View source for Biology:SARS-CoV-2

{{Short description|Virus that causes COVID-19}}
{{pp-30-500|small=yes}}
{{EngvarB|date=May 2021}}
{{Virusbox
| image = Novel Coronavirus SARS-CoV-2.jpg
| image_alt = Electron micrograph of SARS-CoV-2 virions with visible coronae
| image_caption = Colourised [[Engineering:Transmission electron microscopy|transmission electron micrograph]] of SARS-CoV-2 [[Biology:Virus|virion]]s with visible [[Biology:Coronavirus#Etymology|coronae]]
| image2 = Coronavirus. SARS-CoV-2.png
| image2_alt = Illustration of a SARS-CoV-2 virion
| image2_caption = Model of the external structure of the SARS-CoV-2 virion<ref>{{#invoke:cite web ||surname1=Solodovnikov | given1=Alexey |surname2=Arkhipova| given2=Valeria |title = Достоверно красиво: как мы сделали 3D-модель SARS-CoV-2 |trans-title=Truly beautiful: how we made the SARS-CoV-2 3D model  |url = https://nplus1.ru/blog/2021/07/29/sars-cov-2-model |archive-url = https://web.archive.org/web/20210730143142/https://nplus1.ru/blog/2021/07/29/sars-cov-2-model |publisher= N+1 |archive-date=30 July 2021 |date =29 July 2021 |access-date=30 July 2021 |language =ru}}</ref><table cellpadding="0" style="margin:0 auto;">
<tr><td>{{colorbull|1=#005db7|2=round|size=150}} Blue:</td><td>[[Biology:Viral envelope|envelope]]</td></tr>
<tr><td>{{colorbull|1=#02e6ff|2=round|size=150}} Turquoise:</td><td>spike glycoprotein (S)</td></tr>
<tr><td>{{colorbull|1=#ff0c78|2=round|size=150}} Pink:</td><td>envelope proteins (E)</td></tr>
<tr><td>{{colorbull|1=#9bff57|2=round|size=150}} Green:</td><td>membrane proteins (M)</td></tr>
<tr><td>{{colorbull|1=#fe8354|2=round|size=150}} Orange:</td><td>[[Chemistry:Glycan|glycan]]</td></tr></table>
| parent = Sarbecovirus<!--Incertae sedis/Betacoronavirus-->
| species = Severe acute respiratory syndrome–related coronavirus
| virus = Severe acute respiratory syndrome coronavirus 2
| synonyms = * 2019-nCoV<!--Please see [[Biology:Synonym (taxonomy)|Synonym (taxonomy)]] before adding unofficial names here.-->
| subdivision_ranks = Notable variants
| subdivision = <!-- Only include notable variants or strains here-->
* Alpha (B.1.1.7)
* Beta (B.1.351)
* Gamma (P.1)
* Delta (B.1.617.2)
* Omicron (B.1.1.529)
* Full list
}}

'''Severe acute respiratory syndrome coronavirus 2''' ('''SARS‑CoV‑2''')<ref name="CoronavirusStudyGroup" /> is a strain of [[Biology:Coronavirus|coronavirus]] that causes [[Medicine:COVID-19|COVID-19]], the respiratory illness responsible for the COVID-19 pandemic.<ref name="NYT-20210226" /> The virus previously had the [[Biology:Novel coronavirus|provisional name]] '''2019 novel coronavirus''' ('''2019-nCoV'''),<ref name="WHO21Jan2020">{{#invoke:cite report ||title=Surveillance case definitions for human infection with novel coronavirus (nCoV): interim guidance v1, January 2020 |date=January 2020 |publisher=World Health Organization |id=WHO/2019-nCoV/Surveillance/v2020.1 |hdl-access=free |hdl=10665/330376 }}</ref><ref name="CDC-nCoV" /><ref name="CDCAbout">{{#invoke:cite web ||url=https://www.cdc.gov/coronavirus/2019-ncov/about/index.html |title=About Novel Coronavirus (2019-nCoV) |date=11 February 2020 |website=United States Centers for Disease Control and Prevention (CDC) |url-status=live |archive-url=https://web.archive.org/web/20200211105920/https://www.cdc.gov/coronavirus/2019-ncov/about/index.html |archive-date=11 February 2020 |access-date=25 February 2020 }}</ref><ref name="NYT6" /> and has also been called '''human coronavirus 2019''' ('''HCoV-19''' or '''hCoV-19''').<ref name="Zoonotic" /><ref name="Proximal" /><ref name="NEJM-Stability" /><ref name="China natl GeneBank">{{#invoke:cite web ||url=https://db.cngb.org/datamart/disease/DATAdis19/ |title=hCoV-19 Database |publisher=China National GeneBank |access-date=2 June 2020 |archive-url=https://web.archive.org/web/20200617041357/https://db.cngb.org/datamart/disease/DATAdis19/ |archive-date=17 June 2020 |url-status=live}}</ref> <noinclude> First identified in the city of [[Place:Wuhan|Wuhan]], Hubei, China, the [[Organization:World Health Organization|World Health Organization]] designated the outbreak a [[Social:Public health emergency of international concern|public health emergency of international concern]] from January 30, 2020, to May 5, 2023.<ref name="WHO-PHEIC" /><ref name="WHOPandemic" /><ref>{{#invoke:cite web||url=https://www.reuters.com/business/healthcare-pharmaceuticals/covid-is-no-longer-global-health-emergency-who-2023-05-05/|title=WHO declares end to COVID global health emergency|last1=Rigby|first1=Jennifer|last2=Satija|first2=Bhanvi|date=5 May 2023|work=Reuters|access-date=6 May 2023}}</ref></noinclude> SARS‑CoV‑2 is a [[Biology:Positive-sense single-stranded RNA virus|positive-sense single-stranded RNA virus]]<ref name="Machhi2020Sep" /> that is [[Philosophy:Contagious disease|contagious]] in humans.<ref name="Chan24Jan2020" />

SARS‑CoV‑2 is a strain of the species ''severe-acute-respiratory-syndrome-related coronavirus'' (SARSr-CoV), as is [[Biology:SARS-CoV-1|SARS-CoV-1]], the virus that caused the [[Medicine:2002–2004 SARS outbreak|2002–2004 SARS outbreak]].<ref name="CoronavirusStudyGroup" /><ref name="nihSARSr-CoV" /> There are animal-borne coronavirus strains more closely related to SARS-CoV-2, the most closely related being bat coronaviruses, including BANAL-52 and [[Biology:RaTG13|RaTG13]].<ref>{{#invoke:cite journal ||title=Animal coronaviruses and coronavirus disease 2019: Lesson for One Health approach |journal=Open Vet J |date=2020 |volume=10 |issue=3 |doi=10.4314/ovj.v10i3.1 |url=https://www.ajol.info/index.php/ovj/article/view/200858|last1=Poudel |first1=Uddab |last2=Subedi |first2=Deepak |last3=Pantha |first3=Saurav |last4=Dhakal |first4=Santosh |pages=239–251 |pmid=33282694 |pmc=7703617 }}</ref> The virus is of [[Biology:Zoonosis|zoonotic]] origin; its close [[Biology:Sequence homology|genetic similarity]] to bat coronaviruses suggests it emerged from a [[Biology:Bat virome|bat-borne virus]].<ref name=biol/> Research is ongoing as to whether SARS‑CoV‑2 came directly from bats or indirectly through any intermediate hosts.<ref name="WHO-SR22" /> The virus shows little [[Biology:Genetic diversity|genetic diversity]], indicating that the [[Biology:Spillover infection|spillover event]] introducing SARS‑CoV‑2 to humans is likely to have occurred in late 2019.<ref name="early" />

Epidemiological studies estimate that in the period between December 2019 and September 2020 each infection resulted in an average of 2.4–3.4 new infections when no members of the community were [[Medicine:Immunity (medical)|immune]] and no [[Medicine:Infection control|preventive measures]] were taken.<ref name="BillahMiahKhan">{{#invoke:cite journal ||vauthors=Billah MA, Miah MM, Khan MN |title=Reproductive number of coronavirus: A systematic review and meta-analysis based on global level evidence |journal=PLOS ONE |volume=15 |issue=11 |pages=e0242128 |date=11 November 2020 |pmid=33175914 |pmc=7657547 |doi=10.1371/journal.pone.0242128 |bibcode=2020PLoSO..1542128B|doi-access=free }}</ref> However, some subsequent variants have become more infectious.<ref>{{#invoke:cite web||url=https://www.mayoclinic.org/diseases-conditions/coronavirus/expert-answers/covid-variant/faq-20505779|title=COVID-19 variants: What's the concern?|website=Mayo Clinic|date=27 August 2022|access-date=10 October 2022}}</ref> The virus is airborne and primarily spreads between people through close contact and via aerosols and respiratory droplets that are exhaled when talking, breathing, or otherwise exhaling, as well as those produced from coughs and sneezes.<ref>"[https://www.cdc.gov/coronavirus/2019-ncov/prevent-getting-sick/how-covid-spreads.html How Coronavirus Spreads] {{Webarchive|url=https://web.archive.org/web/20200403001235/https://www.cdc.gov/coronavirus/2019-ncov/prepare/transmission.html |date=3 April 2020 }}", Centers for Disease Control and Prevention, Retrieved 14 May 2021.</ref><ref>"[https://www.who.int/news-room/q-a-detail/coronavirus-disease-covid-19-how-is-it-transmitted Coronavirus disease (COVID-19): How is it transmitted?] {{Webarchive|url=https://web.archive.org/web/20201015230546/https://www.who.int/news-room/q-a-detail/coronavirus-disease-covid-19-how-is-it-transmitted |date=15 October 2020 }}", World Health Organization</ref> It [[Biology:Viral entry|enters]] human cells by binding to [[Biology:Angiotensin-converting enzyme 2|angiotensin-converting enzyme 2]] (ACE2), a membrane protein that regulates the renin–angiotensin system.<ref name="HoffmanCell" /><ref>{{#invoke:cite journal || vauthors = Zhao P, Praissman JL, Grant OC, Cai Y, Xiao T, Rosenbalm KE, Aoki K, Kellman BP, Bridger R, Barouch DH, Brindley MA, Lewis NE, Tiemeyer M, Chen B, Woods RJ, Wells L | title = Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor | journal = Cell Host & Microbe | volume = 28 | issue = 4 | pages = 586–601.e6 | date = October 2020 | pmid = 32841605 | pmc = 7443692 | doi = 10.1016/j.chom.2020.08.004 }}</ref>

==Terminology==
[[File:NOVO-NEW-新.2019-nCoV.jpg|thumb|upright|Sign with provisional name "2019-nCoV"|left]]During the initial outbreak in Wuhan, China, various names were used for the virus; some names used by different sources included "the coronavirus" or "Wuhan coronavirus".<ref name="HuangNPR" /><ref name="Fox2020" /> In January 2020, the [[Organization:World Health Organization|World Health Organization]] (WHO) recommended "2019 novel coronavirus" (2019-nCoV)<ref name="CDC-nCoV" /><ref name="WHO-SR10" /> as the provisional name for the virus. This was in accordance with WHO's 2015 guidance<ref name="WHOnamingguidelines" /> against using geographical locations, animal species, or groups of people in disease and virus names.<ref name="TodayNameMixup" /><ref name="EconomistSinophobia" />

On 11 February 2020, the [[Organization:International Committee on Taxonomy of Viruses|International Committee on Taxonomy of Viruses]] adopted the official name "severe acute respiratory syndrome coronavirus 2" (SARS‑CoV‑2).<ref name="COVIDname date" /> To avoid confusion with the disease [[Medicine:SARS|SARS]], the WHO sometimes refers to SARS‑CoV‑2 as "the COVID-19 virus" in public health communications<ref name="QZ-Why" /><ref name="COVIDname public" /> and the name HCoV-19 was included in some research articles.<ref name="Zoonotic" /><ref name="Proximal" /><ref name="NEJM-Stability" /> Referring to COVID-19 as the "Wuhan virus" has been described as dangerous by WHO officials, and as [[Social:Xenophobia|xenophobic]] by many journalists and academics.<ref>{{#invoke:cite web ||url=https://www.nea.org/advocating-for-change/new-from-nea/hate-and-bias-covid-19 |title=Standing Up to Hate and Bias Related to COVID-19 |publisher=National Education Association |date=5 June 2020 |quote=It's racist and it creates xenophobia," University of California at Berkeley Asian American studies lecturer Harvey Dong told ''The Washington Post''. "It's a very dangerous situation."}}</ref><ref>{{#invoke:cite web ||url=https://thehill.com/homenews/administration/488479-who-official-warns-against-calling-it-chinese-virus-says-there-is-no?rl=1 |title=WHO official warns against calling it 'Chinese virus,' says 'there is no blame in this' |work=The Hill |last=Gstalter |first=Morgan |date=19 March 2020 |access-date=15 September 2022 |quote=Ryan is not the first WHO official to push back against the phrase. Director-General Tedros Adhanom Ghebreyesus said earlier this month that the term is "painful to see" and "more dangerous than the virus itself."}}</ref><ref>{{#invoke:cite journal || vauthors = Gover AR, Harper SB, Langton L | title = Anti-Asian Hate Crime During the COVID-19 Pandemic: Exploring the Reproduction of Inequality | journal = American Journal of Criminal Justice | volume = 45 | issue = 4 | pages = 647–667 | date = July 2020 | pmid = 32837171 | pmc = 7364747 | doi = 10.1007/s12103-020-09545-1 }}</ref>

==Infection and transmission==

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Human-to-human [[Medicine:Transmission|transmission]] of SARS‑CoV‑2 was confirmed on 20 January 2020 during the COVID-19 pandemic.<ref name="Chan24Jan2020" /><ref name="LiMar2020" /><ref name="Kessler17Apr2020" /><ref name="Kuo21Jan2020" /> Transmission was initially assumed to occur primarily via respiratory droplets from coughs and sneezes within a range of about {{convert|1.8|m|ft|0|adj=ri1}}.<ref name="CDCTrans" /><ref name="NBCSpread" /> Laser light scattering experiments suggest that speaking is an additional mode of transmission<ref name="Anfrinrud 2020" /><ref name="Stadnytskyi et al 2020" /> and a far-reaching<ref name= "Klompas" /> one, indoors, with little air flow.<ref name= "LivescienceTalkingWorse" /><ref name= "deOliveira" /> Other studies have suggested that the virus may be airborne as well, with aerosols potentially being able to transmit the virus.<ref name="NYT-20200704am" /><ref name="ZZeynep" /><ref name="lew-d-mou" /> During human-to-human transmission, between 200 and 800 infectious SARS‑CoV‑2 virions are thought to initiate a new infection.<ref name="SCI-20201123" /><ref name="NatureTempShedding" /><ref>{{#invoke:cite journal || vauthors = Watanabe T, Bartrand TA, Weir MH, Omura T, Haas CN | title = Development of a dose-response model for SARS coronavirus | journal = Risk Analysis | volume = 30 | issue = 7 | pages = 1129–38 | date = July 2010 | pmid = 20497390 | pmc = 7169223 | doi = 10.1111/j.1539-6924.2010.01427.x | bibcode = 2010RiskA..30.1129W }}</ref> If confirmed, aerosol transmission has biosafety implications because a major concern associated with the risk of working with emerging viruses in the laboratory is the generation of aerosols from various laboratory activities which are not immediately recognizable and may affect other scientific personnel.<ref>{{#invoke:cite journal || vauthors = Artika IM, Ma'roef CN | title = Laboratory biosafety for handling emerging viruses | journal = Asian Pacific Journal of Tropical Biomedicine | volume = 7 | issue = 5 | pages = 483–491 | date = May 2017 | pmid = 32289025 | pmc = 7103938 | doi = 10.1016/j.apjtb.2017.01.020 }}</ref> Indirect contact via [[Medicine:Fomite|contaminated surfaces]] is another possible cause of infection.<ref name="WHO-Workplace" /> Preliminary research indicates that the virus may remain viable on plastic ([[Chemistry:Polypropylene|polypropylene]]) and [[Chemistry:Stainless steel|stainless steel]] (AISI 304) for up to three days, but it does not survive on cardboard for more than one day or on copper for more than four hours.<ref name="NEJM-Stability" /> The virus is inactivated by soap, which destabilizes its [[Biology:Lipid bilayer|lipid bilayer]].<ref name="AtlanticSuccess" /><ref name="NatGeoSoap" /> Viral [[Biology:RNA|RNA]] has also been found in stool samples and semen from infected individuals.<ref name="NEJM-FirstUS" /><ref name="Semen" />

The degree to which the virus is infectious during the [[Medicine:Incubation period|incubation period]] is uncertain, but research has indicated that the [[Biology:Pharynx|pharynx]] reaches peak [[Biology:Viral load|viral load]] approximately four days after infection<ref name="NaturePeakLoad" /><ref name="ScienceFlawed" /> or in the first week of symptoms and declines thereafter.<ref name="LancetLoad" /> The duration of SARS-CoV-2 [[Biology:Viral shedding|RNA shedding]] is generally between 3 and 46 days after symptom onset.<ref>{{#invoke:cite journal || vauthors = Avanzato VA, Matson MJ, Seifert SN, Pryce R, Williamson BN, Anzick SL, Barbian K, Judson SD, Fischer ER, Martens C, Bowden TA, de Wit E, Riedo FX, Munster VJ | title = Case Study: Prolonged Infectious SARS-CoV-2 Shedding from an Asymptomatic Immunocompromised Individual with Cancer | journal = Cell | volume = 183 | issue = 7 | pages = 1901–1912.e9 | date = December 2020 | pmid = 33248470 | pmc = 7640888 | doi = 10.1016/j.cell.2020.10.049 }}</ref>

A study by a team of researchers from the [[Organization:University of North Carolina|University of North Carolina]] found that the nasal cavity is seemingly the dominant initial site of infection, with subsequent [[Medicine:Pulmonary aspiration|aspiration]]-mediated virus-seeding into the lungs in SARS‑CoV‑2 pathogenesis.<ref name="Hou2020" /> They found that there was an infection gradient from high in proximal towards low in distal pulmonary epithelial cultures, with a focal infection in ciliated cells and type 2 pneumocytes in the airway and alveolar regions respectively.<ref name="Hou2020" />

Studies have identified a range of animals—such as cats, ferrets, hamsters, non-human primates, minks, tree shrews, raccoon dogs, fruit bats, and rabbits—that are susceptible and permissive to SARS-CoV-2 infection.<ref>{{#invoke:cite journal || vauthors = Banerjee A, Mossman K, Baker ML | title = Zooanthroponotic potential of SARS-CoV-2 and implications of reintroduction into human populations | journal = Cell Host & Microbe | volume = 29 | issue = 2 | pages = 160–164 | date = February 2021 | pmid = 33539765 | pmc = 7837285 | doi = 10.1016/j.chom.2021.01.004 }}</ref><ref name="oie.int" /><ref name="BronxTiger" /> Some institutions have advised that those infected with SARS‑CoV‑2 restrict their contact with animals.<ref name="USDAtiger" /><ref name="CDCanimals" />

=== Asymptomatic and presymptomatic transmission ===
On 1{{nbsp}}February 2020, the [[Organization:World Health Organization|World Health Organization]] (WHO) indicated that "transmission from [[Medicine:Asymptomatic|asymptomatic]] cases is likely not a major driver of transmission".<ref name="WHO-SR12" /> One meta-analysis found that 17% of infections are asymptomatic, and asymptomatic individuals were 42% less likely to transmit the virus.<ref name="Nogrady2020Nov" />

However, an epidemiological model of the beginning of the outbreak in China suggested that "pre-symptomatic [[Biology:Viral shedding|shedding]] may be typical among documented infections" and that [[Medicine:Subclinical infection|subclinical infection]]s may have been the source of a majority of infections.<ref name="ScienceRapid" /> That may explain how out of 217 on board a cruise liner that docked at [[Place:Montevideo|Montevideo]], only 24 of 128 who tested positive for viral RNA showed symptoms.<ref name="Thorax" /> Similarly, a study of ninety-four patients hospitalized in January and February 2020 estimated patients began shedding virus two to three days before symptoms appear and that "a substantial proportion of transmission probably occurred before first symptoms in the [[Medicine:Index case|index case]]".<ref name="NatureTempShedding" /> The authors later published a correction that showed that shedding began earlier than first estimated, four to five days before symptoms appear.<ref>{{#invoke:cite journal ||last1=He |first1=Xi |last2=Lau |first2=Eric H. Y. |last3=Wu |first3=Peng |last4=Deng |first4=Xilong |last5=Wang |first5=Jian |last6=Hao |first6=Xinxin |last7=Lau |first7=Yiu Chung |last8=Wong |first8=Jessica Y. |last9=Guan |first9=Yujuan |last10=Tan |first10=Xinghua |last11=Mo |first11=Xiaoneng |last12=Chen |first12=Yanqing |last13=Liao |first13=Baolin |last14=Chen |first14=Weilie |last15=Hu |first15=Fengyu |last16=Zhang |first16=Qing |last17=Zhong |first17=Mingqiu |last18=Wu |first18=Yanrong |last19=Zhao |first19=Lingzhai |last20=Zhang |first20=Fuchun |last21=Cowling |first21=Benjamin J. |last22=Li |first22=Fang |last23=Leung |first23=Gabriel M. |title=Author Correction: Temporal dynamics in viral shedding and transmissibility of COVID-19 |journal=Nature Medicine |date=September 2020 |volume=26 |issue=9 |pages=1491–1493 |doi=10.1038/s41591-020-1016-z|pmid=32770170 |pmc=7413015 }}</ref>

=== Reinfection ===
There is uncertainty about reinfection and long-term immunity.<ref name="led-rei" /> It is not known how common reinfection is, but reports have indicated that it is occurring with variable severity.<ref name="led-rei" />

The first reported case of reinfection was a 33-year-old man from Hong Kong who first tested positive on 26 March 2020, was discharged on 15 April 2020 after two negative tests, and tested positive again on 15 August 2020 (142 days later), which was confirmed by whole-genome sequencing showing that the viral genomes between the episodes belong to different [[Biology:Clade|clade]]s.<ref name="to-phyl" /> The findings had the implications that [[Medicine:Herd immunity|herd immunity]] may not eliminate the virus if reinfection is not an uncommon occurrence and that [[Medicine:COVID-19 vaccine|vaccines]] may not be able to provide lifelong protection against the virus.<ref name="to-phyl" />

Another case study described a 25-year-old man from Nevada who tested positive for SARS‑CoV‑2 on 18 April 2020 and on 5 June 2020 (separated by two negative tests). Since genomic analyses showed significant genetic differences between the SARS‑CoV‑2 variant sampled on those two dates, the case study authors determined this was a reinfection.<ref name="till-gen" /> The man's second infection was symptomatically more severe than the first infection, but the mechanisms that could account for this are not known.<ref name="till-gen" />

{{anchor|origin}}

==Reservoir and origin==
<!-- this sub-section is transcluded at Investigations into the origin of COVID-19; please update that page if the section title changes here -->
<noinclude>{{further|Investigations into the origin of COVID-19}}</noinclude>
[[File:SARS-CoV-1 and 2 - mammals as carriers.png|thumb|upright=1.25|Transmission of SARS-CoV-1 and SARS‑CoV‑2 from mammals as biological carriers to humans]]

No [[Biology:Natural reservoir|natural reservoir]] for SARS-CoV-2 has been identified.<ref name="Holmes2021"/> Prior to the emergence of SARS-CoV-2 as a pathogen infecting humans, there had been two previous [[Biology:Zoonosis|zoonosis]]-based coronavirus epidemics, those caused by [[Biology:SARS-CoV-1|SARS-CoV-1]] and [[Biology:MERS-CoV|MERS-CoV]].<ref name=biol>{{#invoke:cite journal ||vauthors=V'kovski P, Kratzel A, Steiner S, Stalder H, Thiel V |title=Coronavirus biology and replication: implications for SARS-CoV-2 |journal=Nat Rev Microbiol |volume=19 |issue=3 |pages=155–170 |date=March 2021 |pmid=33116300 |pmc=7592455 |doi=10.1038/s41579-020-00468-6 |type=Review}}</ref>

The first known infections from SARS‑CoV‑2 were discovered in Wuhan, China.<ref name="NatureZhou" /> The original source of viral transmission to humans remains unclear, as does whether the virus became [[Biology:Pathogen|pathogen]]ic before or after the spillover event.<ref name="Proximal" /><ref name="early" /><ref name="PopSciJan" /> Because many of the early infectees were workers at the Huanan Seafood Market,<ref name="LancetClinical" /><ref name="LancetCharacteristics" /> it has been suggested that the virus might have originated from the market.<ref name="Proximal" /><ref name="nature feb2020" /> However, other research indicates that visitors may have introduced the virus to the market, which then facilitated rapid expansion of the infections.<ref name="early" /><ref name="XivDecoding" /> A March 2021 WHO-convened report stated that human spillover via an intermediate animal host was the most likely explanation, with direct spillover from bats next most likely. Introduction through the food supply chain and the Huanan Seafood Market was considered another possible, but less likely, explanation.<ref name="WHOconvened" /> An analysis in November 2021, however, said that the earliest-known case had been misidentified and that the preponderance of early cases linked to the Huanan Market argued for it being the source.<ref>{{#invoke:cite journal || vauthors = Worobey M | title = Dissecting the early COVID-19 cases in Wuhan | journal = Science | volume = 374 | issue = 6572 | pages = 1202–1204 | date = December 2021 | pmid = 34793199 | doi = 10.1126/science.abm4454 | bibcode = 2021Sci...374.1202W | s2cid = 244403410 }}</ref>

For a virus recently acquired through a cross-species transmission, rapid evolution is expected.<ref>{{#invoke:cite journal || vauthors = Kang L, He G, Sharp AK, Wang X, Brown AM, Michalak P, Weger-Lucarelli J | title = A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptation | journal = Cell | volume = 184 | issue = 17 | pages = 4392–4400.e4 | date = August 2021 | pmid = 34289344 | pmc = 8260498 | doi = 10.1016/j.cell.2021.07.007 }}</ref> The mutation rate estimated from early cases of SARS-CoV-2 was of {{val|6.54|e=-4}} per site per year.<ref name="WHOconvened" /> Coronaviruses in general have high genetic [[Biology:Phenotypic plasticity|plasticity]],<ref>{{#invoke:cite journal || vauthors = Decaro N, Lorusso A | title = Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses | journal = Veterinary Microbiology | volume = 244 | page = 108693 | date = May 2020 | pmid = 32402329 | pmc = 7195271 | doi = 10.1016/j.vetmic.2020.108693 }}</ref> but SARS-CoV-2's viral evolution is slowed by the [[Biology:Proofreading|RNA proofreading]] capability of its replication machinery.<ref name="RobsonF2020Aug" /> For comparison, the viral mutation rate in vivo of SARS-CoV-2 has been found to be lower than that of influenza.<ref>{{#invoke:cite journal || vauthors = Tao K, Tzou PL, Nouhin J, Gupta RK, de Oliveira T, Kosakovsky Pond SL, Fera D, Shafer RW | title = The biological and clinical significance of emerging SARS-CoV-2 variants | journal = Nature Reviews Genetics | volume = 22 | issue = 12 | pages = 757–773 | date = December 2021 | pmid = 34535792 | pmc = 8447121 | doi = 10.1038/s41576-021-00408-x }}</ref>

Research into the natural reservoir of the virus that caused the [[Medicine:2002–2004 SARS outbreak|2002–2004 SARS outbreak]] has resulted in the discovery of many [[Biology:Bat SARS-like coronavirus WIV1|SARS-like bat coronaviruses]], most originating in [[Biology:Horseshoe bat|horseshoe bat]]s. The closest match by far, published in ''Nature (journal)'' in February 2022, were viruses BANAL-52 (96.8% resemblance to SARS‑CoV‑2), BANAL-103 and BANAL-236, collected in three different species of bats in Feuang, Laos.<ref>{{#invoke:cite journal||last1=Temmam|first1=Sarah|last2=Vongphayloth|first2=Khamsing|last3=Salazar|first3=Eduard Baquero|last4=Munier|first4=Sandie|last5=Bonomi|first5=Max|last6=Régnault|first6=Béatrice|last7=Douangboubpha|first7=Bounsavane|last8=Karami|first8=Yasaman|last9=Chretien|first9=Delphine|last10=Sanamxay|first10=Daosavanh|last11=Xayaphet|first11=Vilakhan|date=February 2022|title=Bat coronaviruses related to SARS-CoV-2 and infectious for human cells|journal=Nature|volume=604 |issue=7905 |pages=330–336 |doi=10.1038/s41586-022-04532-4 |pmid=35172323 |bibcode=2022Natur.604..330T |s2cid=246902858 |doi-access=free}}</ref><ref>{{#invoke:cite journal||last=Mallapaty|first=Smriti|date=24 September 2021|title=Closest known relatives of virus behind COVID-19 found in Laos|journal=Nature|language=en|volume=597|issue=7878|page=603|doi=10.1038/d41586-021-02596-2|pmid=34561634 |bibcode=2021Natur.597..603M |s2cid=237626322 |doi-access=free}}</ref><ref>{{#invoke:cite news||title=Newly Discovered Bat Viruses Give Hints to Covid's Origins|date=14 October 2021|url=https://www.nytimes.com/2021/10/14/science/bat-coronaviruses-lab-leak.html|work={{wipe|The New York Times}}}}</ref> An earlier source published in February 2020 identified the virus [[Biology:RaTG13|RaTG13]], collected in bats in Mojiang, Yunnan, China to be the closest to SARS‑CoV‑2, with 96.1% resemblance.<ref name="NatureZhou" /><ref name="NCBI-Bat3" /> None of the above are its direct ancestor.<ref>{{#invoke:cite web ||title=The 'Occam's Razor Argument' Has Not Shifted in Favor of a Lab Leak |url=https://www.snopes.com/news/2021/07/16/lab-leak-evidence/ |website=Snopes.com |date=16 July 2021 |publisher=Snopes |access-date=18 July 2021}}</ref>

[[File:Naturalis Biodiversity Center - RMNH.MAM.33160.b dor - Rhinolophus sinicus - skin.jpeg|thumb|upright=0.8|left|Samples taken from ''Rhinolophus sinicus'', a species of horseshoe bats, show an 80% resemblance to SARS‑CoV‑2.]]
Bats are considered the most likely natural reservoir of SARS‑CoV‑2.<ref name="WHOconvened" /><ref name="LancetBinding" /> Differences between the bat coronavirus and SARS‑CoV‑2 suggest that humans may have been infected via an intermediate host;<ref name="nature feb2020" /> although the source of introduction into humans remains unknown.<ref name="OKeeffeJ2021Mar">{{#invoke:cite book ||vauthors=O'Keeffe J, Freeman S, Nicol A |date=21 March 2021 |title=The Basics of SARS-CoV-2 Transmission |url=https://ncceh.ca/documents/evidence-review/basics-sars-cov-2-transmission |publisher=National Collaborating Centre for Environmental Health (NCCEH) |location=Vancouver, BC |isbn=978-1-988234-54-0 |access-date=12 May 2021 |archive-date=12 May 2021 |archive-url=https://web.archive.org/web/20210512134422/https://ncceh.ca/documents/evidence-review/basics-sars-cov-2-transmission |url-status=live }}</ref><ref name="Holmes2021">{{#invoke:cite journal || vauthors = Holmes EC, Goldstein SA, Rasmussen AL, Robertson DL, Crits-Christoph A, Wertheim JO, Anthony SJ, Barclay WS, Boni MF, Doherty PC, Farrar J |title=The Origins of SARS-CoV-2: A Critical Review |journal=Cell |date=August 2021 | volume = 184 | issue = 19 | pages = 4848–4856 |doi=10.1016/j.cell.2021.08.017| pmid = 34480864 |pmc=8373617 }}</ref>

Although the role of pangolins as an intermediate host was initially posited (a study published in July 2020 suggested that pangolins are an intermediate host of SARS‑CoV‑2-like coronaviruses<ref name="XiaoK2020July" /><ref name="ZhaoJ2020" />), subsequent studies have not substantiated their contribution to the spillover.<ref name="WHOconvened" /> Evidence against this hypothesis includes the fact that pangolin virus samples are too distant to SARS-CoV-2: isolates obtained from pangolins seized in Guangdong were only 92% identical in sequence to the SARS‑CoV‑2 genome (matches above 90 percent may sound high, but in genomic terms it is a wide evolutionary gap<ref>{{#invoke:cite news ||title=Why it's so tricky to trace the origin of COVID-19 |url=https://www.nationalgeographic.com/science/article/why-its-so-tricky-to-trace-the-origin-of-covid-19 |work=Science |publisher=National Geographic |date=10 September 2021 }}</ref>). In addition, despite similarities in a few critical amino acids,<ref name="HuB2020Oct" /> pangolin virus samples exhibit poor binding to the human ACE2 receptor.<ref name="GiovanettiM2020Nov" />

==Phylogenetics and taxonomy==
<!-- this sub-section is transcluded at Investigations into the origin of COVID-19; please update that page if the section title changes here -->
<onlyinclude>
{{Infobox genome
| image         = File:SARS-CoV-2 genome.svg
| caption       = Genomic organisation of isolate Wuhan-Hu-1, the earliest sequenced sample of SARS-CoV-2
| taxId         = 86693
| size          = 29,903 bases
| year          = 2020
| ucsc_assembly = wuhCor1
}}

SARS‑CoV‑2 belongs to the broad family of viruses known as [[Biology:Coronavirus|coronavirus]]es.<ref name="Fox2020">{{#invoke:cite journal ||vauthors=Fox D |title=What you need to know about the novel coronavirus |journal=Nature |date=January 2020 |pmid=33483684 |doi=10.1038/d41586-020-00209-y|s2cid=213064026 }}</ref> It is a [[Biology:Positive-sense single-stranded RNA virus|positive-sense single-stranded RNA]] (+ssRNA) virus, with a single linear RNA segment. Coronaviruses infect humans, other mammals, including livestock and companion animals, and avian species.<ref name="V'kovskik:21">{{#invoke:cite journal ||vauthors=V'kovski P, Kratzel A, Steiner S, Stalder H, Thiel V |title=Coronavirus biology and replication: implications for SARS-CoV-2 |journal=Nature Reviews. Microbiology |volume=19 |issue=3 |pages=155–170 |date=March 2021 |pmid=33116300 |pmc=7592455 |doi=10.1038/s41579-020-00468-6}}</ref> Human coronaviruses are capable of causing illnesses ranging from the [[Medicine:Common cold|common cold]] to more severe diseases such as [[Medicine:Middle East respiratory syndrome|Middle East respiratory syndrome]] (MERS, fatality rate ~34%). SARS-CoV-2 is the seventh known coronavirus to infect people, after 229E, NL63, [[Biology:Human coronavirus OC43|OC43]], [[Biology:Human coronavirus HKU1|HKU1]], [[Biology:Middle East respiratory syndrome-related coronavirus|MERS-CoV]], and the original [[Biology:Severe acute respiratory syndrome coronavirus|SARS-CoV]].<ref name="NEJM-Novel">{{#invoke:cite journal ||vauthors=Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, Zhao X, Huang B, Shi W, Lu R, Niu P, Zhan F, Ma X, Wang D, Xu W, Wu G, Gao GF, Tan W |title=A Novel Coronavirus from Patients with Pneumonia in China, 2019 |journal=The New England Journal of Medicine |volume=382 |issue=8 |pages=727–733 |date=February 2020 |pmid=31978945 |pmc=7092803 |doi=10.1056/NEJMoa2001017}}</ref>

Like the SARS-related coronavirus implicated in the 2003 SARS outbreak, SARS‑CoV‑2 is a member of the subgenus ''[[Biology:Sarbecovirus|Sarbecovirus]]'' (beta-CoV lineage B).<ref name="NextstrainPhylogeny" /><ref name="Wong2019" /> Coronaviruses undergo frequent recombination.<ref name="Singhy:21">{{#invoke:cite journal || vauthors = Singh D, Yi SV | title = On the origin and evolution of SARS-CoV-2 | journal = Experimental & Molecular Medicine | volume = 53 | issue = 4 | pages = 537–547 | date = April 2021 | pmid = 33864026 | pmc = 8050477 | doi = 10.1038/s12276-021-00604-z }}</ref> The mechanism of recombination in unsegmented RNA viruses such as SARS-CoV-2 is generally by copy-choice replication, in which gene material switches from one RNA template molecule to another during replication.<ref>{{#invoke:cite journal || vauthors = Jackson B, Boni MF, Bull MJ, Colleran A, Colquhoun RM, Darby AC, Haldenby S, Hill V, Lucaci A, McCrone JT, Nicholls SM, O'Toole Á, Pacchiarini N, Poplawski R, Scher E, Todd F, Webster HJ, Whitehead M, Wierzbicki C, Loman NJ, Connor TR, Robertson DL, Pybus OG, Rambaut A | title = Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic | journal = Cell | volume = 184 | issue = 20 | pages = 5179–5188.e8 | date = September 2021 | pmid = 34499854 | pmc = 8367733 | doi = 10.1016/j.cell.2021.08.014 | s2cid = 237099659 }}</ref> The SARS-CoV-2 RNA sequence is approximately 30,000 [[Biology:Nucleobase|base]]s in length,<ref name="gisaid" /> relatively long for a coronavirus—which in turn carry the largest genomes among all RNA families.<ref>{{#invoke:cite journal || vauthors = Kim D, Lee JY, Yang JS, Kim JW, Kim VN, Chang H | title = The Architecture of SARS-CoV-2 Transcriptome | journal = Cell | volume = 181 | issue = 4 | pages = 914–921.e10 | date = May 2020 | pmid = 32330414 | pmc = 7179501 | doi = 10.1016/j.cell.2020.04.011 }}</ref> Its genome consists nearly entirely of protein-coding sequences, a trait shared with other coronaviruses.<ref name="Singhy:21" />

[[File:Novel Coronavirus SARS-CoV-2 (49597020718).jpg|thumb|Transmission electron micrograph of SARS‑CoV‑2 virions (red) isolated from a patient during the COVID-19 pandemic|alt=Micrograph of SARS‑CoV‑2 virus particles isolated from a patient]]

A distinguishing feature of SARS‑CoV‑2 is its incorporation of a [[Chemistry:Amino acid#Side chains|polybasic]] site cleaved by [[Biology:Furin|furin]],<ref name="HuB2020Oct" /><ref>{{#invoke:cite journal ||last1=Hossain |first1=Md. Golzar |last2=Tang |first2=Yan-dong |last3=Akter |first3=Sharmin |last4=Zheng |first4=Chunfu |title=Roles of the polybasic furin cleavage site of spike protein in SARS-CoV-2 replication, pathogenesis, and host immune responses and vaccination |journal=Journal of Medical Virology |date=May 2022 |volume=94 |issue=5 |pages=1815–1820 |doi=10.1002/jmv.27539|pmid=34936124 |s2cid=245430230 }}</ref> which appears to be an important element enhancing its virulence.<ref name="KaiWangTo2020">{{#invoke:cite journal || vauthors = To KK, Sridhar S, Chiu KH, Hung DL, Li X, Hung IF, Tam AR, Chung TW, Chan JF, Zhang AJ, Cheng VC, Yuen KY | title = Lessons learned 1 year after SARS-CoV-2 emergence leading to COVID-19 pandemic | journal = Emerging Microbes & Infections | volume = 10 | issue = 1 | pages = 507–535 | date = December 2021 | pmid = 33666147 | pmc = 8006950 | doi = 10.1080/22221751.2021.1898291 }}</ref><noinclude> It was suggested that the acquisition of the furin-cleavage site in the SARS-CoV-2 S protein was essential for zoonotic transfer to humans.<ref name="Mechanisms of SARS-CoV-2 entry into">{{#invoke:cite journal || vauthors = Jackson CB, Farzan M, Chen B, Choe H | title = Mechanisms of SARS-CoV-2 entry into cells | journal = Nature Reviews Molecular Cell Biology | volume = 23 | issue = 1 | pages = 3–20 | date = January 2022 | pmid = 34611326 | pmc = 8491763 | doi = 10.1038/s41580-021-00418-x }}</ref> The furin [[Biology:Protease|protease]] recognizes the canonical [[Chemistry:Peptide|peptide]] sequence [[Chemistry:Arginine|R]]X[<nowiki/>[[Chemistry:Arginine|R]]/[[Chemistry:Lysine|K]]] [[Chemistry:Arginine|R]]↓X where the cleavage site is indicated by a down arrow and X is any [[Chemistry:Amino acid|amino acid]].<ref>{{#invoke:cite journal || vauthors = Braun E, Sauter D | title = Furin-mediated protein processing in infectious diseases and cancer | journal = Clinical & Translational Immunology | volume = 8 | issue = 8 | pages = e1073 | date = 2019 | pmid = 31406574 | pmc = 6682551 | doi = 10.1002/cti2.1073 }}</ref><ref>{{#invoke:cite journal || vauthors = Vankadari N | title = Structure of Furin Protease Binding to SARS-CoV-2 Spike Glycoprotein and Implications for Potential Targets and Virulence | journal = The Journal of Physical Chemistry Letters | volume = 11 | issue = 16 | pages = 6655–6663 | date = August 2020 | pmid = 32787225 | pmc = 7409919 | doi = 10.1021/acs.jpclett.0c01698 }}</ref></noinclude> In SARS-CoV-2 the recognition site is formed by the incorporated 12 [[Biology:Genetic code|codon nucleotide sequence]] CCT CGG CGG GCA which corresponds to the amino acid sequence [[Chemistry:Proline|P]] [[Chemistry:Arginine|RR]] [[Chemistry:Alanine|A]].<ref name=":2" /> This sequence is upstream of an arginine and serine which forms the S1/S2 cleavage site ([[Chemistry:Proline|P]] [[Chemistry:Arginine|RR]] [[Chemistry:Alanine|A]] [[Chemistry:Arginine|R]]↓[[Chemistry:Serine|S]]) of the spike protein.<ref name="PangolinResidue">{{#invoke:cite journal || vauthors = Zhang T, Wu Q, Zhang Z | title = Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak | journal = Current Biology | volume = 30 | issue = 7 | pages = 1346–1351.e2 | date = April 2020 | pmid = 32197085 | pmc = 7156161 | doi = 10.1016/j.cub.2020.03.022 }}</ref> Although such sites are a common naturally-occurring feature of other viruses within the Subfamily Orthocoronavirinae,<ref name=":2">{{#invoke:cite journal || vauthors = Coutard B, Valle C, de Lamballerie X, Canard B, Seidah NG, Decroly E | title = The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade | journal = Antiviral Research | volume = 176 | page = 104742 | date = April 2020 | pmid = 32057769 | pmc = 7114094 | doi = 10.1016/j.cub.2020.03.022 }}</ref> it appears in few other viruses from the [[Biology:Betacoronavirus|Beta-CoV]] genus,<ref>{{#invoke:cite journal || vauthors = Wu Y, Zhao S | title = Furin cleavage sites naturally occur in coronaviruses | journal = Stem Cell Research | volume = 50 | page = 102115 | date = December 2020 | pmid = 33340798 | pmc = 7836551 | doi = 10.1016/j.scr.2020.102115 }}</ref> and it is unique among members of its subgenus for such a site.<ref name="HuB2020Oct" /><!-- COMMENTED OUT PENDING PREPRINT BEING REVIEWED The closest relatives to SARS-CoV2, including BANAL-20-52, RaTG13, Pangolin P4L, and SARS-CoV-1, lack the RRAR insertion.<ref name="Laos">{{#invoke:cite journal || vauthors = Temmam S, Vongphayloth K, Salazar EB, Munier S, Bonomi M, Régnault B, Douangboubpha B, Karami Y, Chretien D, Sanamxay D, Xayaphet V, Paphaphanh P, Lacoste V, Somlor S, Lakeomany K, Phommavanh N, Pérot P, Donati F, Bigot T, Nilges M, Rey F, van der Werf S, Brey P, Eloit M |title=Coronaviruses with a SARS-CoV-2-like receptor-binding domain allowing ACE2-mediated entry into human cells isolated from bats of Indochinese peninsula |journal=Research Square |date=September 2021 |pages= |doi=10.21203/rs.3.rs-871965/v1 |pmid= |pmc= }}</ref> However, --> The furin cleavage site PRRAR↓ is highly similar to that of the [[Biology:Feline coronavirus|feline coronavirus]], an [[Biology:Alphacoronavirus 1|alphacoronavirus 1]] strain.<ref name="feline coronavirus">{{#invoke:cite journal || vauthors = Budhraja A, Pandey S, Kannan S, Verma CS, Venkatraman P | title = The polybasic insert, the RBD of the SARS-CoV-2 spike protein, and the feline coronavirus - evolved or yet to evolve | journal = Biochemistry and Biophysics Reports | volume = 25 | page = 100907 | date = March 2021 | pmid = 33521335 | pmc = 7833556 | doi = 10.1016/j.bbrep.2021.100907 }}</ref>

Viral genetic sequence data can provide critical information about whether viruses separated by time and space are likely to be epidemiologically linked.<ref>{{#invoke:cite journal || vauthors = Worobey M, Pekar J, Larsen BB, Nelson MI, Hill V, Joy JB, Rambaut A, Suchard MA, Wertheim JO, Lemey P | title = The emergence of SARS-CoV-2 in Europe and North America | journal = Science | volume = 370 | issue = 6516 | pages = 564–570 | date = October 2020 | pmid = 32912998 | pmc = 7810038 | doi = 10.1126/science.abc8169 }}</ref> With a sufficient number of sequenced [[Biology:Genome|genome]]s, it is possible to reconstruct a [[Biology:Phylogenetic tree|phylogenetic tree]] of the mutation history of a family of viruses. By 12 January 2020, five genomes of SARS‑CoV‑2 had been isolated from Wuhan and reported by the [[Organization:Chinese Center for Disease Control and Prevention|Chinese Center for Disease Control and Prevention]] (CCDC) and other institutions;<ref name="gisaid">{{#invoke:cite web ||url=https://platform.gisaid.org/epi3/start/CoV2020 |title=CoV2020 |website=GISAID EpifluDB |url-access=registration |url-status=live |archive-url=https://web.archive.org/web/20200112130540/https://platform.gisaid.org/epi3/start/CoV2020 |archive-date=12 January 2020 |access-date=12 January 2020 }}</ref><ref name="VirologicalInitial">{{#invoke:cite web ||url=http://virological.org/t/initial-genome-release-of-novel-coronavirus/319 |title=Initial genome release of novel coronavirus |date=11 January 2020 |website=Virological |url-status=live |archive-url=https://web.archive.org/web/20200112100227/http://virological.org/t/initial-genome-release-of-novel-coronavirus/319 |archive-date=12 January 2020 |access-date=12 January 2020 }}</ref> the number of genomes increased to 42 by 30 January 2020.<ref name="NextstrainJanuary">{{#invoke:cite web ||url=https://nextstrain.org/narratives/ncov/sit-rep/2020-01-30 |title=Genomic analysis of nCoV spread: Situation report 2020-01-30 |website=nextstrain.org |url-status=live <!--Errors loading archive page-->|archive-url=https://web.archive.org/web/20200315182810/https://nextstrain.org/narratives/ncov/sit-rep/2020-01-30 |archive-date=15 March 2020 |access-date=18 March 2020 |vauthors=Bedford T, Neher R, Hadfield N, Hodcroft E, Ilcisin M, Müller N}}</ref> A phylogenetic analysis of those samples showed they were "highly related with at most seven mutations relative to a common ancestor", implying that the first human infection occurred in November or December 2019.<ref name="NextstrainJanuary" /> Examination of the topology of the phylogenetic tree at the start of the pandemic also found high similarities between human isolates.<ref name="Sun2020Trends">{{#invoke:cite journal || vauthors = Sun J, He WT, Wang L, Lai A, Ji X, Zhai X, Li G, Suchard MA, Tian J, Zhou J, Veit M, Su S | title = COVID-19: Epidemiology, Evolution, and Cross-Disciplinary Perspectives | journal = Trends in Molecular Medicine | volume = 26 | issue = 5 | pages = 483–495 | date = May 2020 | pmid = 32359479 | pmc = 7118693 | doi = 10.1016/j.molmed.2020.02.008 }}</ref>  {{As of|2021|August|21|post=,}} 3,422 SARS‑CoV‑2 genomes, belonging to 19 strains, sampled on all continents except Antarctica were publicly available.<ref name="NexstrainApril">{{#invoke:cite web ||title=Genomic epidemiology of novel coronavirus - Global subsampling |url=https://nextstrain.org/ncov/global |date=25 October 2021 |website=Nextstrain|url-status=live|archive-url=https://web.archive.org/web/20200420123520/https://nextstrain.org/ncov/global|archive-date=20 April 2020|access-date=26 October 2021}}</ref>

On 11 February 2020, the [[Organization:International Committee on Taxonomy of Viruses|International Committee on Taxonomy of Viruses]] announced that according to existing rules that compute hierarchical relationships among coronaviruses based on five [[Biology:Conserved sequence|conserved sequence]]s of nucleic acids, the differences between what was then called 2019-nCoV and the virus from the 2003 SARS outbreak were insufficient to make them separate viral species. Therefore, they identified 2019-nCoV as a virus of ''[[Biology:Severe acute respiratory syndrome–related coronavirus|Severe acute respiratory syndrome–related coronavirus]]''.<ref>{{#invoke:cite journal ||author=Coronaviridae Study Group of the International Committee on Taxonomy of Viruses |title=The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 |journal=Nature Microbiology |volume=5 |issue=4 |pages=536–544 |date=April 2020 |pmid=32123347 |pmc=7095448 |doi=10.1038/s41564-020-0695-z}}</ref></onlyinclude>

In July 2020, scientists reported that a more infectious SARS‑CoV‑2 variant with spike protein variant G614 has replaced D614 as the dominant form in the pandemic.<ref name="Medicalxpress.com">{{#invoke:cite news ||title=New, more infectious strain of COVID-19 now dominates global cases of virus: study |url=https://medicalxpress.com/news/2020-07-infectious-strain-covid-dominates-global.html |access-date=16 August 2020 |work=medicalxpress.com  |archive-date=17 November 2020 |archive-url=https://web.archive.org/web/20201117010819/https://medicalxpress.com/news/2020-07-infectious-strain-covid-dominates-global.html |url-status=live}}</ref><ref name="Korber et al 2020">{{#invoke:cite journal ||vauthors=Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO, Montefiori DC |title=Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus |journal=Cell |volume=182 |issue=4 |pages=812–827.e19 |date=August 2020 |pmid=32697968 |pmc=7332439 |doi=10.1016/j.cell.2020.06.043 | doi-access = free}}</ref>

Coronavirus genomes and subgenomes encode six [[Biology:Open reading frame|open reading frame]]s (ORFs).<ref name="Dhama2020">{{#invoke:cite journal ||vauthors=Dhama K, Khan S, Tiwari R, Sircar S, Bhat S, Malik YS, Singh KP, Chaicumpa W, Bonilla-Aldana DK, Rodriguez-Morales AJ |title=Coronavirus Disease 2019-COVID-19 |journal=Clinical Microbiology Reviews |volume=33 |issue=4 |date=September 2020 |pmid=32580969 |pmc=7405836 |doi=10.1128/CMR.00028-20}}</ref> In October 2020, researchers discovered a possible [[Biology:Overlapping gene|overlapping gene]] named ''ORF3d'', in the SARS‑CoV‑2 [[Biology:Genome|genome]]. It is unknown if the protein produced by ''ORF3d'' has any function, but it provokes a strong immune response. ''ORF3d'' has been identified before, in a variant of coronavirus that infects [[Biology:Pangolin|pangolin]]s.<ref name="SA-20201111">{{#invoke:cite news ||vauthors=Dockrill P |title=Scientists Just Found a Mysteriously Hidden 'Gene Within a Gene' in SARS-CoV-2 |url=https://www.sciencealert.com/scientists-find-mysterious-gene-within-gene-hidden-in-the-coronavirus-genome |date=11 November 2020 |work=ScienceAlert |access-date=11 November 2020 |archive-date=17 November 2020 |archive-url=https://web.archive.org/web/20201117010827/https://www.sciencealert.com/scientists-find-mysterious-gene-within-gene-hidden-in-the-coronavirus-genome |url-status=live}}</ref><ref name="EL-20201001">{{#invoke:cite journal ||vauthors=Nelson CW, Ardern Z, Goldberg TL, Meng C, Kuo CH, Ludwig C, Kolokotronis SO, Wei X |title=Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic |journal=eLife |volume=9 |date=October 2020 |pmid=33001029 |pmc=7655111 |doi=10.7554/eLife.59633 |doi-access=free}}</ref>

=== Phylogenetic tree ===

==== Variants ====
[[File:Novel Coronavirus SARS-CoV-2 (50960620707) (cropped).jpg|thumb|False-colour [[Engineering:Transmission electron microscopy|transmission electron micrograph]] of a B.1.1.7 variant coronavirus. The variant's increased transmissibility is believed to be due to changes in the structure of the spike proteins, shown here in green.]]
There are many thousands of variants of SARS-CoV-2, which can be grouped into the much larger [[Biology:Clade|clade]]s.<ref name="Koyama2020June" /> Several different clade nomenclatures have been proposed. Nextstrain divides the variants into five clades (19A, 19B, 20A, 20B, and 20C), while [[Organization:GISAID|GISAID]] divides them into seven (L, O, V, S, G, GH, and GR).<ref name="Alm2020Aug" />

Several notable variants of SARS-CoV-2 emerged in late 2020. The [[Organization:World Health Organization|World Health Organization]] has currently declared five variants of concern, which are as follows:<ref>{{#invoke:cite web ||last=World Health Organization |date=27 November 2021 |title=Tracking SARS-CoV-2 variants |url=https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/ |url-status=live |access-date=28 November 2021 |website=[[Organization:World Health Organization|World Health Organization]] |archive-date=6 June 2021 |archive-url=https://web.archive.org/web/20210606183718/https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/ }}</ref>
* '''Alpha''': Lineage B.1.1.7 emerged in the {{wipe|United Kingdom}} in September 2020, with evidence of increased transmissibility and virulence. Notable mutations include N501Y and P681H.
** An E484K mutation in some lineage B.1.1.7 virions has been noted and is also tracked by various public health agencies.
* '''Beta''': Lineage B.1.351 emerged in {{wipe|South Africa}} in May 2020, with evidence of increased transmissibility and changes to antigenicity, with some public health officials raising alarms about its impact on the efficacy of some vaccines. Notable mutations include K417N, E484K and N501Y.
* '''Gamma''': Lineage P.1 emerged in {{wipe|Brazil}} in November 2020, also with evidence of increased transmissibility and virulence, alongside changes to antigenicity. Similar concerns about vaccine efficacy have been raised. Notable mutations also include K417N, E484K and N501Y.
* '''Delta''': Lineage B.1.617.2 emerged in {{wipe|India}} in October 2020. There is also evidence of increased transmissibility and changes to antigenicity.
* '''Omicron''': Lineage B.1.1.529 emerged in Botswana in November 2021.

Other notable variants include 6 other WHO-designated variants under investigation and Cluster 5, which emerged among [[Biology:Mink|mink]] in Denmark and resulted in a mink euthanasia campaign rendering it virtually extinct.<ref name="WHO2020_Cluster5" />

== Virology ==

===Virus structure===

[[File:Coronavirus virion structure.svg|alt=Figure of a spherical SARSr-CoV virion showing locations of structural proteins forming the viral envelope and the inner nucleocapsid|thumb|right|Structure of a [[Biology:SARSr-CoV|SARSr-CoV]] virion]]

Each SARS-CoV-2 virion is {{convert|60|–|140|nm|lk=in}} in diameter;<ref name="NEJM-Novel" /><ref name="LancetCharacteristics" /> its mass within the global human populace has been estimated as being between 0.1 and 10 kilograms.<ref>{{#invoke:cite journal ||vauthors = Sender R, Bar-On YM, Gleizer S, Bernsthein B, Flamholz A, Phillips R, Milo R | title = The total number and mass of SARS-CoV-2 virions |url=https://www.medrxiv.org/content/10.1101/2020.11.16.20232009v2 |journal=MedRxiv: The Preprint Server for Health Sciences | date = April 2021 | pmid = 33236021 | pmc = 7685332 | doi = 10.1101/2020.11.16.20232009 }}</ref> Like other coronaviruses, SARS-CoV-2 has four structural proteins, known as the S (spike), E (envelope), M (membrane), and N (nucleocapsid) proteins; the N protein holds the RNA genome, and the S, E, and M proteins together create the [[Biology:Viral envelope|viral envelope]].<ref name="WuStructure" /> Coronavirus S proteins are [[Chemistry:Glycoprotein|glycoprotein]]s and also type I [[Biology:Membrane protein|membrane protein]]s (membranes containing a single [[Biology:Transmembrane domain|transmembrane domain]] oriented on the extracellular side).<ref name="Mechanisms of SARS-CoV-2 entry into"/> They are divided into two functional parts (S1 and S2).<ref name="V'kovskik:21" /> In SARS-CoV-2, the spike protein, which has been imaged at the atomic level using [[Engineering:Cryogenic electron microscopy|cryogenic electron microscopy]],<ref name="SCI-20200219" /><ref name="GZM-20200220" /> is the protein responsible for allowing the virus to attach to and fuse with the [[Biology:Cell membrane|membrane]] of a host cell;<ref name="WuStructure" /> specifically, its S1 [[Biology:Protein subunit|subunit]] catalyzes attachment, the S2 subunit fusion.<ref name="CEBMcoronaviruses" />
[[File:6VSB spike protein SARS-CoV-2 monomer in homotrimer.png|thumb|upright|alt=SARS‑CoV‑2 spike homotrimer focusing upon one protein subunit with an ACE2 binding domain highlighted|SARS‑CoV‑2 spike [[Chemistry:Homotrimer|homotrimer]] with one protein subunit highlighted. The ACE2 binding domain is magenta.]]

=== Genome ===
As of early 2022, about 7 million SARS-CoV-2 genomes had been sequenced and deposited into public databases and another 800,000 or so were added each month.<ref>{{#invoke:cite journal ||last1=Sokhansanj |first1=Bahrad A. |last2=Rosen |first2=Gail L. |date=26 April 2022 |editor-last=Gaglia |editor-first=Marta M. |title=Mapping Data to Deep Understanding: Making the Most of the Deluge of SARS-CoV-2 Genome Sequences |journal=mSystems |language=en |volume=7 |issue=2 |pages=e00035–22 |doi=10.1128/msystems.00035-22|pmid=35311562 |pmc=9040592 |issn=2379-5077}}</ref> By September 2023, the [[Organization:GISAID|GISAID]] EpiCoV database contained more than 16 million genome sequences.<ref>{{Cite web |title=GISAID - gisaid.org |url=https://gisaid.org |access-date=2023-09-16 |website=gisaid.org |language=en}}</ref> 

SARS-CoV-2 has a linear, [[Biology:Sense (molecular biology)|positive-sense]], single-stranded RNA genome about 30,000 bases long.<ref name="V'kovskik:21" /> Its genome has a bias against [[Biology:GC-content|cytosine (C) and guanine (G) nucleotides]], like other coronaviruses.<ref>{{#invoke:cite journal ||vauthors=Kandeel M, Ibrahim A, Fayez M, Al-Nazawi M |title=From SARS and MERS CoVs to SARS-CoV-2: Moving toward more biased codon usage in viral structural and nonstructural genes |journal=Journal of Medical Virology |volume=92 |issue=6 |pages=660–666 |date=June 2020 |pmid=32159237 |pmc=7228358 |doi=10.1002/jmv.25754}}</ref> The genome has the highest composition of [[Chemistry:Uridine|U]] (32.2%), followed by [[Chemistry:Adenosine|A]] (29.9%), and a similar composition of [[Chemistry:Guanine|G]] (19.6%) and [[Chemistry:Cytosine|C]] (18.3%).<ref name=":02">{{#invoke:cite journal ||vauthors=Hou W |title=Characterization of codon usage pattern in SARS-CoV-2 |journal=Virology Journal |volume=17 |issue=1 |page=138 |date=September 2020 |pmid=32928234 |pmc=7487440 |doi=10.1186/s12985-020-01395-x|doi-access=free}}</ref> The [[Biology:GC skew|nucleotide bias]] arises from the mutation of guanines and cytosines to adenosines and [[Chemistry:Uracil|uracil]]s, respectively.<ref name=":12">{{#invoke:cite journal ||vauthors=Wang Y, Mao JM, Wang GD, Luo ZP, Yang L, Yao Q, Chen KP |title=Human SARS-CoV-2 has evolved to reduce CG dinucleotide in its open reading frames |journal=Scientific Reports |volume=10 |issue=1 |page=12331 |date=July 2020 |pmid=32704018 |doi=10.1038/s41598-020-69342-y |pmc=7378049|bibcode=2020NatSR..1012331W }}</ref> The mutation of CG dinucleotides is thought to arise to avoid the [[Biology:Antiviral protein|zinc finger antiviral protein]] related defense mechanism of cells,<ref>{{#invoke:cite journal ||vauthors=Rice AM, Castillo Morales A, Ho AT, Mordstein C, Mühlhausen S, Watson S, Cano L, Young B, Kudla G, Hurst LD |title=Evidence for Strong Mutation Bias toward, and Selection against, U Content in SARS-CoV-2: Implications for Vaccine Design |journal=Molecular Biology and Evolution |volume=38 |issue=1 |pages=67–83 |date=January 2021 |pmid=32687176 |doi=10.1093/molbev/msaa188 |pmc=7454790}}</ref> and to lower the energy to unbind the genome during replication and [[Biology:Translation|translation]] (adenosine and uracil [[Biology:Base pair|base pair]] via two [[Chemistry:Hydrogen bond|hydrogen bond]]s, cytosine and guanine via three).<ref name=":12" /> The depletion of CG dinucleotides in its genome has led the virus to have a noticeable [[Biology:Codon usage bias|codon usage bias]]. For instance, arginine's six different codons have a [[Biology:Codon usage bias#Methods of analysis|relative synonymous codon usage]] of AGA (2.67), CGU (1.46), AGG (.81), CGC (.58), CGA (.29), and CGG (.19).<ref name=":02" /> A similar codon usage bias trend is seen in other SARS–related coronaviruses.<ref>{{#invoke:cite journal ||vauthors=Gu H, Chu DK, Peiris M, Poon LL |title=Multivariate analyses of codon usage of SARS-CoV-2 and other betacoronaviruses |journal=Virus Evolution |volume=6 |issue=1 |pages=veaa032 |date=January 2020 |pmid=32431949 |doi=10.1093/ve/veaa032 |pmc=7223271}}</ref>

=== Replication cycle ===
Virus infections start when viral particles bind to host surface cellular receptors.<ref>{{#invoke:cite journal ||vauthors=Wang Q, Zhang Y, Wu L, Niu S, Song C, Zhang Z, Lu G, Qiao C, Hu Y, Yuen KY, Wang Q, Zhou H, Yan J, Qi J |title=Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2 |journal=Cell |volume=181 |issue=4 |pages=894–904.e9 |date=May 2020 |pmid=32275855 |pmc=7144619 |doi=10.1016/j.cell.2020.03.045}}</ref> [[Biology:Protein structure prediction|Protein modeling]] experiments on the spike protein of the virus soon suggested that SARS‑CoV‑2 has sufficient affinity to the receptor angiotensin converting enzyme 2 (ACE2) on human cells to use them as a mechanism of [[Biology:Viral entry|cell entry]].<ref name="SCLSModeling" /> By 22 January 2020, a group in China working with the full virus genome and a group in the United States using [[Biology:Reverse genetics|reverse genetics]] methods independently and experimentally demonstrated that ACE2 could act as the receptor for SARS‑CoV‑2.<ref name="NatureZhou" /><ref name="Letko22Jan2020" /><ref name="NatMicLetko" /><ref name="ElSahly" /> Studies have shown that SARS‑CoV‑2 has a higher affinity to human ACE2 than the original SARS virus.<ref name="SCI-20200219" /><ref name="NIH-Structure" /> SARS‑CoV‑2 may also use [[Biology:Basigin|basigin]] to assist in cell entry.<ref name="CD147" />

Initial spike protein priming by transmembrane protease, serine 2 (TMPRSS2) is essential for entry of SARS‑CoV‑2.<ref name="HoffmanCell" /> The host protein [[Biology:Neuropilin 1|neuropilin 1]] (NRP1) may aid the virus in host cell entry using ACE2.<ref name="CuervoNZ2020Nov" /> After a SARS‑CoV‑2 virion attaches to a target cell, the cell's TMPRSS2 cuts open the spike protein of the virus, exposing a fusion peptide in the S2 subunit, and the host receptor ACE2.<ref name="CEBMcoronaviruses" /> After fusion, an [[Biology:Endosome|endosome]] forms around the virion, separating it from the rest of the host cell. The virion escapes when the [[Chemistry:PH|pH]] of the endosome drops or when [[Biology:Cathepsin|cathepsin]], a host [[Chemistry:Cysteine|cysteine]] protease, cleaves it.<ref name="CEBMcoronaviruses" /> The virion then releases RNA into the cell and forces the cell to produce and disseminate [[Biology:Viral replication|copies of the virus]], which infect more cells.<ref name="econ-anatomy-killer" />

SARS‑CoV‑2 produces at least three [[Biology:Virulence factor|virulence factor]]s that promote shedding of new virions from host cells and inhibit [[Biology:Immune response|immune response]].<ref name="WuStructure" /> Whether they include downregulation of ACE2, as seen in similar coronaviruses, remains under investigation (as of May 2020).<ref name="BMJ-Best-Practice" />

{{Multiple image | align = center | direction = horizontal | total_width = 500 | image1 = SARS-CoV-2 49531042877.jpg | alt1 = SARS-CoV-2 emerging from a human cell | image2 = SARS-CoV-2 scanning electron microscope image.jpg | alt2 = SARS-CoV-2 virions emerging from a human cell | footer_align = center | footer = Digitally colourised scanning electron micrographs of SARS-CoV-2 virions (yellow) emerging from human cells [[Biology:Cell culture|cultured]] in a laboratory}}

== Treatment and drug development ==
Very few drugs are known to effectively inhibit SARS‑CoV‑2. [[Chemistry:Masitinib|Masitinib]] is a clinically safe drug and was recently found to inhibit its main [[Biology:Protease|protease]], 3CLpro and showed >200-fold reduction in viral titers in the lungs and nose in mice. However, it is not approved for the treatment of COVID-19 in humans as of August 2021.<ref>{{#invoke:cite journal || vauthors = Drayman N, DeMarco JK, Jones KA, Azizi SA, Froggatt HM, Tan K, Maltseva NI, Chen S, Nicolaescu V, Dvorkin S, Furlong K, Kathayat RS, Firpo MR, Mastrodomenico V, Bruce EA, Schmidt MM, Jedrzejczak R, Muñoz-Alía MÁ, Schuster B, Nair V, Han KY, O'Brien A, Tomatsidou A, Meyer B, Vignuzzi M, Missiakas D, Botten JW, Brooke CB, Lee H, Baker SC, Mounce BC, Heaton NS, Severson WE, Palmer KE, Dickinson BC, Joachimiak A, Randall G, Tay S | title = Masitinib is a broad coronavirus 3CL inhibitor that blocks replication of SARS-CoV-2 | journal = Science | volume = 373 | issue = 6557 | pages = 931–936 | date = August 2021 | pmid = 34285133 | doi = 10.1126/science.abg5827 | pmc = 8809056 | bibcode = 2021Sci...373..931D | doi-access = free }}</ref>{{update inline|date=May 2022}}  In December 2021, the {{wipe|United States}} granted emergency use authorization to Nirmatrelvir/ritonavir for the treatment of the virus;<ref name="fda-factsheet">{{#invoke:cite tech report ||title=Fact sheet for healthcare providers: Emergency Use Authorization for Paxlovid |number=LAB-1492-0.8 |publisher=[[Company:Pfizer|Pfizer]] |date=22 December 2021 |url=https://www.fda.gov/media/155050/download |format=PDF |archive-url=https://web.archive.org/web/20211223210430/https://www.fda.gov/media/155050/download |archive-date=23 December 2021 |url-status=live}}</ref> the [[Social:European Union|European Union]], {{wipe|United Kingdom}}, and {{wipe|Canada}} followed suit with full authorization soon after.<ref name="Paxlovid EPAR">{{#invoke:cite web || title=Paxlovid EPAR | website=[[Organization:European Medicines Agency|European Medicines Agency]] (EMA) | date=24 January 2022 | url=https://www.ema.europa.eu/en/medicines/human/EPAR/paxlovid | access-date=3 February 2022}} Text was copied from this source which is copyright European Medicines Agency. Reproduction is authorized provided the source is acknowledged.</ref><ref name="MHRA PR 20211231">{{#invoke:cite press release || title = Oral COVID-19 antiviral, Paxlovid, approved by UK regulator | url = https://www.gov.uk/government/news/oral-covid-19-antiviral-paxlovid-approved-by-uk-regulator | publisher = Medicines and Healthcare products Regulatory Agency | date = 31 December 2021 }}</ref><ref name="Health Canada PR 20220117">{{#invoke:cite press release || title = Health Canada authorizes Paxlovid for patients with mild to moderate COVID-19 at high risk of developing serious disease | website=Health Canada | date=17 January 2022 | url=https://www.canada.ca/en/health-canada/news/2022/01/health-canada-authorizes-paxlovidtm-for-patients-with-mild-to-moderate-covid-19-at-high-risk-of-developing-serious-disease.html | access-date=24 April 2022}}</ref>  One study found that Nirmatrelvir/ritonavir reduced the risk of hospitalization and death by 88%.<ref name="FDA PR 20211222">{{#invoke:cite press release || title=FDA Authorizes First Oral Antiviral for Treatment of COVID-19 | website=U.S. [[Organization:Food and Drug Administration|Food and Drug Administration]] (FDA) | date=22 December 2021 | url=https://www.fda.gov/news-events/press-announcements/coronavirus-covid-19-update-fda-authorizes-first-oral-antiviral-treatment-covid-19 | access-date=22 December 2021}} {{PD-notice}}</ref>

[[Biology:COVID Moonshot|COVID Moonshot]] is an international collaborative open-science project started in March 2020 with the goal of developing an un-patented oral [[Biology:Antiviral drug|antiviral drug]] for treatment of SARS-CoV-2.<ref name="Whipple">{{#invoke:cite news || vauthors = Whipple T |title=Moonshot is the spanner in the Covid-19 works the country needs |url=https://www.thetimes.co.uk/article/moonshot-is-the-spanner-in-the-covid-19-works-the-country-needs-bnf0z5t7t |access-date=5 November 2021 |work=The Times |date=23 October 2021}}</ref>

==Epidemiology==

Retrospective tests collected within the Chinese surveillance system revealed no clear indication of substantial unrecognized circulation of SARS‑CoV‑2 in Wuhan during the latter part of 2019.<ref name="WHOconvened" />

A meta-analysis from November 2020 estimated the [[Medicine:Basic reproduction number|basic reproduction number]] (<math>R_0</math>) of the virus to be between 2.39 and 3.44.<ref name="BillahMiahKhan"/> This means each infection from the virus is expected to result in 2.39 to 3.44 new infections when no members of the community are [[Medicine:Immunity (medical)|immune]] and no [[Medicine:Infection control|preventive measures]] are taken. The reproduction number may be higher in densely populated conditions such as those found on [[Engineering:Cruise ship|cruise ship]]s.<ref name="Rocklov" /> Human behavior affects the R0 value and hence estimates of R0 differ between different countries, cultures, and social norms. For instance, one study found relatively low R0 (~3.5) in Sweden, Belgium and the Netherlands, while Spain and the US had significantly higher R0 values (5.9 to 6.4, respectively).<ref>{{#invoke:cite journal || vauthors = Ke R, Romero-Severson E, Sanche S, Hengartner N | title = Estimating the reproductive number R<sub>0</sub> of SARS-CoV-2 in the United States and eight European countries and implications for vaccination | journal = Journal of Theoretical Biology | volume = 517 | page = 110621 | date = May 2021 | pmid = 33587929 | pmc = 7880839 | doi = 10.1016/j.jtbi.2021.110621 | bibcode = 2021JThBi.51710621K }}</ref> 
{| class="wikitable"
|+Reproductive value R0 of SARS-CoV-2 variants
!Variant
!R0
!Source
|-
|Reference/ancestral strain
|~2.8
|<ref>{{#invoke:cite journal || vauthors = Liu Y, Gayle AA, Wilder-Smith A, Rocklöv J | title = The reproductive number of COVID-19 is higher compared to SARS coronavirus | journal = Journal of Travel Medicine | volume = 27 | issue = 2 | pages = taaa021 | date = March 2020 | pmid = 32052846 | pmc = 7074654 | doi = 10.1093/jtm/taaa021 }}</ref>
|-
|Alpha (B.1.1.7)
|(40-90% higher than previous variants)
|<ref>{{#invoke:cite journal || vauthors = Davies NG, Abbott S, Barnard RC, Jarvis CI, Kucharski AJ, Munday JD, Pearson CA, Russell TW, Tully DC, Washburne AD, Wenseleers T, Gimma A, Waites W, Wong KL, van Zandvoort K, Silverman JD, Diaz-Ordaz K, Keogh R, Eggo RM, Funk S, Jit M, Atkins KE, Edmunds WJ | title = Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England | journal = Science | volume = 372 | issue = 6538 | pages = eabg3055 | date = April 2021 | pmid = 33658326 | pmc = 8128288 | doi = 10.1126/science.abg3055 }}</ref>
|-
|Delta (B.1.617.2)
|~5 (3-8)
|<ref>{{#invoke:cite journal || vauthors = Liu Y, Rocklöv J | title = The reproductive number of the Delta variant of SARS-CoV-2 is far higher compared to the ancestral SARS-CoV-2 virus | journal = Journal of Travel Medicine | volume = 28 | issue = 7 | pages = taab124 | date = October 2021 | pmid = 34369565 | pmc = 8436367 | doi = 10.1093/jtm/taab124 }}</ref>
|}
There have been about 96,000 confirmed cases of infection in mainland China.<ref name="JHU_ticker" /> While the proportion of infections that result in confirmed cases or progress to diagnosable disease remains unclear,<ref name="STAT-Severity" /> one mathematical model estimated that 75,815 people were infected on 25 January 2020 in Wuhan alone, at a time when the number of confirmed cases worldwide was only 2,015.<ref name="pmid32014114" /> Before 24 February 2020, over 95% of all deaths from [[Medicine:COVID-19|COVID-19]] worldwide had occurred in Hubei province, where Wuhan is located.<ref name="GuardianLeap" /><ref name="SunChinaAfrica" /> As of {{Cases in the COVID-19 pandemic|date|editlink=|ref=no}}, the percentage had decreased to {{percentage|3216|{{Cases in the COVID-19 pandemic|deaths|editlink=no|ref=no}}|sigfig=2}}.{{Cases in the COVID-19 pandemic|ref=yes}}

As of {{Cases in the COVID-19 pandemic|date|editlink=|ref=no}}, there have been {{Cases in the COVID-19 pandemic|confirmed|editlink=no|ref=no}} total confirmed cases of SARS‑CoV‑2 infection in the ongoing pandemic.{{Cases in the COVID-19 pandemic|ref=yes}} The total number of deaths attributed to the virus is {{Cases in the COVID-19 pandemic|deaths|editlink=no|ref=no}}.{{Cases in the COVID-19 pandemic|ref=yes}}
{{clear}}

== See also ==
* [[Biology:3C-like protease|3C-like protease]] (NS5)

== References ==
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<ref name="NatureZhou">{{#invoke:cite journal ||vauthors=Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, Si HR, Zhu Y, Li B, Huang CL, Chen HD, Chen J, Luo Y, Guo H, Jiang RD, Liu MQ, Chen Y, Shen XR, Wang X, Zheng XS, Zhao K, Chen QJ, Deng F, Liu LL, Yan B, Zhan FX, Wang YY, Xiao GF, Shi ZL |title=A pneumonia outbreak associated with a new coronavirus of probable bat origin |journal=Nature |volume=579 |issue=7798 |pages=270–273 |date=March 2020 |pmid=32015507 |pmc=7095418 |doi=10.1038/s41586-020-2012-7 |bibcode=2020Natur.579..270Z}}</ref>

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<ref name="NCBI-Bat">{{#invoke:cite journal ||date=15 February 2020 |title=Bat SARS-like coronavirus isolate bat-SL-CoVZC45, complete genome |url=https://www.ncbi.nlm.nih.gov/nuccore/MG772933 |access-date=15 February 2020 |website=[[Organization:National Center for Biotechnology Information|National Center for Biotechnology Information]] (NCBI) |archive-url=https://web.archive.org/web/20200604011749/https://www.ncbi.nlm.nih.gov/nuccore/MG772933 |archive-date=4 June 2020 |url-status=live}}</ref>
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<ref name="NCBI-Bat2">{{#invoke:cite journal ||date=15 February 2020 |title=Bat SARS-like coronavirus isolate bat-SL-CoVZXC21, complete genome |url=https://www.ncbi.nlm.nih.gov/nuccore/MG772934 |access-date=15 February 2020 |website=[[Organization:National Center for Biotechnology Information|National Center for Biotechnology Information]] (NCBI) |archive-url=https://web.archive.org/web/20200604011744/https://www.ncbi.nlm.nih.gov/nuccore/MG772934 |archive-date=4 June 2020 |url-status=live}}</ref>
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<ref name="NCBI-Bat3">{{#invoke:cite web ||url=https://www.ncbi.nlm.nih.gov/nuccore/1802633852 |title=Bat coronavirus isolate RaTG13, complete genome |date=10 February 2020 |website=[[Organization:National Center for Biotechnology Information|National Center for Biotechnology Information]] (NCBI) |access-date=5 March 2020 |archive-url=https://web.archive.org/web/20200515133838/https://www.ncbi.nlm.nih.gov/nuccore/1802633852 |archive-date=15 May 2020 |url-status=live}}</ref>

<ref name="PopSciJan">{{#invoke:cite web ||url=https://www.popsci.com/story/health/wuhan-coronavirus-china-wet-market-wild-animal/ |title=We're still not sure where the Wuhan coronavirus really came from |date=28 January 2020 |website=Popular Science |url-status=live |archive-url=https://archive.today/20200130003350/https://www.popsci.com/story/health/wuhan-coronavirus-china-wet-market-wild-animal/ |archive-date=30 January 2020 |access-date=30 January 2020 |vauthors=Eschner K}}</ref>

<ref name="Proximal">{{#invoke:cite journal ||vauthors=Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF |title=The proximal origin of SARS-CoV-2 |journal=Nature Medicine |volume=26 |issue=4 |pages=450–452 |date=April 2020 |pmid=32284615 |pmc=7095063 |doi=10.1038/s41591-020-0820-9}}</ref>

<ref name="RobsonF2020Aug">{{#invoke:cite journal ||vauthors=Robson F, Khan KS, Le TK, Paris C, Demirbag S, Barfuss P, Rocchi P, Ng WL |title=Coronavirus RNA Proofreading: Molecular Basis and Therapeutic Targeting [published correction appears in Mol Cell. 2020 Dec 17;80(6):1136-1138] |journal=Molecular Cell |volume=79 |issue=5 |pages=710–727 |date=August 2020 |pmid=32853546 |pmc=7402271 |doi=10.1016/j.molcel.2020.07.027}}</ref>

<ref name="WHOconvened">{{#invoke:cite book ||last1=Joint WHO-China Study Team |title=WHO-convened global study of origins of SARS-CoV-2: China Part |date=30 March 2021 |publisher=World Health Organization |location=Geneva, Switzerland |url=https://www.who.int/publications-detail-redirect/who-convened-global-study-of-origins-of-sars-cov-2-china-part |access-date=31 May 2023 |language=en}}</ref>

<ref name="XiaoK2020July">{{#invoke:cite journal ||vauthors=Xiao K, Zhai J, Feng Y, Zhou N, Zhang X, Zou JJ, Li N, Guo Y, Li X, Shen X, Zhang Z, Shu F, Huang W, Li Y, Zhang Z, Chen RA, Wu YJ, Peng SM, Huang M, Xie WJ, Cai QH, Hou FH, Chen W, Xiao L, Shen Y |title=Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins |journal=Nature |volume=583 |issue=7815 |pages=286–289 |date=July 2020 |pmid=32380510 |doi=10.1038/s41586-020-2313-x |s2cid=218557880 | doi-access = free |bibcode=2020Natur.583..286X}}</ref>

<ref name="XivDecoding">{{#invoke:cite journal || vauthors = Yu WB, Tang GD, Zhang L, Corlett RT | title = Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2 / HCoV-19) using whole genomic data | journal = Zoological Research | volume = 41 | issue = 3 | pages = 247–257 | date = May 2020 | pmid = 32351056 | pmc = 7231477 | doi = 10.24272/j.issn.2095-8137.2020.022 }}</ref>

<ref name="ZhaoJ2020">{{#invoke:cite journal || vauthors = Zhao J, Cui W, Tian BP | title = The Potential Intermediate Hosts for SARS-CoV-2 | journal = Frontiers in Microbiology | volume = 11 | issue =  | page = 580137 | date = 2020 | pmid = 33101254 | pmc = 7554366 | doi = 10.3389/fmicb.2020.580137 | doi-access = free }}</ref>

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<ref name="ZhouCellJune2021">{{#invoke:cite journal || vauthors = Zhou H, Ji J, Chen X, Bi Y, Li J, Wang Q, Hu T, Song H, Zhao R, Chen Y, Cui M, Zhang Y, Hughes AC, Holmes EC, Shi W | title = Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses | journal = Cell | volume = 184 | issue = 17 | pages = 4380–4391.e14 | date = August 2021 | pmid = 34147139 | pmc = 8188299 | doi = 10.1016/j.cell.2021.06.008 }}</ref>
-->
<section end=LDRs for Reservoir and origin />

<!-- Refs used by everything else (except section Reservoir and origin); further division coming. -->

<ref name="Alm2020Aug">{{#invoke:cite journal ||vauthors=Alm E, Broberg EK, Connor T, Hodcroft EB, Komissarov AB, Maurer-Stroh S, Melidou A, Neher RA, O'Toole Á, Pereyaslov D |title=Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020 |journal=Euro Surveillance |volume=25 |issue=32 |date=August 2020 |pmid=32794443 |pmc=7427299 |doi=10.2807/1560-7917.ES.2020.25.32.2001410}}</ref>

<ref name="Anfrinrud 2020">{{#invoke:cite journal ||vauthors=Anfinrud P, Stadnytskyi V, Bax CE, Bax A |title=Visualizing Speech-Generated Oral Fluid Droplets with Laser Light Scattering |journal=The New England Journal of Medicine |volume=382 |issue=21 |pages=2061–2063 |date=May 2020 |pmid=32294341 |pmc=7179962 |doi=10.1056/NEJMc2007800}}</ref>

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<ref name="AtlanticSuccess">{{#invoke:cite web ||url=https://www.theatlantic.com/science/archive/2020/03/biography-new-coronavirus/608338/ |title=Why the Coronavirus Has Been So Successful |date=20 March 2020 |website=The Atlantic |url-status=live |archive-url=https://web.archive.org/web/20200320161836/https://www.theatlantic.com/science/archive/2020/03/biography-new-coronavirus/608338/ |archive-date=20 March 2020 |access-date=20 March 2020 |vauthors=Yong E}}</ref>

<ref name="BMJ-Best-Practice">{{#invoke:cite web ||vauthors=Beeching NJ, Fletcher TE, Fowler R |url=https://bestpractice.bmj.com/topics/en-us/3000168/pdf/3000168.pdf |access-date=25 May 2020 |title=BMJ Best Practice: Coronavirus Disease 2019 (COVID-19) |website=BMJ  |date=22 May 2020 |archive-url=https://web.archive.org/web/20200613123054/https://bestpractice.bmj.com/topics/en-us/3000168/pdf/3000168.pdf |archive-date=13 June 2020 |url-status=live}}</ref>

<ref name="BronxTiger">{{#invoke:cite news ||vauthors=Goldstein J |url=https://www.nytimes.com/2020/04/06/nyregion/bronx-zoo-tiger-coronavirus.html |title=Bronx Zoo Tiger Is Sick with the Coronavirus |date=6 April 2020 |work={{wipe|The New York Times}} |access-date=10 April 2020 |archive-url=https://web.archive.org/web/20200409094808/https://www.nytimes.com/2020/04/06/nyregion/bronx-zoo-tiger-coronavirus.html |archive-date=9 April 2020 |url-status=live}}</ref>

<ref name="CD147">{{#invoke:cite journal || vauthors = Wang K, Chen W, Zhang Z, Deng Y, Lian JQ, Du P, Wei D, Zhang Y, Sun XX, Gong L, Yang X, He L, Zhang L, Yang Z, Geng JJ, Chen R, Zhang H, Wang B, Zhu YM, Nan G, Jiang JL, Li L, Wu J, Lin P, Huang W, Xie L, Zheng ZH, Zhang K, Miao JL, Cui HY, Huang M, Zhang J, Fu L, Yang XM, Zhao Z, Sun S, Gu H, Wang Z, Wang CF, Lu Y, Liu YY, Wang QY, Bian H, Zhu P, Chen ZN | title = CD147-spike protein is a novel route for SARS-CoV-2 infection to host cells | journal = Signal Transduction and Targeted Therapy | volume = 5 | issue = 1 | page = 283 | date = December 2020 | pmid = 33277466 | pmc = 7714896 | doi = 10.1038/s41392-020-00426-x | s2cid = 214725955 | doi-access = free | biorxiv = 10.1101/2020.03.14.988345 }}</ref>

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<ref name="CDCanimals">{{#invoke:cite web ||url=https://www.cdc.gov/coronavirus/2019-ncov/daily-life-coping/animals.html |title=If You Have Animals—Coronavirus Disease 2019 (COVID-19) |date=13 April 2020 |website=Centers for Disease Control and Prevention (CDC)  |access-date=16 April 2020 |archive-url=https://web.archive.org/web/20200401163720/https://www.cdc.gov/coronavirus/2019-ncov/daily-life-coping/animals.html |archive-date=1 April 2020 |url-status=live}}</ref>

<ref name="CDC-nCoV">{{#invoke:cite web ||url=https://www.cdc.gov/coronavirus/2019-ncov/hcp/faq.html |title=Healthcare Professionals: Frequently Asked Questions and Answers |date=11 February 2020 |website=United States Centers for Disease Control and Prevention (CDC) |url-status=live |archive-url=https://web.archive.org/web/20200214023335/https://www.cdc.gov/coronavirus/2019-ncov/hcp/faq.html |archive-date=14 February 2020 |access-date=15 February 2020}}</ref>

<ref name="CDCTrans">{{#invoke:cite web ||url=https://www.cdc.gov/coronavirus/2019-ncov/about/transmission.html |title=How COVID-19 Spreads |date=27 January 2020 |website=U.S. Centers for Disease Control and Prevention (CDC) |url-status=live |archive-url=https://web.archive.org/web/20200128152653/https://www.cdc.gov/coronavirus/2019-ncov/about/transmission.html |archive-date=28 January 2020 |access-date=29 January 2020}}</ref>

<ref name="CEBMcoronaviruses">{{#invoke:cite web ||vauthors=Aronson JK |title=Coronaviruses – a general introduction |date=25 March 2020 |access-date=24 May 2020 |url=https://www.cebm.net/covid-19/coronaviruses-a-general-introduction/ |website=Centre for Evidence-Based Medicine, Nuffield Department of Primary Care Health Sciences, University of Oxford |archive-url=https://web.archive.org/web/20200522053938/https://www.cebm.net/covid-19/coronaviruses-a-general-introduction/ |archive-date=22 May 2020}}</ref>

<!-- <ref name="CellWalls">{{#invoke:cite journal ||vauthors=Walls AC, Park YJ, Tortorici MA, Wall A, McGuire AT, Veesler D |title=Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein |journal=Cell |volume=181 |issue=2 |pages=281–292.e6 |date=April 2020 |pmid=32155444 |pmc=7102599 |doi=10.1016/j.cell.2020.02.058}}</ref> -->

<ref name="Chan24Jan2020">{{#invoke:cite journal ||vauthors=Chan JF, Yuan S, Kok KH, To KK, Chu H, Yang J, Xing F, Liu J, Yip CC, Poon RW, Tsoi HW, Lo SK, Chan KH, Poon VK, Chan WM, Ip JD, Cai JP, Cheng VC, Chen H, Hui CK, Yuen KY |title=A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster |journal=Lancet |volume=395 |issue=10223 |pages=514–523 |date=February 2020 |pmid=31986261 |pmc=7159286 |doi=10.1016/S0140-6736(20)30154-9}}</ref>

<!-- <ref name="CNBC2020Oct">{{#invoke:cite news ||vauthors=Meredith S |title=A new coronavirus variant is seen spreading across Europe, research says |url=https://www.cnbc.com/2020/10/29/coronavirus-variant-seen-spreading-across-europe-research-says.html |access-date=10 November 2020 |work=CNBC |date=29 October 2020 }}</ref> -->

<ref name="CoronavirusStudyGroup">{{#invoke:cite journal ||title=The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 |journal=Nature Microbiology |volume=5 |issue=4 |pages=536–544 |date=April 2020 |pmid=32123347 |pmc=7095448 |doi=10.1038/s41564-020-0695-z |author1=Coronaviridae Study Group of the International Committee on Taxonomy of Viruses}}</ref>

<ref name="COVIDname date">{{#invoke:cite web ||url=https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/naming-the-coronavirus-disease-(covid-2019)-and-the-virus-that-causes-it |title=Naming the coronavirus disease (COVID-2019) and the virus that causes it |publisher=World Health Organization |url-status=live |archive-url=https://web.archive.org/web/20200228035651/https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/naming-the-coronavirus-disease-(covid-2019)-and-the-virus-that-causes-it |archive-date=28 February 2020 |access-date=14 December 2020 |quote=ICTV announced "severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)" as the name of the new virus on 11 February 2020. This name was chosen because the virus is genetically related to the coronavirus responsible for the SARS outbreak of 2003. While related, the two viruses are different.}}</ref>

<ref name="COVIDname public">{{#invoke:cite web ||url=https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/naming-the-coronavirus-disease-(covid-2019)-and-the-virus-that-causes-it |title=Naming the coronavirus disease (COVID-2019) and the virus that causes it |publisher=World Health Organization |url-status=live |archive-url=https://web.archive.org/web/20200228035651/https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/naming-the-coronavirus-disease-(covid-2019)-and-the-virus-that-causes-it |archive-date=28 February 2020 |access-date=14 December 2020 |quote=From a risk communications perspective, using the name SARS can have unintended consequences in terms of creating unnecessary fear for some populations.{{nbsp}}... For that reason and others, WHO has begun referring to the virus as "the virus responsible for COVID-19" or "the COVID-19 virus" when communicating with the public. Neither of these designations {{sic|is|nolink=y}} intended as replacements for the official name of the virus as agreed by the ICTV. }}</ref>

<ref name="CuervoNZ2020Nov">{{#invoke:cite journal ||vauthors=Zamorano Cuervo N, Grandvaux N |title=ACE2: Evidence of role as entry receptor for SARS-CoV-2 and implications in comorbidities |journal=eLife |volume=9 |issue= |date=November 2020 |pmid=33164751 |pmc=7652413 |doi=10.7554/eLife.61390|doi-access=free}}</ref>

<ref name= "deOliveira" >{{#invoke:cite journal ||vauthors=de Oliveira PM, Mesquita LC, Gkantonas S, Giusti A, Mastorakos E |title=Evolution of spray and aerosol from respiratory releases: theoretical estimates for insight on viral transmission |journal= Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences|volume=477 |issue=2245 |page=20200584 |date=January 2021 |pmid=33633490 |pmc=7897643 |doi=10.1098/rspa.2020.0584 |s2cid=231643585 | doi-access = free |bibcode=2021RSPSA.47700584D}}</ref>

<ref name="econ-anatomy-killer">{{#invoke:Cite magazine ||date=12 March 2020 |title=Anatomy of a Killer: Understanding SARS-CoV-2 and the drugs that might lessen its power |url=https://www.economist.com/briefing/2020/03/12/understanding-sars-cov-2-and-the-drugs-that-might-lessen-its-power |magazine=[[Finance:The Economist|The Economist]] |archive-url=https://web.archive.org/web/20200314010231/https://www.economist.com/briefing/2020/03/12/understanding-sars-cov-2-and-the-drugs-that-might-lessen-its-power |archive-date=14 March 2020 |access-date=14 March 2020 |url-status=live }}</ref>

<ref name="EconomistSinophobia">{{#invoke:cite news ||author= |title=The coronavirus spreads racism against—and among—ethnic Chinese |url=https://www.economist.com/china/2020/02/17/the-coronavirus-spreads-racism-against-and-among-ethnic-chinese |newspaper=[[Finance:The Economist|The Economist]] |date=17 February 2020|access-date= 17 February 2020|archive-url= https://web.archive.org/web/20200217223902/https://www.economist.com/china/2020/02/17/the-coronavirus-spreads-racism-against-and-among-ethnic-chinese|archive-date= 17 February 2020|url-status= live}}</ref>

<ref name="ElSahly">{{#invoke:cite journal ||vauthors=((El Sahly HM)) |title=Genomic Characterization of the 2019 Novel Coronavirus |url=https://www.jwatch.org/na50823/2020/02/06/genomic-characterization-2019-novel-coronavirus |url-status=live |journal=The New England Journal of Medicine |archive-url=https://web.archive.org/web/20200217184052/https://www.jwatch.org/na50823/2020/02/06/genomic-characterization-2019-novel-coronavirus |archive-date=17 February 2020 |access-date=9 February 2020 }}</ref>

<ref name="GuardianLeap">{{#invoke:cite news ||url=https://www.theguardian.com/world/2020/jan/30/coronavirus-deaths-leap-in-china-as-countries-struggle-to-evacuate-citizens |title=Coronavirus deaths leap in China as countries struggle to evacuate citizens |date=30 January 2020 |work={{wipe|The Guardian}} |access-date=10 March 2020 |url-status=live |archive-url=https://web.archive.org/web/20200206150542/https://www.theguardian.com/world/2020/jan/30/coronavirus-deaths-leap-in-china-as-countries-struggle-to-evacuate-citizens |archive-date=6 February 2020 |vauthors=Boseley S, McCurry J}}</ref>

<ref name="GZM-20200220">{{#invoke:cite web ||url=https://gizmodo.com/scientists-create-atomic-level-image-of-the-new-coronav-1841795715 |title=Scientists Create Atomic-Level Image of the New Coronavirus's Potential Achilles Heel |date=19 February 2020 |website=Gizmodo |url-status=live |archive-url=https://web.archive.org/web/20200308070019/https://gizmodo.com/scientists-create-atomic-level-image-of-the-new-coronav-1841795715 |archive-date=8 March 2020 |access-date=13 March 2020 |vauthors=Mandelbaum RF}}</ref>

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<ref name="HoffmanCell">{{#invoke:cite journal ||vauthors=Hoffmann M, Kleine-Weber H, Schroeder S, Krüger N, Herrler T, Erichsen S, Schiergens TS, Herrler G, Wu NH, Nitsche A, Müller MA, Drosten C, Pöhlmann S |title=SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor |journal=Cell |volume=181 |issue=2 |pages=271–280.e8 |date=April 2020 |pmid=32142651 |pmc=7102627 |doi=10.1016/j.cell.2020.02.052}}</ref>

<ref name="Hou2020">{{#invoke:cite journal ||vauthors=Hou YJ, Okuda K, Edwards CE, Martinez DR, Asakura T, Dinnon KH, Kato T, Lee RE, Yount BL, Mascenik TM, Chen G, Olivier KN, Ghio A, Tse LV, Leist SR, Gralinski LE, Schäfer A, Dang H, Gilmore R, Nakano S, Sun L, Fulcher ML, Livraghi-Butrico A, Nicely NI, Cameron M, Cameron C, Kelvin DJ, de Silva A, Margolis DM, Markmann A, Bartelt L, Zumwalt R, Martinez FJ, Salvatore SP, Borczuk A, Tata PR, Sontake V, Kimple A, Jaspers I, O'Neal WK, Randell SH, Boucher RC, Baric RS |title=SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract |journal=Cell |volume=182 |issue=2 |pages=429–446.e14 |date=July 2020 |pmid=32526206 |pmc=7250779 |doi=10.1016/j.cell.2020.05.042 | doi-access = free}}</ref>

<ref name="HuangNPR">{{#invoke: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? |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 |vauthors=Huang P}}</ref>

<ref name="Kessler17Apr2020">{{#invoke:cite news ||vauthors=Kessler G |url=https://www.washingtonpost.com/politics/2020/04/17/trumps-false-claim-that-who-said-coronavirus-was-not-communicable/ |title=Trump's false claim that the WHO said the coronavirus was 'not communicable' |date=17 April 2020 |newspaper=The Washington Post |access-date=17 April 2020 |archive-url=https://archive.today/20200417193804/https://www.washingtonpost.com/politics/2020/04/17/trumps-false-claim-that-who-said-coronavirus-was-not-communicable/ |archive-date=17 April 2020}}</ref>

<ref name= "Klompas" >{{#invoke:cite journal ||vauthors=Klompas M, Baker MA, Rhee C |title=Airborne Transmission of SARS-CoV-2: Theoretical Considerations and Available Evidence |journal=JAMA |volume=324 |issue=5 |pages=441–442 |date=August 2020 |pmid=32749495 |doi=10.1001/jama.2020.12458 |quote=Investigators have demonstrated that speaking and coughing produce a mixture of both droplets and aerosols in a range of sizes, that these secretions can travel together for up to 27 feet, that it is feasible for SARS-CoV-2 to remain suspended in the air and viable for hours, that SARS-CoV-2 RNA can be recovered from air samples in hospitals, and that poor ventilation prolongs the amount of time that aerosols remain airborne. |s2cid=220500293|doi-access=free }}</ref>

<ref name="Koyama2020June">{{#invoke:cite journal ||vauthors=Koyama T, Platt D, Parida L |title=Variant analysis of SARS-CoV-2 genomes |journal=Bulletin of the World Health Organization |volume=98 |issue=7 |pages=495–504 |date=July 2020 |pmid=32742035 |pmc=7375210 |doi=10.2471/BLT.20.253591 |quote=We detected in total 65776 variants with 5775 distinct variants.}}</ref>

<ref name="Kuo21Jan2020">{{#invoke:cite news ||vauthors=Kuo L |url=https://www.theguardian.com/world/2020/jan/20/coronavirus-spreads-to-beijing-as-china-confirms-new-cases |title=China confirms human-to-human transmission of coronavirus |date=21 January 2020 |work={{wipe|The Guardian}} |access-date=18 April 2020 |archive-url=https://web.archive.org/web/20200322001315/https://www.theguardian.com/world/2020/jan/20/coronavirus-spreads-to-beijing-as-china-confirms-new-cases |archive-date=22 March 2020 |url-status=live}}</ref>

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<ref name="WuStructure">{{#invoke:cite journal ||vauthors=Wu C, Liu Y, Yang Y, Zhang P, Zhong W, Wang Y, Wang Q, Xu Y, Li M, Li X, Zheng M, Chen L, Li H |title=Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods |journal=Acta Pharmaceutica Sinica B |volume=10 |issue=5 |pages=766–788 |date=May 2020 |pmid=32292689 |pmc=7102550 |doi=10.1016/j.apsb.2020.02.008}}</ref>

<ref name="Zoonotic">{{#invoke:cite journal ||vauthors=Wong G, Bi YH, Wang QH, Chen XW, Zhang ZG, Yao YG |title=Zoonotic origins of human coronavirus 2019 (HCoV-19 / SARS-CoV-2): why is this work important? |journal=Zoological Research |volume=41 |issue=3 |pages=213–219 |date=May 2020 |pmid=32314559 |pmc=7231470 |doi=10.24272/j.issn.2095-8137.2020.031}}</ref>

<ref name="ZZeynep">{{#invoke:cite web ||url=https://www.theatlantic.com/health/archive/2020/07/why-arent-we-talking-more-about-airborne-transmission/614737/ |title=We Need to Talk About Ventilation |vauthors=Tufekci Z |publisher=The Atlantic |date=30 July 2020|access-date=8 September 2020|archive-date=17 November 2020|archive-url=https://web.archive.org/web/20201117010832/https://www.theatlantic.com/health/archive/2020/07/why-arent-we-talking-more-about-airborne-transmission/614737/|url-status=live}}</ref>

}}

== Further reading ==
{{Refbegin}}
{{Refend}}

== External links ==
{{Zoonotic viral diseases|state=collapsed}}
{{Viral systemic diseases|state=collapsed}}
{{subject bar|commons = y|commons-search = Category:SARS-CoV-2|species = y|species-search = |voy = y|voy-search = SARS-CoV-2|n = y|n-search = SARS-CoV-2|wikt = y|wikt-search = |b = y|b-search = SARS-CoV-2|q = y|q-search = SARS-CoV-2|s = y|s-search = "SARS-CoV-2"|v = y|v-search = |d = y|d-search = Q82069695 | portal1=COVID-19 | portal2=Medicine | portal13=Viruses}}
{{Medical resources| ICD10 = {{ICD10|U07.1}}}}
{{Taxonbar|from=Q82069695}}

[[Category:Infraspecific virus taxa]]
[[Category:Zoonoses]]

{{Sourceattribution|SARS-CoV-2}}