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Coronaviridae


Bat-borne virus

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Bat-borne virus

A bat-borne virus is any virus whose primary reservoir is any species of bat. The viruses species include coronaviruses, hantaviruses, lyssaviruses, SARS coronavirus, rabies virus, nipah virus, lassa virus, Henipavirus, Ebola virus and Marburg virus. Bat-borne viruses are among the most important of the emerging viruses.[1][2][3] Transmission Bat-borne viruses are transmitted via bat bite and transfer via saliva, as well as aerosolization of saliva, feces, and/or urine. Like rabies virus, newly emerging bat-borne viruses can be transmitted to humans directly by bats. These include Ebola virus, SARS, and the Chinese respiratory syndrome coronavirus.[4][5] Left unrecognized and untreated, the interval between transmission of rabies virus strains until the disease manifests in the victims, varies from hours to years. Most victims are not aware of either having been bitten by a bat or exposed to a bat's secretions. This can be due to a lack of awareness of a bat's presence in the same space, such as when sleep

Hantaviridae

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Hantaviruses

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Coronaviridae

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Bat SARS-like coronavirus WIV1

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Bat SARS-like coronavirus WIV1

Bat SARS-like coronavirus WIV1, (Bat SL-CoV-WIV1) also sometimes called SARS-like coronavirus WIV1, is a newly identified CoV isolated from Chinese rufous horseshoe bats. The discovery confirms that bats are the natural reservoir of the SARS virus. Phylogenetic analysis shows the possibility of direct transmission of SARS from bats to humans without the intermediary Chinese civets, as previously believed. It is a single-stranded, enveloped, positive-sense RNA betacoronavirus.[1][2] See also Severe acute respiratory syndrome (SARS) References Xing-Yi Ge; Jia-Lu Li; Xing-Lou Yang; et al. (2013). "Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor". Nature. 503 (7477): 535–8. doi:10.1038/nature12711. PMC 5389864. PMID 24172901. Naik, Gautam. "Study: Bat-to-Human Leap Likely for SARS-Like Virus - WSJ.com". Online.wsj.com. Retrieved 2013-10-31.

Coronaviridae

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Bat-borne viruses

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Animal virology

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Coronaviridae

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Coronaviridae

Coronaviridae is a family of enveloped, positive-sense, single-stranded RNA viruses. The viral genome is 26–32 kilobases in length. The particles are typically decorated with large (~20 nm), club- or petal-shaped surface projections (the "peplomers" or "spikes"), which in electron micrographs of spherical particles create an image reminiscent of the solar corona. The newest addition is the 2019-nCoV, showing so far a lower mortality rate than the MERS- and SARS-coronavirus members. Virology Diagram of coronavirus virion structure The 5' and 3' ends of the genome have a cap and poly(A) tract, respectively. The viral envelope, obtained by budding through membranes of the endoplasmic reticulum (ER) and/or Golgi apparatus, invariably contains two virus-specified (glyco)protein species, S and M. Glycoprotein S comprises the large surface projections, while M is a triple-spanning transmembrane protein. Toroviruses and a select subset of coronaviruses (in particular the members of subgroup A in the genus Betaco

Nidovirales

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Virus families

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Coronaviridae

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2012 Middle East respiratory syndrome coronavirus outbreak

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2012 Middle East respiratory syndrome coronavirus outbreak

Since 2012, an outbreak of Middle East respiratory syndrome coronavirus has affected several countries, primarily in its namesake, the Middle East. The virus, which causes Middle East respiratory syndrome (MERS), is a newly emerged betacoronavirus that was first identified in a patient from Saudi Arabia in April 2012. Sporadic cases, small clusters, and large outbreaks have been reported in 24 countries, with over 1,000 cases of the virus and over 400 deaths.[11] Coronavirus Most infections with human coronaviruses are mild and associated with common colds. The six coronaviruses known to infect humans are in the alpha and beta genera. Both MERS-CoV and SARS-CoV (severe acute respiratory syndrome) are betacoronaviruses.[12][13] Global surveillance of potential epidemics and preparation has improved since and because of the SARS epidemic, and MERS is being closely monitored.[14][notes 1] The Fourth Meeting of the International Health Regulations Emergency Committee concerning MERS-CoV was held on 4 Decembe

Middle East respiratory syndrome

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CS1 Persian-language sources (fa)

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Coronavirus frameshifting stimulation element

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Coronavirus frameshifting stimulation element

In molecular biology, the coronavirus frameshifting stimulation element is a conserved stem-loop of RNA found in coronaviruses that can promote ribosomal frameshifting. Such RNA molecules interact with a downstream region to form a pseudoknot structure; the region varies according to the virus but pseudoknot formation is known to stimulate frameshifting. In the classical situation, a sequence 32 nucleotides downstream of the stem is complementary to part of the loop. In other coronaviruses, however, another stem-loop structure around 150 nucleotides downstream can interact with members of this family to form kissing stem-loops and stimulate frameshifting.[1] Other RNA families identified in the coronavirus include the SL-III cis-acting replication element (CRE), the coronavirus 3' stem-loop II-like motif (s2m), the coronavirus packaging signal and the coronavirus 3' UTR pseudoknot. During protein synthesis, rapidly changing conditions in the cell can cause ribosomal pausing. In coronaviruses, this can affec

Coronaviridae

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Cis-regulatory RNA elements

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Coronavirus

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Coronavirus

A coronavirus is one of a number of viruses that cause diseases in mammals and birds. In humans, the viruses cause respiratory infections, including the common cold, which are typically mild, though rarer forms such as SARS, MERS and COVID-19 can be lethal. Symptoms vary in other species: in chickens, they cause an upper respiratory disease, while in cows and pigs coronaviruses cause diarrhea. There are no vaccines or antiviral drugs to prevent or treat human coronavirus infections. Coronaviruses comprise the subfamily Orthocoronavirinae in the family Coronaviridae, in the order Nidovirales.[5][6] They are enveloped viruses with a positive-sense single-stranded RNA genome and a nucleocapsid of helical symmetry. The genome size of coronaviruses ranges from approximately 26 to 32 kilobases, the largest among known RNA viruses. The name coronavirus is derived from the Latin corona, meaning "crown" or "halo", which refers to the characteristic appearance of the virus particles (virions): they have a fringe remin

Coronaviridae

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Coronavirus 3' UTR pseudoknot

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Coronavirus 3' UTR pseudoknot

The Coronavirus 3' UTR pseudoknot is an RNA structure found in the coronavirus genome. Coronaviruses contain 30 kb single-stranded positive-sense RNA genomes. The 3' UTR region of these coronavirus genomes contains a conserved ~55 nucleotide pseudoknot structure which is necessary for viral genome replication.[1] The mechanism of cis-regulation is unclear, but this element is postulated to function in the plus-strand. Other RNA families identified in the coronavirus include the coronavirus SL-III cis-acting replication element (CRE), the coronavirus frameshifting stimulation element, the coronavirus 3' stem-loop II-like motif (s2m) and the coronavirus packaging signal. References Williams GD, Chang RY, Brian DA (October 1999). "A phylogenetically conserved hairpin-type 3' untranslated region pseudoknot functions in coronavirus RNA replication". Journal of Virology. 73 (10): 8349–8355. PMC 112852. PMID 10482585. External links Page for Coronavirus 3' UTR pseudoknot at Rfam

Coronaviridae

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Cis-regulatory RNA elements

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Coronavirus SL-III cis-acting replication element

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Coronavirus SL-III cis-acting replication element

The coronavirus SL-III cis-acting replication element (CRE) is an RNA element that regulates defective interfering (DI) RNA replication.[1] Other RNA families identified in the coronavirus include the coronavirus 3' stem-loop II-like motif (s2m), the coronavirus frameshifting stimulation element, the coronavirus packaging signal and the coronavirus 3' UTR pseudoknot. See also Cardiovirus cis-acting replication element (CRE) Citrus tristeza virus replication signal References Raman S, Bouma P, Williams GD, Brian DA (June 2003). "Stem-loop III in the 5' untranslated region is a cis-acting element in bovine coronavirus defective interfering RNA replication". Journal of Virology. 77 (12): 6720–6730. doi:10.1128/JVI.77.12.6720-6730.2003. PMC 156170. PMID 12767992. External links Page for Coronavirus SL-III cis-acting replication element (CRE) at Rfam

Coronaviridae

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Cis-regulatory RNA elements

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Slippery sequence

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Slippery sequence

Tandem slippage of 2 tRNAs at rous sarcoma virus slippery sequence. After the frameshift, new base pairings are correct at the first and second nucleotides but incorrect at wobble position. E, P, and A sites of the ribosome are indicated. Location of growing polypeptide chain is not indicated in image because there is not yet consensus on whether the −1 slip occurs before or after polypeptide is transferred from P-site tRNA to A-site tRNA (in this case from the Asn tRNA to the Leu tRNA).[1] A slippery sequence is a small section of codon nucleotide sequences (usually UUUAAAC) that controls the rate and chance of ribosomal frameshifting. A slippery sequence causes a faster ribosomal transfer which in turn can cause the reading ribosome to "slip." This allows a tRNA to shift by 1 base (−1) after it has paired with its anticodon, changing the reading frame.[2][3][4][5][6] A −1 frameshift triggered by a sequence like such is a Programmed −1 Ribosomal Frameshift. It is followed by a spacer region, and an RNA sec

Coronaviridae

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Cis-regulatory RNA elements

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Gene expression

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Porcine coronavirus HKU15

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Porcine coronavirus HKU15

Porcine coronavirus HKU15 (PorCoV HKU15) is a virus first discovered in a surveillance study in Hong Kong, China,[1] and first reported to be associated with porcine diarrhea in February 2014. In February 2014, PorCoV HKU15 was identified in pigs with clinical diarrhea disease in the U.S. state of Ohio.[2] The complete genome of one US strain has been published.[3] Since then, it has been identified in pig farms in Canada.[4] The virus has been referred to as Porcine coronavirus HKU15, Swine deltacoronavirus and Porcine deltacoronavirus. References Woo, P. C.; Lau, S. K.; Lam, C. S.; Lau, C. C.; Tsang, A. K.; Lau, J. H.; Bai, R; Teng, J. L.; Tsang, C. C.; Wang, M; Zheng, B. J.; Chan, K. H.; Yuen, K. Y. (2012). "Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus". Journal of Virology. 86 (7): 3995–400

Coronaviridae

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Animal virology

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Gammacoronavirus

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Gammacoronavirus

Gammacoronavirus is one of the four genera, Alpha-, Beta-, Gamma-, and Deltacoronavirus, in the subfamily Orthocoronavirinae of the family Coronaviridae. They are enveloped, positive-sense, single-stranded RNA viruses of zoonotic origin. Coronaviruses infect both animals and humans. While the alpha and beta genera are derived from the bat gene pool, the gamma and delta genera are derived from the avian and pig gene pools.[2] Gamma-CoV also known as coronavirus group 3 are the avian coronaviruses. See also Animal viruses Positive/negative-sense RNA virus References "Virus Taxonomy: 2018 Release" (html). International Committee on Taxonomy of Viruses (ICTV). October 2018. Retrieved 24 January 2019. Woo PC, Lau SK, Lam CS, Lau CC, Tsang AK, Lau JH, Bai R, Teng JL, Tsang CC, Wang M, Zheng BJ, Chan KH, Yuen KY (2012). "Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian

Gammacoronaviruses

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Coronaviridae

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Coronavirus packaging signal

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Coronavirus packaging signal

The Coronavirus packaging signal is a conserved cis-regulatory element found in Coronavirus which has an important role in regulating the packaging of the viral genome into the capsid. As part of the viral life cycle, within the infected cell, the viral genome becomes associated with viral proteins and assembles into new infective progeny viruses This process is called packaging and is vital for viral replication. This virus has positive-sense single-stranded RNA genome. A short region (190 base pairs) in the viral genome was identified that interacts with a viral envelope protein (protein M) and enables the viral RNA to be specificity packaged into virions.[1][2] Other RNA families identified in the coronavirus include the SL-III cis-acting replication element (CRE), the coronavirus frameshifting stimulation element, the coronavirus 3' stem-loop II-like motif (s2m) and the coronavirus 3' UTR pseudoknot. See also Bacteriophage pRNA References Qin L, Xiong B, Luo C, et al. (2003). "Identification of p

Coronaviridae

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Cis-regulatory RNA elements

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Kissing stem-loop

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Kissing stem-loop

An example of an RNA stem-loop. If now a second RNA stem-loop has complementary base-sequence, the two loops can base pair resulting in a kissin loop. This animated GIF shows two RNA loops (orange and green) bind to each other in a structure called a kissing loop. The two RNA loops interact through stacking interactions and through hydrogen bonding (interacting bases shown in space-filling representation). Adapted from Proteopedia page. A kissing stem-loop, or kissing stem loop interaction, is formed in RNA when two bases between two hairpin loops pair. These intra- and intermolecular kissing interactions are important in forming the tertiary or quaternary structure of many RNAs.[1] RNA kissing interactions, also called loop-loop pseudoknots, occur when the unpaired nucleotides in one hairpin loop, base pair with the unpaired nucleotides in another hairpin loop.[2] When the hairpin loops are located on separate RNA molecules, their intermolecular interaction is called a kissing complex. These interaction

Coronaviridae

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Cis-regulatory RNA elements

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Torovirus

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Torovirus

Torovirus is a genus of viruses in the order Nidovirales, in the family Tobaniviridae, in the subfamily Torovirinae.[1] They primarily infect vertebrates.,[2][3] especially cattle, pig, and horse.[4] There are currently three species in this genus including the type species Equine torovirus.[5] Diseases associated with this genus include: gastroenteritis,[4] which commonly presents in mammals,[6] but rarely in humans.[7] Torovirus is the sole genus in the monotypic subfamily Torovirinae.[5] Torovirus is also a monotypic taxon, containing only one subgenus, Renitovirus.[5] Structure Torovirus particles share characteristics with members of the related family Coronaviridae; they are round, pleomorphic, enveloped viruses about 120 to 140 nm in diameter. The virus particle has surface spike proteins that are club-shaped and are evenly dispersed over the surface. A nucleocapsid that is doughnut-shaped with helical symmetry is present.[4][8] Genus Structure Symmetry Capsid Genomic arrangement Genomic segmentat

Nidovirales

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Coronaviridae

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Orthocoronavirinae

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Orthocoronavirinae

Orthocoronavirinae is one of two subfamilies in the family Coronaviridae. It is subdivided into the genera Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus. These include phylogenetically compact genogroups of enveloped, positive-sense, single-stranded RNA and with a nucleocapsid of helical symmetry. The genomic size of coronaviruses ranges from approximately 26 to 32 kilobases, extraordinarily large for an RNA virus. Their numbers are growing rapidly with several novel coronaviruses being recently discovered including Middle East respiratory syndrome coronavirus MERS-CoV discovered in 2012.[3][4] Taxonomy The genus Alphacoronavirus (formerly known as Coronavirus group 1 (CoV-1)) includes subgroups 1a and 1b, which are prototyped by human coronavirus 229E (HCoV-229E) and HCoV-NL63, as well as the newly established species alphacoronavirus 1 (including porcine transmissible gastroenteritis virus [TGEV]), respectively. The genus Betacoronavirus (formerly Betacoronavirus group 2 (Cov-2

Virus subfamilies

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Coronaviridae

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Coronavirus respiratory syndrome

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Coronavirus respiratory syndrome

Coronavirus respiratory syndrome or coronavirus pneumonia or coronavirus flu or coronavirus respiratory syndrome pneumonia, or variant, is a disease caused by members of the coronavirus (CoV) group. It may refer to: Middle East respiratory syndrome (MERS) disease caused by MERS-CoV virus, first occurring in an outbreak 2012–2014, and since recurring Severe acute respiratory syndrome (SARS) disease caused by SARS-CoV virus, first occurring in an outbreak 2002–2004 2019-nCoV acute respiratory disease (2019-nCoV-ARD) caused by 2019-nCoV, first occurring in an ongoing outbreak starting in 2019 See also Acute respiratory distress syndrome (ARDS) Coronavirus outbreak Coronaviridae Pneumonia

Syndromes affecting the respiratory system

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Coronaviridae

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Pneumonia

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Middle East respiratory syndrome coronavirus outbreak

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Middle East respiratory syndrome coronavirus outbreak

Middle East respiratory syndrome coronavirus outbreak (MERS outbreak) may refer to: 2012 Middle East respiratory syndrome coronavirus outbreak (2012 MERS outbreak) 2015 Middle East respiratory syndrome outbreak in South Korea (2015 MERS outbreak) 2018 Middle East respiratory syndrome outbreak (2018 MERS outbreak) See also Middle East respiratory syndrome (MERS), a disease Middle East respiratory syndrome coronavirus (MERS-CoV), a virus Coronavirus outbreak

Coronaviridae

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Middle East respiratory syndrome

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2019–20 Wuhan coronavirus outbreak

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2019–20 Wuhan coronavirus outbreak

The 2019–20 coronavirus outbreak is an ongoing epidemic of coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2, which started in December 2019. It was first identified in Wuhan, capital of Hubei province China, after 41 people presented with pneumonia of no clear cause. It can spread between people, with the time from exposure to onset of symptoms generally between 2 and 14 days.[5] Symptoms may include fever, cough, and shortness of breath.[6] Complications may include pneumonia and acute respiratory distress syndrome. There is no vaccine or specific antiviral treatment, with efforts typically to management symptoms and support functioning.[7] Hand washing is recommended to prevent spread of the disease.[8] Anyone who is suspected of carrying the virus is advised to monitor their health for two weeks, wear a mask, and seek medical advice by calling a doctor rather than directly visiting a clinic.[9] As of 19 February 2020, 75,662 cases have been confirmed, including in all provinces of China and more t

2010s medical outbreaks

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2019 health disasters

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2020 disasters in Asia

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2019–20 Wuhan coronavirus outbreak by country and territory

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2019–20 Wuhan coronavirus outbreak by country and territory

Map of the 2019–20 Wuhan coronavirus outbreak (as of 15 February 2020):   Region of origin (Mainland China)   Confirmed cases reported   Suspected cases reported 2019–20 COVID-19 outbreak by country and territory[1] Country or territory[a] Confirmed Deaths Recoveries[b] China (mainland)[c] 66,492 1,523 8,096 International conveyance[d] 218 0 – Singapore 67 0 17 Hong Kong 56 1 1 Japan 41 1 11 Thailand 33 0 13 South Korea 28 0 7 Malaysia 19 0 3 Taiwan 18 0 1 Germany 16 0 1 Vietnam 16 0 7 Australia 15 0 6 United States 15 0 3 France 11 0 3 Macau 10 0 3 United Kingdom 9 0 1 Canada 8 0 1 United Arab Emirates 8 0 1 India 3 0 1 Italy 3 0 – Philippines 3 1 2 Russia 2 0 2 Spain 2 0 1 Belgium 1 0 – Cambodia 1 0 1 Egypt 1 0 – Finland 1 0 1 Nepal 1 0 1 Sri Lanka 1 0 1 Sweden 1 0 – 29 territories 67

2019 health disasters

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2020 disasters in Asia

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2010s medical outbreaks

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Novel coronavirus

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Novel coronavirus

Look up nCoV or novel coronavirus in Wiktionary, the free dictionary. A novel coronavirus (nCoV) is any recently discovered coronavirus of medical significance not yet permanently named. Although coronaviruses are endemic in humans and infections are normally mild (such as the common cold, which is caused by human coronaviruses in about 15% of cases), cross-species transmission has produced some unusually virulent strains which can cause viral pneumonia and in serious cases even acute respiratory distress syndrome.[1][2][3] Species The following viruses could initially be referred to as "novel coronavirus", often with retroactive addition of the year of discovery, before being given a permanent designation: Human pathogenic novel coronaviridae species Initial name Officially named Informal names Original host[a] Place of discovery Disease caused 2019-nCoV severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)[b][4][5] SARS virus 2 snakes, pangolins, bats Wuhan, China coronavirus disea

Coronaviridae

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Chinese coronavirus

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Chinese coronavirus

Chinese coronavirus may refer to: Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2), first reported in Wuhan, Hubei, China; in December 2019 Severe acute respiratory syndrome-related coronavirus (SARS-CoV), first reported in Foshan, Guangdong, China; in November 2002 See also Coronavirus (CoV) Coronaviridae Coronavirus outbreak (disambiguation) Coronavirus respiratory syndrome (disambiguation) novel coronavirus (nCoV)

Coronaviridae

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Coronavirus outbreak

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Coronavirus outbreak

Coronavirus outbreak is an outbreak of disease caused by coronavirus infections. It may refer to: 2019–20 Wuhan coronavirus outbreak 2018 Middle East respiratory syndrome outbreak (2018 MERS outbreak) 2015 Middle East respiratory syndrome outbreak in South Korea (2015 MERS outbreak) 2012 Middle East respiratory syndrome coronavirus outbreak (2012 MERS outbreak) 2003 SARS outbreak See also Coronavirus respiratory syndrome Coronaviridae

Disease outbreaks

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Set indices

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Coronaviridae

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Coronavirus disease

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Coronavirus disease

Look up COVID in Wiktionary, the free dictionary. Characteristics of patients who have been infected with SARS-CoV-2, MERS-CoV, and SARS-CoV[1] SARS-CoV-2[a] MERS-CoV SARS-CoV Demographic Detection date December 2019 June 2012 November 2002 Detection place Wuhan, China Jeddah, Saudi Arabia Guangdong, China Age average 49 56 39.9 Age range 21–76 14–94 1–91 Male:female ratio 2.7:1 3.3:1 1:1.25 Confirmed cases 835[b] 2494 8096 Case fatality rate 25[b] (2.9%) 858 (37%) 744 (10%) Health-care workers 16[c] 9.8% 23.1% Symptoms Fever 40 (98%) 98% 99–100% Dry cough 31 (76%) 47% 29–75% Dyspnoea 22 (55%) 72% 40–42% Diarrhoea 1 (3%) 26% 20–25% Sore throat 0 21% 13–25% Ventilatory support 9.8% 80% 14–20% Notes Symptoms were based on the first 41 patients. Data as of 23 January 2020. Data as of 21 January 2020; other data up to 21 January 2020. Published on 24 January 2020. A coronavirus disease (COVID),[2][3] coronavirus respiratory syndrome, coronav

Pneumonia

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Set indices

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Zoonoses

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