. ICTV gave named the virus Porcine epidemic diarrhea virus in 1995.[74] An epidemic broke out from China in 2010 that spread throughout the world. A virulent strain emerged in US between 2013 and 2015. It affected pigs of all ages, and mortality was as high as 95% among the the suckling piglets. Another severe outbreak occurred in Germany in 2014 that spread to other European countries.[75]

Bat coronaviruses

Reagan and his colleagues at the University of Maryland were the first to investigate bats as a potential sources of coronavirus in 1956. They experimentally inoculated 44 cave bats or little brown bats (Myotis lucifugus) with IBV and found that all of them developed the symptoms of infectious bronchitis. Their report reads:

50 percent of the bats exposed to the infectious bronchitis virus showed symptoms or death in the intracerebral, intraperitoneal, intradermal, intracardiac and intraocular groups; 75 percent in the intranasal and intrarectal groups; 100 percent in the intraoral group; and 25 percent intralingual and intramuscular group, whereas the controls appeared normal.[76]

But nothing was known of the real nature of bats as reservoirs of coronaviruses until the epidemic of severe acute respiratory syndrome of humans in 2002/2003. When the virus, SARS-CoV was identified in the early 2003,[77] the Himalayan palm civets (Paguma larvata) found in a live-animal market in Guangdong, China, were established as the source of the infection a few months later.[78] Further studies showed that civets were not the natural hosts of the virus, but horseshoe bats (Rhinilophus species) are the actual carriers.[79][80] Among all vertebrate hosts, bats are known to harbour the most variety of coronaviruses, with more than 30 species identified.[81][82] According to diversity estimate, there may be 3,200 species of coronaviruses in bats.[83]

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