There are only 3 occurrences of coronavirus in the HE Corpus.
The initiative wanted honour the memory of Dr Carlo Urbani who died of SARS in Hanoi in 2003, having contracted the coronavirus infection during his investigation work on the epidemics.
Implementation of GHSA will draw on USAID experience addressing highly dangerous pathogens, including Severe Acute Respiratory Syndrome (SARS), avian influenzas, Middle East Respiratory Syndrome (MERS) coronavirus , as well as lessons from ongoing global efforts to establish prevention, preparedness, and response capabilities for the possible spread of viruses across borders.
Figure 1.4 Selected emerging and re-emerging infectious diseases: 1996–2004 Ebola and Crimean– Congo haemorrhagic fever; Influenza H5N1; Hantavirus; Lassa fever; Monkeypox; Nipah; Hendra; New variant Creutzfeld–Jakob disease; Rift Valley fever; SARS coronavirus; Venezuelan equine encephalomyelitis; Yellow fever; West Nile fever; Cryptosporidiosis; Leptospirosis; Lyme borreliosis; Escherichia coli O157; Multidrug-resistant Salmonella.
To better examine the concept of coronavirus, a linguistic analysis was conducted on the COVID-19 corpus released as part of the COVID-19 Open Research Dataset (CORD-19).
There are 102,683 occurrences of coronavirus found in 17,931 articles that were published in different 2672 journals between 1970 and 2020.
are a highly diverse group or family of large enveloped spherical and pleomorphic viruses
belong to the order Nidovirales, family Coronaviridae, and kingdom Orthocoronavirinae
are subdivided into 4 genera: α, β, γ, and δ
display a
crown-like outer structure characterised by bulbous and widely-spaced projections
diameter of 60-140 nanometres
contain a very large non-segmented, single-stranded, and positive sense RNA (ssRNA) genome of 27-34 kilobases in length complexed with a basic nucleocapsid protein to form a helical capsid
infect mammals and birds
may induce systemic diseases
are prone to
rapid mutations during transmission
interspecies transmission
zoonotic (from non-human to human) transmission
cause from mild infections to death
respiratory infections
enteric infections
neurological infections
hepatitis
serositis
of which 7 species were found to affect humans
Based on infected organism:
Calf coronavirus
Human coronavirus (HCV/HCoV)
Bovine coronavirus
Feline coronavirus
Cheetah coronavirus
Asian leopard cat coronavirus
Civet cat coronavirus
Murine coronavirus
Parker's rat coronavirus (RCV)
Rat sialodacryoadenitis virus (RCV-SDA)
Longquan mouse coronavirus
Porcine coronavirus
Canine coronavirus
Avian coronavirus
Pigeon coronavirus
Pheasant coronavirus
Canada goose coronavirus (CGCoV)
Blue-winged teal coronavirus
Guinea fowl coronavirus
Turkey coronavirus
Equine coronavirus
Bubaline coronavirus
Bat coronavirus
Pipistrellus bat coronavirus
Tylonycteris bat coronavirus
Miniopterus bat coronavirus
Zaria bat coronavirus
Rosettus bat coronavirus
Rhinolophus bat coronavirus
Scotophilus bar coronavirus
HKU6 bat coronavirus
HKU6-1 bat coronavirus
Chinese ferret badger coronavirus
Sable antelope coronavirus
Dromedary camel coronavirus
Bottlenose dolphin coronavirus
Beluga whale coronavirus
White-tailed deer coronavirus
Based on pathogenicity
pathogenic coronavirus
non-pathogenic coronavirus
innocuous coronavirus
harmless coronavirus
asymptomatic coronavirus
mild coronavirus
lethal conoravirus
avirulent coronavirus
highly pathogenic human coronavirus
Based on affected organism and system
Porcine respiratory coronavirus
Canine respiratory coronavirus
Feline enteric coronavirus
Canine enteric coronavirus
Human respiratory coronavirus
Bovine enteric coronavirus
Human enteric coronavirus
Calf enteric coronavirus
Ferret enteric coronavirus
Turkey enteric coronavirus
Bovine respiratory coronavirus
Mouse neurotropic coronavirus
Rabbit enteric coronavirus
Swine enteric coronavirus
Bat enteric coronavirus
Based on the disease caused:
Porcine hemagglutinating encephalomyelitis coronavirus (PHE-CoV/PHEV)
Swine acute diarrhoea syndrome coronavirus (SADS-CoV)
Severe acute respiratory syndrome coronavirus (SARS-CoV)
Middle East respiratory syndrome coronavirus (MERS-CoV)
Mouse hepatitis coronavirus
[Porcine] transmissible gastroenteritis coronavirus (TGEV)
Feline infectious peritonitis [corona]virus (FIPV)
Porcine epidemic diarrhoea coronavirus (PEDV)
Avian infectious bronchitis coronavirus (IBV)
Neonatal calf diarrhoea coronavirus (NCDCV)
Human pneumonia-associated coronavirus
Bat SARS-like coronavirus
BCoV-like human enteric coronavirus
SARS-like coronavirus
SARS-associated coronavirus
MERS-like coronavirus
MERS-related coronavirus
common-cold coronavirus
PED coronavirus
Covid-19 coronavirus
Based on geographical location
Wuhan coronavirus
British coronavirus
Danish coronavirus
Based on affected system/tissue:
respiratory coronavirus
enteric coronavirus
neurotropic coronavirus
gastrointestinal coronavirus
neurovirulent coronavirus
nasopharungeal coronavirus
pantropic coronavirus
Based on transmission
zoonotic coronavirus
epizootic swine coronavirus
fecal coronavirus
Based on taxonomy
Alphacoronavirus
Betacoronavirus
Gammacoronavirus
Deltacoronavirus
Based on viral morphology
trimeric coronavirus
trimeric human coronavirus
trimeric SARS coronavirus
enveloped RNA coronavirus
single-stranded RNA coronavirus
Based on human manipulation
chimeric coronavirus
UV-inactivated coronavirus
attenuated coronavirus
A sample of 226 contexts containing mentions of coronavirus components were extracted. Most mentions are centred on the following components: RNA genome, protein repertoires and structural proteins.
largest RNA genome identified to date
very plastic, which means that coronaviruses have a high potential for evolution, adaption, and interspecies jumping.
encodes:
four major structural proteins: spike (S), nucleocapsid (N), membrane (M), and envelope (E)
hemaggulitin-esterase (HE) protein, not found in all coronaviruses
non-structural proteins
accessory proteins
Protein repertoire of the coronaviruses consists of four main structural and approximately 16 major non-structural proteins.
Coronavirus consists four main proteins, spike (S), membrane (M), envelope (E) and nucleocapsid (N).
characterised in 2003
mediates entry of coronavirus
constitutes the outermost component in a coronavirus virion particle
forms a structure (known as peplomers or spikes) that protrude from the envelope that encloses the round nucleocapsid.
governs binding to host cell receptors and virus entry into cells
plays important roles in inducing a protective immune response, and in virus attachment, membrane fusion, and viral pathogenicity
primarily targeted by monoclonal antibodies (mAbs)
all coronavirus vaccine candidates are directed against it because it is the most immunological component of coronaviruses .
genetically variable, which increases the difficulty of generating a vaccine
a key factor in host specificity
the most abundant component of the coronavirus
plays important roles in virus assembly by interacting with S and N proteins
critical components required for assembly of coronavirus virions and virus-like particle
highly conserved, approaching the level of conservation of some of the viral enzymes and replicase accessory proteins from pp1a
differs from other viral proteins in terms of its structure, processing, and intracellular transport
its expression might be sufficient to trigger the formation of virus-like particles (VLPs).
suggested to induce innate immunity including interferon production.
proposed to play a role in innate immune response to coronaviruses
a minor component
plays an important role in virion assembly
regulates virion assembly and release
its expression might be sufficient to trigger the formation of virus-like particles (VLPs)
forms VLPs upon co-expression with M proteins
binds to the genomic RNA and encapsidates it to form a helical nucleocaspid.
found on the membrane of some coronaviruses
makes up a second shorter spike protein on some coronaviruses
may increase viral infectivity
presumably promotes virus spread and entry in vivo by facilitating the reversible attachment of the virus
highly conserved components of the coronavirus lifecycle that mediate viral replication
include:
3C-like protease (3CLpro)
papain-like protease (PLpro)
RNA-dependent RNA polymerase (RdRp)
The spike (S) protein is the most discussed structural protein. This may be due to its role in inducing a protective immune response, which makes it the target of all vaccine candidates.
Currently, there are at least seven known human coronaviruses (2019-nCoV, SARS-CoV, MERS-CoV, HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1), where many of them, including severe acute respiratory syndrome-related coronavirus (SARS-CoV) and Middle East respiratory syndrome-related coronavirus (MERS-CoV), were shown to be transmitted from bats.
To date, 7 pathogenic HCoVs (Figure 2A and 2B) have been found [1, 27] : (i) 2019-nCoV, SARS-CoV, MERS-CoV, HCoV-OC43, and HCoV-HKU1 are b genera, and (ii) HCoV-NL63 and HCoV-229E are a genera.
The following histogram represents the occurrences of human coronavirus acronyms across time. Please note that nCoV stands for novel coronavirus, an expression used to refer to new identified coronaviruses before a denomination is agreed upon. This linguistic analysis found three variants for MERS-CoV (also referred to as hCoV-EMC and MERS-hCoV-EMC) as well as two variants for SARS-CoV-2 (also referred to as 2019-nCoV).
As can be seen, it is no surprise that SARS-CoV, MERS-CoV and SARS-CoV-2 are the most mentioned human coronaviruses in the corpus. These are highly pathogenic and caused epidemics. It is worth noting that mentions of other less harmful human coronaviruses increased after the 2002-2003 SARS outbreak. Even though some of human viruses were identified prior to 2002, the corpus contains significantly more occurrences thereafter than in previous years. This indicates that research in human coronaviruses truly exploded after the 2002-2003 SARS outbreak.
The following section contains summaries of all human coronaviruses known to date. These summaries are based on definitional contexts extracted from the corpus.
is a betacoronavirus
discovered in the 1960s.
circulates in humans globally
whose ancestors were identified in domestic animals such as cattle and swine
is known to cause
self-limiting mild upper respiratory tract infections
common colds, frequently
pneumonia in older adults, neonates and immunocompromised patients
gastrointestinal symptoms
winter outbreaks at 2-4 year intervals in temperate regions
is a alphacoronavirus
discovered in the 1960s.
circulates in humans globally
is likely to have originated from bats
similar coronaviruses were identified in dromedaries
is known to cause
self-limiting mild upper respiratory tract infections (common colds)
lower respiratory tract infections in children
infections symptomatically indistinguishable from influenza A viruses and rhinoviruses.
winter outbreaks at 2-4 year intervals in temperate regions
is a alphacoronavirus
discovered in 2004 in a child with bronchiolitis in The Netherlands
circulates in humans globally
whose incidence peaks during spring, early summer and winter
is known to cause
self-limiting mild upper respiratory tract infections (common colds)
lower respiratory tract infection in children
conjunctivitis, fever, bronchiolitis
gastrointestinal symptoms
is a betacoronavirus
discovered in 2005 in a elderly man with pneumonia and bronchiolitis in Hong Kong
circulates in humans globally
whose incidence peaks during winter
is known to cause
mild upper respiratory tract infections (common colds)
pneumonia in older adults, young children and immunocompromised patients
stands for severe acute respiratory syndrome coronavirus
is a betacoronavirus
discovered in 2002 during an outbreak of 300 cases of rapidly progressive pneumonia in the province of Guangdong, China
believed to have originated from bats
identified in several wild animal species and live animal markets
infected 8,096 confirmed cases
killed 774 people globally
has an incubation period of 1-4 days
spread across 26 countries
is known to cause severe acute respiratory syndrome (SARS)
lower respiratory tract infection with symptoms including fever, malaise and lymphocytopenia
diarrhoea, haematological disorders, pulmonary vasculitis, thrombosis
systemic infection
death (approx. 10% mortality rate)
sheds in respiratory secretions, stool and urine
stands for Middle East respiratory syndrome coronavirus
is a betacoronavirus
once known as human coronavirus Erasmus Medical Center/2012 (HCoV-EMC/2012)
discovered in 2012 in a elderly man with severe pneumonia and renal failure in Jeddah, Saudi Arabia
believed to have originated from bats
transmitted from camels
infected 2,468 confirmed cases
killed 851 people globally
spread across 27 countries
is known to cause severe acute respiratory syndrome (SARS)
mild to severe self-limiting upper and lower respiratory tract infection
severe community acquired pneumonia (CAP)
sheds in respiratory secretions and stool to a lesser extent
stands for severe acute respiratory syndrome coronavirus 2
is a betacoronavirus
once known as 2019 novel human coronavirus (2019-nCoV)
discovered in December 2019 in lung airway epithelial cells of a patient with pneumonia in Wuhan, China
believed to have originated from bats
is closely related to a group of severe acute respiratory syndrome-related coronaviruses (SARSr-CoV), showing 96% identity to a bat coronavirus)
is known to cause Coronavirus Disease 2019 (COVID-19)
less severe infection than SARS-CoV
mild to severe lower respiratory tract infection
mild fever (37.3 °C -38.5 °C) and irritant dry cough
pneumonia, characterised by fever, cough, dyspnoea, bilateral pulmonary infiltrates and acute respiratory injury (more severe in aged than younger patients)
acute respiratory distress syndrome (ARDS)
kidney tubular damage through direct cytotoxicity
lung epithelia damage
spleen damage, myocardial dysfunction, hepatic injury and acute renal failure
sheds in respiratory secretions and stool
This linguistic analysis looks at 402 different collocations of coronavirus. The following visualisation contains 13 types of collocations. Each collocate constitutes a bubble whose size represents its frequency in the corpus and whose colour represents its type of collocation (grammar relations). You can reduce and increase the number of collocates shown by setting a desired range with the frequency slider control.
Coronaviruses are primarily described agents, a pathogens, viruses and causes.
Top collocates described as coronavirus are generic terms such as virus, agent, pathogen, as well as denominations for specific coronaviruses:
MERS-CoV
SARS-CoV
TGEV ([Porcine] transmissible gastroenteritis coronavirus)
IBV (Avian infectious bronchitis coronavirus)
PEDV (Porcine epidemic diarrhoea coronavirus)
2019-nCoV
SARS-CoV-2
Top nouns modified by coronavirus are infection, protein, virus, genome, disease and replication. This highlights two key processes in which coronaviruses participate (infection and replication), which cause disease. It also includes the two most discussed coronavirus components, as explained previously.
Coronavirus is modified by adjectives and nouns referring to:
the disease it causes: SARS (Severe Acute Respiratory Syndrome), MERS (Middle East Respiratory Syndrome)
the type of organism it infects: human, feline, bovine, porcine, enteric, canine, murine, bat
Collocates before against coronavirus are nouns designating objects and activities that combat coronaviruses. Top collocates include antibody, activity, vaccine, protection, response, efficacy and inhibitor.
Collocates before by coronavirus are verbs such as cause, infect, induce, encode, follow, and the noun infection.
Collocates before for coronavirus are
terms pertaining to testing (positive, negative, test, report, result, RT-PCR, seropositive, seronegative);
microbiology terms (receptor, protein);
vaccine; and reservoir.
Top collocates before with coronavirus include infection, infect, associate, patient, challenge and inoculate.
The preposition to is also very productive and links nouns, verbs and adjectives to coronavirus. Top collocates are are:
antibody, immunity and antiserum, because combating coronaviruses involves the immune system;
relate, similar, similarity, identical and compare, because when identifying coronaviruses it is important to establish a lineage by comparison;
due, because it coronaviruses are causes for diseases;
exposure and expose, because individuals come into contact with coronaviruses; and
belong, because coronaviruses are classified into taxons.
The preposition of is very productive and links varied concepts with coronavirus:
taxonomical terms (strain, type, member, form)
microbiology terms designating parts (protein, sequence, genome, glycoprotein, gene)
processes (outbreak, emergence, identification, replication, detection, transmission, spread, pathogenesis)
Coronaviruses are
isolated
inactivated
neutralised
amplified
controlled
purified
extracted
inhibited
Coronaviruses are
discovered
identified
detected
confirmed
recognised
determined
Coronaviruses are
characterised
described
studied
sequenced
Coronaviruses
emerge
originate
Coronaviruses are
named
termed
designated
called
Coronaviruses
spread
circulate
Coronaviruses are
transmitted
propagated
Coronaviruses are
shed
excreted
Coronaviruses
bud
infect
mutate
replicate
This histogram represents the number of occurrences of coronavirus, together with scientific articles published each year with at least one occurrence.
Occurrences increased sharply in the 2002-2003 period, which coincides with the outbreak of SARS, a respiratory disease caused by a type of coronavirus.
As of 2003, the number of published articles has increased steadily in parallel with an great rise in occurrences. This means that articles from 2003 onwards contain more occurrences of coronavirus, which suggests that publications have become more specific.
This shows the evolution of coronavirus in the vast Google Books corpus, which gives you a general idea of the evolution of the term in English books between 1800 and 2012. Values are expressed as a percentage of the total corpus instead of occurrences.
Please note that this is not a domain-specific corpus. However, it provides an overview of coronavirus across domains.
Mentions of coronavirus increased steadily from 1966 until 1983 when it first peaked. It sustained high values for over two decades until 2004, when it finally plummets to pre-1965 values.
Subsequent to the WHO declaration, the United States Surgeon General proclaimed a formal advisory to cancel elective surgeries at hospitals due to the concern that elective procedures may contribute to the spreading of the coronavirus within facilities and use up medical resources needed to manage a potential surge of coronavirus cases [6] . The announcement escalated to a nationwide debate regarding the safety and feasibility of continuing to perform elective surgical procedures during the COVID-19 pandemic [7, 8] . Many health care professionals erroneously interpreted the Surgeon General's recommendation as a "blanket directive" to cancel all elective procedures in the Country [9] . This notion was vehemently challenged in an open letter to the Surgeon General on behalf of United States hospitals [10] .
Although the efficacy of antiviral therapy is still uncertain, combination treatment based on the inhibition of viral replication might reduce the inflammatory injury, and can allow the body to gradually produce enough virus-specific antibodies to clear the virus through the immune response, and ultimately cure the disease. There is a great debate on the use of corticosteroids for coronavirus infection such as severe acute respiratory syndrome (SARS) [11, 12] and Middle East respiratory syndrome (MERS) [13, 14] , and the data of systemic corticosteroid treatment in critical COVID-19 are lacking. The findings of this study support the use of corticosteroids in severe COVID-19. Early use (immediately on admission or within the first three days of hospitalization) might relatively rapid control the disease progress or avoid disease further deterioration.
As described above, neutrophilia was related to severe 2019 novel coronavirus pneumonia and composite endpoint. However, up to now most of the research have focused on the role of lymphocyte in 2019 novel coronavirus pneumonia. We think that the role of neutrophila in 2019 novel coronavirus pneumonia shouldn't be ignored and further related researches are needed in the future.
In vitro experiments also showed a strong antiviral effect of chloroquine on a recombinant HCoV-O43 coronavirus [45] . Although chloroquine was reported to be active against Middle East respiratory syndrome coronavirus (MERS-CoV) in vitro [46] , this observation remains controversial [47] .
We have read with great interest the Correspondence by Shibo Jiang and colleagues, in which they propose a name change for the newly emerged coronavirus, which was recently designated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the Coronavirus Study Group of the International Committee on Taxonomy of Viruses. The authors argued that the use of SARS in the virus name could confuse the public about the disease that it causes; in addition, they noted that the name SARS-CoV-2 is not consistent with the disease name chosen by WHO, coronavirus disease 2019.
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