Severe acute respiratory syndrome coronavirus 2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)[2][3] is the strain of coronavirus that causes coronavirus disease 2019 (COVID-19), the respiratory illness responsible for the COVID-19 pandemic. Colloquially known as simply the coronavirus, it was previously referred to by its provisional name, 2019 novel coronavirus (2019-nCoV),[4][5][6][7] and has also been called human coronavirus 2019 (HCoV-19 or hCoV-19).[8][9][10][11] The World Health Organization declared the outbreak a Public Health Emergency of International Concern on 30 January 2020, and a pandemic on 11 March 2020.[12][13]

This article is about the virus strain that causes COVID-19. For the strain that causes SARS, see Severe acute respiratory syndrome coronavirus. For the species to which both strains belong, see Severe acute respiratory syndrome-related coronavirus.

Severe acute respiratory syndrome coronavirus 2
Transmission electron micrograph of SARS-CoV-2 virions with visible coronae
Illustration of a SARS-CoV-2 virion[1]     Red protrusions: spike proteins (S)[1]     Grey coating: the envelope, composed mainly of lipids, which can be destroyed with alcohol or soap[1]     Yellow deposits: envelope proteins (E)[1]     Orange deposits: membrane proteins (M)[1]
Virus classification
(unranked): Virus
Realm: Riboviria
Kingdom: Orthornavirae
Phylum: Pisuviricota
Class: Pisoniviricetes
Order: Nidovirales
Family: Coronaviridae
Genus: Betacoronavirus
Subgenus: Sarbecovirus
Species:
Severe acute respiratory syndrome–related coronavirus
Strain:
Severe acute respiratory syndrome coronavirus 2
Synonyms
  • 2019-nCoV

SARS-CoV-2 is a Baltimore class IV[14] positive-sense single-stranded RNA virus[15] that is contagious in humans.[16] As described by the U.S. National Institutes of Health, it is the successor to SARS-CoV-1,[10][17] the strain that caused the 2002–2004 SARS outbreak.

Taxonomically, SARS-CoV-2 is a strain of severe acute respiratory syndrome-related coronavirus (SARSr-CoV).[2] It is believed to have zoonotic origins and has close genetic similarity to bat coronaviruses, suggesting it emerged from a bat-borne virus.[18][19][20][9] There is no evidence yet to link an intermediate animal reservoir, such as a pangolin, to its introduction to humans.[21][22] The virus shows little genetic diversity, indicating that the spillover event introducing SARS-CoV-2 to humans is likely to have occurred in late 2019.[23]

Epidemiological studies estimate each infection results in 1.4 to 3.9 new ones when no members of the community are immune and no preventive measures taken. The virus primarily spreads between people through close contact and via respiratory droplets produced from coughs or sneezes.[24][25] It mainly enters human cells by binding to the receptor angiotensin converting enzyme 2 (ACE2).[18][26][27][28]

HeLa cells engineered to express ACE2 become susceptible to SARS-CoV-2 infection.

Terminology
See also: Trump administration communication during the COVID-19 pandemic § Terminology
The name "2019-nCoV" in use in a trilingual sign at a Lisbon health facility in February 2020.

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",[29][30][31] or "Wuhan virus".[32] In January 2020, the World Health Organisation recommended "2019 novel coronavirus" (2019-nCov)[33][5] as the provisional name for the virus. This was in accordance with WHO's 2015 guidance[34] against using geographical locations, animal species, or groups of people in disease and virus names.[35][36] On 11 February 2020, the International Committee on Taxonomy of Viruses adopted the official name "severe acute respiratory syndrome coronavirus 2" (SARS-CoV-2).[21] To avoid confusion with the disease SARS, the WHO sometimes refers to SARS-CoV-2 as "the COVID-19 virus" in public health communications[37][38] and the name HCoV-19 was included in some research articles.[8][9][10] The general public often call both SARS-CoV-2 and the disease it causes "coronavirus". U.S. President Donald Trump referred to the virus as the "Chinese virus" in tweets, interviews, and White House press briefings.[39][40][41]

Virology

Infection and transmission
Part of a series on the
COVID-19 pandemic
 COVID-19 Portal
Main article: Transmission of COVID-19

Human-to-human transmission of SARS-CoV-2 was confirmed on 20 January 2020, during the COVID-19 pandemic.[16][42][43][44] Transmission was initially assumed to occur primarily via respiratory droplets from coughs and sneezes within a range of about 1.8 metres (6 ft).[25][45] Laser light scattering experiments suggest speaking as an additional mode of transmission.[46][47] Other studies have suggested that the virus may be airborne as well.[48]

Indirect contact via contaminated surfaces is another possible cause of infection.[49] Preliminary research indicates that the virus may remain viable on plastic (polypropylene) and stainless steel (AISI 304) for up to three days, but does not survive on cardboard for more than one day or on copper for more than four hours;[10] the virus is inactivated by soap, which destabilises its lipid bilayer.[50][51] Viral RNA has also been found in stool samples and semen from infected individuals.[52][53]

The degree to which the virus is infectious during the incubation period is uncertain, but research has indicated that the pharynx reaches peak viral load approximately four days after infection[54][55] or the first week of symptoms, and declines after.[56] On 1 February 2020, the World Health Organization (WHO) indicated that "transmission from asymptomatic cases is likely not a major driver of transmission".[57] However, an epidemiological model of the beginning of the outbreak in China suggested that "pre-symptomatic shedding may be typical among documented infections" and that subclinical infections may have been the source of a majority of infections.[58] That may explain how out of 217 on board a cruise liner that docked at Montevideo, only 24 of 128 who tested positive for viral RNA showed symptoms.[59] Similarly, a study of ninety-four patients hospitalized in January and February 2020 estimated patients shed the greatest amount of virus two to three days before symptoms appear and that "a substantial proportion of transmission probably occurred before first symptoms in the index case".[60]

There is some evidence of human-to-animal transmission of SARS-CoV-2, including examples in felids.[61][62] Some institutions have advised those infected with SARS-CoV-2 to restrict contact with animals.[63][64]

On 3 July 2020, a preliminary scientific paper reported that a major genetic risk factor of the Covid-19 virus was inherited from archaic Neanderthals 60,000 years ago. The paper has yet to undergo peer review.[65][66]

Reservoir and zoonotic origin
Transmission of SARS-CoV-1 and SARS-CoV-2 from mammals as biological carriers to humans

The first known infections from the SARS-CoV-2 strain were discovered in Wuhan, China.[18] The original source of viral transmission to humans remains unclear, as does whether the strain became pathogenic before or after the spillover event.[23][67][9] Because many of the first individuals found to be infected by the virus were workers at the Huanan Seafood Market,[68][69] it has been suggested that the strain might have originated from the market.[9][70] However, other research indicates that visitors may have introduced the virus to the market, which then facilitated rapid expansion of the infections.[23][71] A phylogenetic network analysis of 160 early coronavirus genomes sampled from December 2019 to February 2020 revealed that the virus type most closely related to the bat coronavirus was most abundant in Guangdong, China, and designated type "A". The predominant type among samples from Wuhan, "B", is more distantly related to the bat coronavirus than the ancestral type "A".[72][73]

Research into the natural reservoir of the virus strain that caused the 2002–2004 SARS outbreak has resulted in the discovery of many SARS-like bat coronaviruses, most originating in the Rhinolophus genus of horseshoe bats. Phylogenetic analysis indicates that samples taken from Rhinolophus sinicus show a resemblance of 80% to SARS-CoV-2.[20][74][75] Phylogenetic analysis also indicates that a virus from Rhinolophus affinis, collected in Yunnan province and designated RaTG13, has a 96% resemblance to SARS-CoV-2.[18][76]

Samples taken from Rhinolophus sinicus, a species of horseshoe bats, show a 80% resemblance to SARS-CoV-2.

Bats were initially considered to be the most likely natural reservoir of SARS-CoV-2,[77][78] which means that they harbour the virus for long periods of time with no pathogenic effects. Regarding the animal source of infection into humans, the differences between the bat coronavirus sampled at the time and SARS-CoV-2 suggested that humans were infected via an intermediate host. Arinjay Banerjee, a virologist at McMaster University, notes that "the SARS virus shared 99.8% of its genome with a civet coronavirus, which is why civets were considered the source."[70] Although studies had suggested some likely candidates, the number and identities of intermediate hosts remains uncertain.[79] Nearly half of the strain's genome had a phylogenetic lineage distinct from known relatives.[80]

The pangolin coronavirus has up to 92% resemblance to SARS-CoV-2.[81]

A phylogenetics study published in 2020 indicates that pangolins are a reservoir host of SARS-CoV-2-like coronaviruses.[82] However, there is no direct evidence to link pangolins as an intermediate host of SARS-CoV-2 at this moment. While there is scientific consensus that bats are the ultimate source of coronaviruses, it is hypothesized that a SARS-CoV-2-like coronavirus originated in pangolins, jumped back to bats, and then jumped to humans, resulting in SARS-CoV-2. Based on whole genome sequence similarity, a pangolin coronavirus candidate strain was found to be less similar than RaTG13, but more similar than other bat coronaviruses to SARS-CoV-2.[81] Therefore, based on maximum parsimony, a specific population of bats is more likely to have directly transmitted SARS-CoV-2 to humans than a pangolin, while an evolutionary ancestor to bats was the source of general coronaviruses.[83]

A metagenomics study published in 2019 had previously revealed that SARS-CoV, the strain of the virus that causes SARS, was the most widely distributed coronavirus among a sample of Sunda pangolins.[84] On 7 February 2020, South China Agricultural University in Guangzhou announced that researchers discovered a pangolin sample with a particular coronavirus – a single nucleic acid sequence of the virus was "99% similar" to that of a protein-coding RNA of SARS-CoV-2.[85] The authors state that "the receptor-binding domain of the S protein [that binds to the cell surface receptor during infection] of the newly discovered Pangolin-CoV is virtually identical to that of 2019-nCoV, with one amino acid difference."[86] Microbiologists and geneticists in Texas have independently found evidence of reassortment in coronaviruses suggesting involvement of pangolins in the origin of SARS-CoV-2.[87] The majority of the viral RNA is related to a variation of bat coronaviruses. The spike protein appears to be a notable exception, however, possibly acquired through a more recent recombination event with a pangolin coronavirus.[88] Structural analysis of the receptor binding domain (RBD) and human angiotensin-converting enzyme 2 (ACE2) complex[89] revealed key mutations on the RBD, such as F486 and N501, which form contacts with ACE2.[90] These residues are found in the pangolin coronavirus.[90]

Pangolins are protected under Chinese law, but their poaching and trading for use in traditional Chinese medicine remains common in the black market.[91][92] Deforestation, wildlife farming and trade in unsanitary conditions increases the risk of new zoonotic diseases, biodiversity experts have warned.[93][94][95]

It is unlikely that SARS-CoV-2 was genetically engineered. According to computational simulations on protein folding, the RBD of the spike protein of SARS-CoV-2 should have unremarkable binding affinity. In actuality, however, it has very efficient binding to the human ACE2 receptor. To expose the RBD for fusion, furin proteases must first cleave the S protein. Furin proteases are abundant in the respiratory tract and lung epithelial cells. Additionally, the backbone of the virus does not resemble any previously described in scientific literature used for genetic modification. The possibility that the virus could have gained the necessary adaptations through cell culture in a laboratory setting is challenged by scientists who assert that "the generation of the predicted O-linked glycans... suggest[s] the involvement of an immune system."[96][9]

Phylogenetics and taxonomy
Genomic information
Genomic organisation of isolate Wuhan-Hu-1, the earliest sequenced sample of SARS-CoV-2
NCBI genome ID86693
Genome size29,903 bases
Year of completion2020
Genome browser (UCSC)

SARS-CoV-2 belongs to the broad family of viruses known as coronaviruses.[30] It is a positive-sense single-stranded RNA (+ssRNA) virus, with a single linear RNA segment. Other coronaviruses are capable of causing illnesses ranging from the common cold to more severe diseases such as Middle East respiratory syndrome (MERS, fatality rate ~34%). It is the seventh known coronavirus to infect people, after 229E, NL63, OC43, HKU1, MERS-CoV, and the original SARS-CoV.[97]

Like the SARS-related coronavirus strain implicated in the 2003 SARS outbreak, SARS-CoV-2 is a member of the subgenus Sarbecovirus (beta-CoV lineage B).[98][99] Its RNA sequence is approximately 30,000 bases in length.[15] SARS-CoV-2 is unique among known betacoronaviruses in its incorporation of a polybasic cleavage site, a characteristic known to increase pathogenicity and transmissibility in other viruses.[9][100][101]

With a sufficient number of sequenced genomes, it is possible to reconstruct a phylogenetic tree of the mutation history of a family of viruses. By 12 January 2020, five genomes of SARS-CoV-2 had been isolated from Wuhan and reported by the Chinese Center for Disease Control and Prevention (CCDC) and other institutions;[15][102] the number of genomes increased to 42 by 30 January 2020.[103] 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.[103] As of 7 May 2020, 4,690 SARS-CoV-2 genomes sampled on six continents were publicly available.[104]

On 11 February 2020, the International Committee on Taxonomy of Viruses announced that according to existing rules that compute hierarchical relationships among coronaviruses on the basis of five conserved sequences of nucleic acids, the differences between what was then called 2019-nCoV and the virus strain from the 2003 SARS outbreak were insufficient to make them separate viral species. Therefore, they identified 2019-nCoV as a strain of Severe acute respiratory syndrome-related coronavirus.[2]

Structural biology
Structure of a SARSr-CoV virion

Each SARS-CoV-2 virion is 50–200 nanometres in diameter.[69] 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 viral envelope.[105] The spike protein, which has been imaged at the atomic level using cryogenic electron microscopy,[106][107] is the protein responsible for allowing the virus to attach to and fuse with the membrane of a host cell;[105] specifically, its S1 subunit catalyzes attachment, the S2 subunit fusion.[108]

SARS-CoV-2 spike homotrimer with one protein subunit highlighted. The ACE2 binding domain is magenta.

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 cell entry.[109] By 22 January 2020, a group in China working with the full virus genome and a group in the United States using reverse genetics methods independently and experimentally demonstrated that ACE2 could act as the receptor for SARS-CoV-2.[18][110][26][111] Studies have shown that SARS-CoV-2 has a higher affinity to human ACE2 than the original SARS virus strain.[106][112] SARS-CoV-2 may also use basigin to assist in cell entry.[113]

Initial spike protein priming by transmembrane protease, serine 2 (TMPRSS2) is essential for entry of SARS-CoV-2.[27] After a SARS-CoV-2 virion attaches to a target cell, the cell's protease TMPRSS2 cuts open the spike protein of the virus, exposing a fusion peptide in the S2 subunit, and the host receptor ACE2.[108] After fusion, an endosome forms around the virion, separating it from the rest of the host cell. The virion escapes when the pH of the endosome drops or when cathepsin, a host cysteine protease, cleaves it.[108] The virion then releases RNA into the cell and forces the cell to produce and disseminate copies of the virus, which infect more cells.[114]

SARS-CoV-2 produces at least three virulence factors that promote shedding of new virions from host cells and inhibit immune response.[105] Whether they include downregulation of ACE2, as seen in similar coronaviruses, remains under investigation (as of May 2020).[82]

Digitally colourised scanning electron micrographs of SARS-CoV-2 virions (yellow) emerging from human cells cultured in a laboratory

Epidemiology
Main article: COVID-19 pandemic
Transmission electron micrograph of SARS-CoV-2 virions (red) isolated from a patient during the COVID-19 pandemic

Based on the low variability exhibited among known SARS-CoV-2 genomic sequences, the strain is thought to have been detected by health authorities within weeks of its emergence among the human population in late 2019.[23][115] The earliest case of infection currently known is dated back to 17 November 2019 or possibly 1 December 2019.[116] The virus subsequently spread to all provinces of China and to more than 150 other countries in Asia, Europe, North America, South America, Africa, and Oceania.[117] Human-to-human transmission of the virus has been confirmed in all these regions.[118] On 30 January 2020, SARS-CoV-2 was designated a Public Health Emergency of International Concern by the WHO,[119][12] and on 11 March 2020 the WHO declared it a pandemic.[13][120]

The basic reproduction number () of the virus has been estimated to be between 1.4 and 3.9.[121][122] This means each infection from the virus is expected to result in 1.4 to 3.9 new infections when no members of the community are immune and no preventive measures are taken. The reproduction number may be higher in densely populated conditions such as those found on cruise ships.[123] Many forms of preventive efforts may be employed in specific circumstances in order to reduce the propagation of the virus.

There have been about 82,000 confirmed cases of infection in mainland China.[117] While the proportion of infections that result in confirmed cases or progress to diagnosable disease remains unclear,[124] 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.[125] Before 24 February 2020, over 95% of all deaths from COVID-19 worldwide had occurred in Hubei province, where Wuhan is located.[126][127] As of 16 August 2020, the percentage had decreased to 0.42%.[117]

As of 16 August 2020, there have been 21,480,111 total confirmed cases of SARS-CoV-2 infection in the ongoing pandemic.[117] The total number of deaths attributed to the virus is 771,518.[117] Many recoveries from confirmed infections go unreported, but at least 13,462,165 people have recovered from confirmed infections.[117]

gollark: .··
gollark: Just stop this madness and add THIS VERSION.
gollark: `pacman -S help-command`
gollark: It's a 421x421 PNG.
gollark: That looks stupid.

See also
  • Decoding COVID-19 – 2020 PBS film documentary about the 2019–2020 COVID-19 pandemic

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