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'''Severe acute respiratory syndrome coronavirus 2''' ('''SARS-CoV-2'''),<ref name="CoronavirusStudyGroup" /><ref name=":2">{{Cite news|url=https://www.bbc.com/news/world-asia-china-51466362|title=Coronavirus disease named Covid-19|date=11 February 2020|work=[[BBC News Online]] | archive-url=https://web.archive.org/web/20200215204154/https://www.bbc.com/news/world-asia-china-51466362 | archive-date=15 February 2020 | url-status=live | access-date=15 February 2020}}</ref> formerly known as the '''2019 novel coronavirus''' ('''2019-nCoV'''),<ref name=WHO21Jan2020>{{cite report | vauthors = ((World Health Organization)) | year = 2020 | title = Surveillance case definitions for human infection with novel coronavirus (nCoV): interim guidance v1, January 2020 | author-link = World Health Organization | publisher = World Health Organization | hdl = 10665/330376 | id = WHO/2019-nCoV/Surveillance/v2020.1 | hdl-access = free }}</ref><ref>{{cite web | title=Healthcare Professionals: Frequently Asked Questions and Answers | website=U.S. [[Centers for Disease Control and Prevention]] (CDC) | date=11 February 2020 | url=https://www.cdc.gov/coronavirus/2019-ncov/hcp/faq.html | access-date=15 February 2020 | archive-url=https://web.archive.org/web/20200214023335/https://www.cdc.gov/coronavirus/2019-ncov/hcp/faq.html | archive-date=14 February 2020 | url-status=live }}</ref> is a [[positive-sense single-stranded RNA virus]].<ref>{{cite web|url=http://www.chinacdc.cn/dfdt/201912/t20191226_209404.html|title=中国疾病预防控制中心|publisher=[[Chinese Center for Disease Control and Prevention]]|location=People's Republic of China|language=Chinese|accessdate=9 January 2020|archive-url=https://web.archive.org/web/20200206072618/http://www.chinacdc.cn/dfdt/201912/t20191226_209404.html|archive-date=6 February 2020|url-status=live}}</ref><ref name=":xinhuanet9Jan2020">{{cite news|url=http://www.xinhuanet.com/english/2020-01/09/c_138690570.htm|title=New-type coronavirus causes pneumonia in Wuhan: expert|accessdate=9 January 2020|url-status=live|archive-url=https://web.archive.org/web/20200109084208/http://www.xinhuanet.com/english/2020-01/09/c_138690570.htm|archive-date=9 January 2020|agency=Xinhua|location=People's Republic of China}}</ref><ref name=":gisaid">{{cite web|url=https://platform.gisaid.org/epi3/start/CoV2020|title=CoV2020|website=GISAID EpifluDB|url-status=live|accessdate=12 January 2020|url-access=registration|archive-url=https://web.archive.org/web/20200112130540/https://platform.gisaid.org/epi3/start/CoV2020|archive-date=12 January 2020}}</ref> It is [[Contagious disease|contagious]] among humans and is the cause of [[coronavirus disease 2019]] (COVID-19).<ref name="Chan24Jan2020" /> {{As of|February 2020}}, there is no [[vaccine]].<ref name="Reut_NIH_Moderna_3months" />
'''Severe acute respiratory syndrome coronavirus 2''' ('''SARS-CoV-2'''),<ref name="CoronavirusStudyGroup" /><ref name=":2">{{Cite news|url=https://www.bbc.com/news/world-asia-china-51466362|title=Coronavirus disease named Covid-19|date=11 February 2020|work=[[BBC News Online]] | archive-url=https://web.archive.org/web/20200215204154/https://www.bbc.com/news/world-asia-china-51466362 | archive-date=15 February 2020 | url-status=live | access-date=15 February 2020}}</ref> formerly known as the '''2019''' [[novel coronavirus]] ('''2019-nCoV'''),<ref name=WHO21Jan2020>{{cite report | vauthors = ((World Health Organization)) | year = 2020 | title = Surveillance case definitions for human infection with novel coronavirus (nCoV): interim guidance v1, January 2020 | author-link = World Health Organization | publisher = World Health Organization | hdl = 10665/330376 | id = WHO/2019-nCoV/Surveillance/v2020.1 | hdl-access = free }}</ref><ref>{{cite web | title=Healthcare Professionals: Frequently Asked Questions and Answers | website=U.S. [[Centers for Disease Control and Prevention]] (CDC) | date=11 February 2020 | url=https://www.cdc.gov/coronavirus/2019-ncov/hcp/faq.html | access-date=15 February 2020 | archive-url=https://web.archive.org/web/20200214023335/https://www.cdc.gov/coronavirus/2019-ncov/hcp/faq.html | archive-date=14 February 2020 | url-status=live }}</ref> is a [[positive-sense single-stranded RNA virus]].<ref>{{cite web|url=http://www.chinacdc.cn/dfdt/201912/t20191226_209404.html|title=中国疾病预防控制中心|publisher=[[Chinese Center for Disease Control and Prevention]]|location=People's Republic of China|language=Chinese|accessdate=9 January 2020|archive-url=https://web.archive.org/web/20200206072618/http://www.chinacdc.cn/dfdt/201912/t20191226_209404.html|archive-date=6 February 2020|url-status=live}}</ref><ref name=":xinhuanet9Jan2020">{{cite news|url=http://www.xinhuanet.com/english/2020-01/09/c_138690570.htm|title=New-type coronavirus causes pneumonia in Wuhan: expert|accessdate=9 January 2020|url-status=live|archive-url=https://web.archive.org/web/20200109084208/http://www.xinhuanet.com/english/2020-01/09/c_138690570.htm|archive-date=9 January 2020|agency=Xinhua|location=People's Republic of China}}</ref><ref name=":gisaid">{{cite web|url=https://platform.gisaid.org/epi3/start/CoV2020|title=CoV2020|website=GISAID EpifluDB|url-status=live|accessdate=12 January 2020|url-access=registration|archive-url=https://web.archive.org/web/20200112130540/https://platform.gisaid.org/epi3/start/CoV2020|archive-date=12 January 2020}}</ref> It is [[Contagious disease|contagious]] among humans and is the cause of [[coronavirus disease 2019]] (COVID-19).<ref name="Chan24Jan2020" /> {{As of|February 2020}}, there is no [[vaccine]].<ref name="Reut_NIH_Moderna_3months" />


SARS-CoV-2 is the cause of the ongoing [[2019–20 coronavirus outbreak]], a [[Public Health Emergency of International Concern]] that originated in [[Wuhan]], China.<ref name="NYT 20200130" /> Because of this connection, the virus is sometimes referred to informally, among other nicknames, as the "'''Wuhan coronavirus'''".<ref name="HuangNPR">{{Cite web|url=https://www.npr.org/sections/goatsandsoda/2020/01/22/798277557/how-does-wuhan-coronavirus-compare-to-mers-sars-and-the-common-cold|title=How Does Wuhan Coronavirus Compare with MERS, SARS and the Common Cold?|last=Huang|first=Pien|date=22 January 2020|website=[[NPR]]|url-status=live|archive-url=https://web.archive.org/web/20200202094021/https://www.npr.org/sections/goatsandsoda/2020/01/22/798277557/how-does-wuhan-coronavirus-compare-to-mers-sars-and-the-common-cold|archive-date=2 February 2020|access-date=3 February 2020|name-list-format=vanc}}</ref><ref name="Fox2020">{{cite journal|last1=Fox|first1=Dan|year=2020|title=What you need to know about the Wuhan coronavirus|journal=Nature|doi=10.1038/d41586-020-00209-y|issn=0028-0836|name-list-format=vanc}}</ref>
SARS-CoV-2 is the cause of the ongoing [[2019–20 coronavirus outbreak]], a [[Public Health Emergency of International Concern]] that originated in [[Wuhan]], China.<ref name="NYT 20200130" /> Because of this connection, the virus is sometimes referred to informally, among other nicknames, as the "'''Wuhan coronavirus'''".<ref name="HuangNPR">{{Cite web|url=https://www.npr.org/sections/goatsandsoda/2020/01/22/798277557/how-does-wuhan-coronavirus-compare-to-mers-sars-and-the-common-cold|title=How Does Wuhan Coronavirus Compare with MERS, SARS and the Common Cold?|last=Huang|first=Pien|date=22 January 2020|website=[[NPR]]|url-status=live|archive-url=https://web.archive.org/web/20200202094021/https://www.npr.org/sections/goatsandsoda/2020/01/22/798277557/how-does-wuhan-coronavirus-compare-to-mers-sars-and-the-common-cold|archive-date=2 February 2020|access-date=3 February 2020|name-list-format=vanc}}</ref><ref name="Fox2020">{{cite journal|last1=Fox|first1=Dan|year=2020|title=What you need to know about the Wuhan coronavirus|journal=Nature|doi=10.1038/d41586-020-00209-y|issn=0028-0836|name-list-format=vanc}}</ref>

Revision as of 01:36, 19 February 2020

This article is about the virus strain. For the disease, see 2019-nCoV acute respiratory disease. For the outbreak, see 2019–20 coronavirus outbreak. For the species of virus to which this strain belongs, see Severe acute respiratory syndrome-related coronavirus.

Severe acute respiratory syndrome coronavirus 2
Illustration of a SARS-CoV-2 virion
Illustration of a SARS-CoV-2 virion
Cross-sectional illustration of a SARS-CoV-2 virion showing internal components
Cross-sectional illustration of a SARS-CoV-2 virion showing internal components
Virus classification Edit this classification
(unranked): Virus
Realm: Riboviria
Kingdom: Orthornavirae
Phylum: Pisuviricota
Class: Pisoniviricetes
Order: Nidovirales
Family: Coronaviridae
Genus: Betacoronavirus
Subgenus: Sarbecovirus
Species:
Severe acute respiratory syndrome-related coronavirus
Strain:
Severe acute respiratory syndrome coronavirus 2
SARS-CoV-2 is located in China
SARS-CoV-2
Wuhan, China, the epicenter of the only recorded outbreak
Synonyms
  • 2019-nCoV
  • COVID-19 virus

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2),[1][2] formerly known as the 2019 novel coronavirus (2019-nCoV),[3][4] is a positive-sense single-stranded RNA virus.[5][6][7] It is contagious among humans and is the cause of coronavirus disease 2019 (COVID-19).[8] As of February 2020, there is no vaccine.[9]

SARS-CoV-2 is the cause of the ongoing 2019–20 coronavirus outbreak, a Public Health Emergency of International Concern that originated in Wuhan, China.[10] Because of this connection, the virus is sometimes referred to informally, among other nicknames, as the "Wuhan coronavirus".[11][12]

SARS-CoV-2 has strong genetic similarity to known bat coronaviruses, making a zoonotic origin in bats likely,[13][14][15] although an intermediate reservoir such as a pangolin is thought to be involved.[16][17] From a taxonomic perspective SARS-CoV-2 is classified as a strain of the species severe acute respiratory syndrome-related coronavirus.[1]

Name

During the ongoing 2019–20 coronavirus outbreak, the World Health Organization (WHO) originally recommended use of the temporary designation "2019-nCoV" (2019 novel coronavirus) to refer to the virus. However, this led to concerns that the absence of an official name might lead to the use of prejudicial informal names, and in common parlance the virus was often referred to as "the new coronavirus", "Wuhan coronavirus", or simply "coronavirus".[18][19] Per 2015 WHO guidelines on the naming of viruses and diseases,[19][20] the International Committee on Taxonomy of Viruses (ICTV) announced that it would introduce a suitable official name for the virus.[18]

On 11 February 2020, the ICTV introduced the name "severe acute respiratory syndrome coronavirus 2" (SARS-CoV-2) to refer to the virus strain previously known as 2019-nCoV.[1] Earlier the same day, the WHO officially renamed the disease caused by the virus strain from 2019-nCoV acute respiratory disease to "coronavirus disease 2019" (COVID-19).[21][2]

Virology

Infection

Human-to-human transmission of the virus has been confirmed[8] and occurs primarily via respiratory droplets from coughs and sneezes within a range of about 6 feet (1.8 m).[22][23] Viral RNA has also been found in stool samples from infected patients.[24]

It is possible that the virus can be infectious even during the incubation period, but this has not been proven,[25] and the WHO stated on 1 February 2020 that "transmission from asymptomatic cases is likely not a major driver of transmission" at this time.[26]

Reservoir

Animals sold for food were originally suspected to be the reservoir or intermediary hosts of SARS-CoV-2 because many of the first individuals found to be infected by the virus were workers at the Huanan Seafood Market.[27] A market selling live animals for food was also blamed in the SARS outbreak in 2003; such markets are considered to be incubators for novel pathogens.[28] The outbreak has prompted a temporary ban on the trade and consumption of wild animals in China.[29][30] However, some researchers have suggested that the Huanan Seafood Market may not be the original source of viral transmission to humans.[31][32]

Research into the origin of the 2003 SARS outbreak has resulted in the discovery of many SARS-like bat coronaviruses, most originating in the Rhinolophus genus of horseshoe bats. Two genome sequences from Rhinolophus sinicus published in 2015 and 2017 show a resemblance of 80% to 2019-nCoV.[33][34][15] A third virus genome from Rhinolophus affinis, "RaTG13" collected in Yunnan province, has a 96% resemblance to 2019-nCoV.[13][35] For comparison, this amount of variation among viruses is similar to the amount of mutation observed over ten years in the H3N2 human influenza virus strain.[36]

Researchers from Guangzhou claim to have found a "99% identical" viral genome in a pangolin sample.[37] As of 12 February 2020, the sequence remains unavailable, and all information comes from a university announcement.[38] Pangolins are protected under Chinese law, but poaching and trading of pangolins for traditional medicine remains common. A metagenomic study published in 2019 previously revealed that SARS-CoV was the most widely distributed coronavirus among a sample of Malayan pangolins.[39] Microbiologists and geneticists in Texas have independently found evidence of recombination in coronaviruses suggesting pangolin origins of SARS-CoV-2; they acknowledged remaining unknown factors while urging continued examination of other mammals.[40]

Phylogenetics and taxonomy

Genomic information
Genomic organisation of SARS-CoV-2
NCBI genome IDMN908947
Genome size29,903 bases
Year of completion2020

SARS-CoV-2 belongs to the broad family of viruses known as coronaviruses. It is a positive-sense single-stranded RNA (+ssRNA) virus. Other coronaviruses are capable of causing illnesses ranging from the common cold to more severe diseases such as Middle East respiratory syndrome (MERS). It is the seventh known coronavirus to infect people, after 229E, NL63, OC43, HKU1, MERS-CoV, and the original SARS-CoV.[41]

Like the SARS-related coronavirus strain implicated in the 2003 SARS outbreak, SARS-CoV-2 is a member of the subgenus Sarbecovirus (Beta-CoV lineage B).[42][27][43] Its RNA sequence is approximately 30,000 bases in length.[7]

With a sufficient number of sequenced genomes, it is possible to reconstruct a phylogenetic tree of the mutation history of a family of viruses. By 12 January 2020, five genomes of 2019-nCoV had been isolated from Wuhan and reported by the Chinese Center for Disease Control and Prevention (CCDC) and other institutions;[7][44] the number of genomes increased to 81 by 11 February 2020.[45] A phylogenic analysis of the samples shows they are "highly related with at most seven mutations relative to a common ancestor", implying that the first human infection occurred in November or December 2019.[45]

On 11 February 2020, ICTV announced that according to existing rules that compute hierarchical relationships among coronaviruses on the basis of five conserved sequences of nucleic acids, the differences between 2019-nCoV and the virus strain from the 2003 SARS outbreak are insufficient to make 2019-nCoV a separate viral species. Therefore, they identified 2019-nCoV as a strain of severe acute respiratory syndrome-related coronavirus.[1]

Structural biology

See also: Open reading frame
Ribbon diagram of M(pro) protease], a prospective target for antiviral drugs against 2019-nCoV
Ribbon diagram of M(pro) protease, a prospective target for antiviral drugs against 2019-nCoV

Protein modeling experiments on the spike (S) protein of the virus suggest that it has sufficient affinity to the angiotensin converting enzyme 2 (ACE2) receptors of human cells to use them as a mechanism of cell entry.[46] On 22 January 2020, a group in China working with the full virus genome and a group in the United States using reverse genetics methods independently and experimentally demonstrated that ACE2 could act as the receptor for 2019-nCoV.[47][48][49]

To look for potential protease inhibitors, the viral 3C-like protease M(pro) from the ORF1a polyprotein has also been modeled for drug docking experiments. Innophore has produced two computational models based on SARS protease,[50] and the Chinese Academy of Sciences has produced an unpublished experimental structure of a recombinant 2019-nCoV protease.[51] In addition, researchers have modeled the structures of all mature peptides in the 2019-nCov genome using I-TASSER and Swiss-model.[52][53]

Digitally colorized electron micrographs of SARS-CoV-2
  • SARS-CoV-2 (yellow) emerging from a human cell
    SARS-CoV-2 (yellow) emerging from a human cell
  • SARS-CoV-2 virions with visible coronae
    SARS-CoV-2 virions with visible coronae
  • SARS-CoV-2 virions with visible coronae
    SARS-CoV-2 virions with visible coronae
  • SARS-CoV-2 (yellow) emerging from a human cell
    SARS-CoV-2 (yellow) emerging from a human cell

Epidemiology

Main article: 2019–20 Wuhan coronavirus outbreak

The first known human infection by the strain occurred in early December 2019.[54][31] Proliferation of SARS-CoV-2 was first detected in Wuhan, China, in mid-December 2019, likely originating from a single infected animal.[31] The virus subsequently spread to all provinces of China and to more than two dozen other countries in Asia, Europe, North America, Africa, and Oceania.[55] Human-to-human spread of the virus has been confirmed in all of these regions[8][56][57][58] except Africa.[59] On 30 January 2020, 2019-nCoV was designated a Public Health Emergency of International Concern by the WHO.[10][60]

As of 18 February 2020 (03:45 UTC), there were 73,334 confirmed cases of infection, of which 72,438 were within mainland China.[55] One mathematical model estimated the number of people infected in Wuhan alone at 75,815 as of 25 January 2020.[61] Nearly all cases outside China have occurred in people who either traveled from Wuhan, or were in direct contact with someone who traveled from the area.[62][63] While the proportion of infections that result in confirmed infection or progress to diagnosable disease remains unclear,[64][65] the total number of deaths attributed to the virus was 1,873 as of 18 February 2020 (03:45 UTC); over 95% of all deaths have occurred in Hubei province,[55] where Wuhan is located.

The basic reproduction number (, pronounced R-nought or R-zero)[66] of the virus has been estimated to be between 1.4 and 3.9.[67][68][69][70] This means that, when unchecked, the virus typically results in 1.4 to 3.9 new cases per established infection. It has been established that the virus is able to transmit along a chain of at least four people.[71]

Vaccine research

Many organizations are using published genomes to develop possible vaccines against 2019-nCoV.[9]

In China, the Chinese Center for Disease Control and Prevention is developing a vaccine.[72][73] The University of Hong Kong has announced that a vaccine is under development, but they have yet to proceed to animal testing.[74] Shanghai East Hospital is also developing a vaccine in partnership with the biotechnology company Stemirna Therapeutics.[74]

Elsewhere, three vaccine projects are being supported by the Coalition for Epidemic Preparedness Innovations (CEPI), including projects by the biotechnology companies Moderna and Inovio Pharmaceuticals and another by the University of Queensland.[75] The United States National Institutes of Health (NIH) is cooperating with Moderna to create an RNA vaccine matching a spike of the coronavirus surface, and intends to start human trials by May 2020.[9] Inovio Pharmaceuticals is developing a DNA-based vaccination and collaborating with a Chinese firm in order to speed its acceptance by regulatory authorities in China, hoping to perform human trials of the vaccine in the summer of 2020.[76] In Australia, the University of Queensland is investigating the potential of a molecular clamp vaccine that would genetically modify viral proteins in order to stimulate an immune reaction.[75]

In an independent project, the Public Health Agency of Canada has authorized the International Vaccine Centre (VIDO-InterVac) at the University of Saskatchewan to begin work on a vaccine.[77] VIDO-InterVac aims to start animal testing in March 2020 and human testing in 2021.[77]

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Further reading

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